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MOPRO 15.02 DOCUMENTATION
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Laboratoire de Cristallographie, Resonance Magnetique et Modelisations

Faculte des Sciences et Technologies - CNRS - Universite de Lorraine
Boulevard des Aiguillettes.
BP 70239 54506 Vandoeuvre-les-Nancy Cedex France

http://crm2.univ-lorraine.fr/lab/software/mopro/download-mopro/
last update : 2015-02

contact email : christian.jelsch@univ-lorraine.fr




Christian Jelsch , Benoit Guillot , Slawomir Domagala , Bertrand Fournier , Ignasi Mata , Christian Iordache




**********************************************************************
1 - INTRODUCTION
**********************************************************************

* MOPRO is a crystallographic program dedicated to
** the charge density refinement of small molecules and biological macromolecules at subatomic resolution (d ~0.4-0.7 Angstrom)
** the crystallographic refinement of structures at atomic resolution(d~ 0.7 - 1 .3A) using a multipolar atom model with parameters transferred from a charge density databank.
The program uses the Hansen & Coppens atom model for electron density refinement:
RHO(R) = RHOcore(R) Core (spherical)
+ Pval K**3 RHOval ( K R ) Spherical Valence
+ sum K'**3 Rl(K'*R) Plm Ylm(Theta,Phi) Multipolar Valence
where R is the distance to atomic nucleus.
Ylm are spherical harmonic functions.
Rl are radial functions of Slater type.
Rl(r) = zeta**(Nl+3) r**Nl exp(-zeta*r) / (Nl+2)!

The least squares algorithm minimizes the crystallographic residual wR2(F) or wR2(I).
The following crystallographic statistics are given after each refinement cycle :
RF = sum | Fo - Fc | / sum Fo
RI = sum | Io - Ic | / sum Io
wR2F = [ sum [ (Fo-Fc)/sigFo ]^2 / sum [ (Fo/sigFo)^2 ] ] ^1/2
wR2I = [ sum [ (Io-Ic)/sigIo ]^2 / sum [ (Io/sigIo)^2 ] ] ^1/2
g.o.f. [ sum [ (Fo-Fc)/sigFo ]^2 / ( Nobs - Nvar ) ] ^1/2

Import2MoPro

Import2MoPro is an interactive program to import molecular structure files:
from SHELXL , CIF , PDB , MOLLY , XYZ & MoPro formats.
The program does also Database Transfer: see $ Database Transfer.
The atomic local axes to define the multipoles are automatic computed according to bonding and maximal symmetry criteria.

VMoPro

VMoPro is a vizualisation Interactive Program for the related properties:
- Fourier Syntheis Electron Density : m*Fo - n*Fc
- Deformation of Dynamic Electron Density : Fmul-Fsph
- Deformation of Static Electron Density
- Electrostic Potential
- Gradient of Total Static Electron Density
- Laplacian of Total Static Electron Density
Lapl = d2Rho/dx2 + d2Rho/dy2 + d2Rho/dz2
- Critical points, where Grad(Rho) = 0

Grids are computed :
- in a projection plane (PL option)
VMOPro can then create a postscript image.
- in 3D XPLOR-CNS format
XPLOR maps shall be displayed with other programs (Pymol...)
- in 3D cube format
cube maps can be displayed with Molekel, vmd, Gaussview ...
A 1D grid can be generated using the PL option, but by specifying the same Value for Ymin and Ymax.
The VMoPro program can display the generated 2D postscript images (plot1.ps) by calling "gsview32.exe" (ghostscript, ghostview, versions 4.5 or before).
Other programs to display postcript are : CorelDraw , xv, Adobe ImageReady

Flat-Solvent

This program generates structure factors ( Fcalc PHIcalc ) of the molecular envelope for bulk solvent correction in case of macromolecules. (Fokine et al., Acta Cryst D, 2002)
The program is interactive and needs a pdb coordinates file as input.

MoProGUI

MoProGUI is the Graphical User Interface of the MoPro/VMoPro suite of software.
It is written in JAVA language and works on PC windows, linux & Mac.
The MoProGUI requires the java version 6 (or version 5 for Mac) JAVA6 is downloadable at http://java.sun.com/javase/downloads/index.jsp.
java -version tells you the version of java installed on your computer.

MoProView

MoProView is a Molecular Viewer.
It has Graphical User Interface with some menus enabling computation of VMoPro maps.
Available on PC windows.

**********************************************************************
2 - LIST OF MoPro FILES
**********************************************************************

Run MoPro in a unix/linux or dos terminal by typing: MoPro.exe mopro_input_file_name on PC-Windows, by clicking on the MoPro.exe icon.
The working directory is indicated in the file "mopro.ini" in the line "FILE DIR".
The following input files are compulsory for the execution of MoPro:
- mopro input file : the MoPro commands input file. (default = "mopro.inp")
- parameters_file## : molecular structure including atomic coordinates, thermal displacement and charge density (multipoles) parameters. The end of the file name designates the version number.

The following files are compulsory for crystallographic refinements:
- reflection_file : the diffraction data.
- mopro.tab : atomic orbitals and scattering factors table.
- WAVEF : description of atomic wave functions

The following files are optional:
- "mopro.ini" : to indicate path to working directory and some library files.
- RESTRAIN : list of restraints to apply during the refinement.
- CONSTRAIN : list of constraints to apply during the refinement.
- asf_Kissel.dat : anomalous scattering table for atoms (Kissel,1995)
- Parameters_selection : indicates the parameters of the model to be refined

The following files are normal output of MoPro:
- parameters_file##+1 : the molecular structure after refinements.

The Version number is incremented by 1.
e.g. the output of "peptide01" is "peptide02"

An output file "mopro.out02", which is identical to "mopro.out", is also created.
- "mopro.out" : in which are listed the parameters shifts, agreement factors, disagreeable reflections etc...
- "RESTRAIN.log" : list the results of restraints applied during the refinement.
- "CONSTRAIN.log" : list the results of constraints applied during the refinement.
- "ref.template" : this file is a template for the parameters selection file. This way, if you don't know how to generate it, do only a structure factors calculation with your model to get this template file.
- "ref.current" : this file indicates which parameters were refined during the last cycle.
- "mopro.check" : retrieves the lines read in input files and lists some subroutines used. This file is useful to find the cause of an error when the program fails to run.

**********************************************************************
3 - FILES DESCRIPTION
**********************************************************************

*

**********************************************************************
3.1 - THE MOLECULAR PARAMETERS FILE
**********************************************************************

* To describe a MoPro molecular parameters file, lets take the simple example of a water molecule.
In the file below, there are 3 atoms, named OW, H1 and H2.
For the hydrogen atoms, Z is directed towards OW.
For the oxygen atom, the Z axis is the inner bisecting direction of the H1-OW-H2 triplet, while X is along the outer bisecting direction.
! Example of parameters file
! you can insert comments with lines beginning by !

WSIG 1. 0.
! SPACE GROUP P 21

SCALE 3 7.5647 -0.13 0.23 ! 3 scale factors

CELL 10.7107 6.6140 8.4967 90.00 97.133 90.0 0.7107

SYMM 2 P CENTRO
X , Y , Z
-X , 1/2+Y, -Z

! EQUIV ! ORTEP code of molecular internal symmetries

UOVER 0.0000 ISO

EXTIN 0.0000

SOLVT 0.00000 50.00000
! SOLVT ENV 0.35 50. !! F = Fmodel + Fsolv

! dummy atoms definition
DUMMY 1
DUMY 0.345 0.445 0.143 D1 0 ! #4 dummy atom
! dummy atoms may be used for local axes definition.
! The first dummy atom has atom number NA+1,
! where NA is the number of normal atoms in the structure.
! residue number of dummy atoms is 0.

! anomalous contribution multiplier
FMULT 1.00000

KAPPA 2
1.000000 1.000000 6. 0. ! #1 OW HOH 1
1.160000 1.000000 1. 0. ! #2 H1 HOH 1

ATOMS 3

ATOM 1 OW HOH 1 0.60011 -0.18260 -0.06259 1.000 1 O
bZX H1 H2 OCT K1 V0 Q0
UANI 0.016464 0.019319 0.024018 0.007591 0.008773 0.011924
6.000 0. 0. 0. 0. 0. 0. 0. 0. 0.
0. 0. 0. 0. 0. 0. 0.

ATOM 2 H1 HOH 1 0.52872 -0.22696 -0.01034 1.000 1 H
ZX OW H2 DIP K2 V0 Q0
UISO 0.027838
1.000 0. 0. 0. 0.

ATOM 3 H2 HOH 1 0.54648 -0.11688 -0.09235 1.000 1 H
ZX OW H1 DIP K2 V1_H1 Q0
UISO 0.037540

ANHAR 1 5 ! number_of_anharmonic_atoms max_order
5 ! C 1 atom_number
> 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00
0.00E+00 0.00E+00
0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00
0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00
0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00
0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00
0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00


In this molecule the thermal motion description is respectively anisotropic for the oxygen atom and isotropic for the hydrogen ones.
A kappa1:kappa2 parameter set is defined for OW and (H1=H2).
Most are compulsory keywords in the MoPro molecular parameters file.

! SPACE_GROUP P 21
Optional space group name

WSIG Ws ...
Optional weighting scheme. See definition of WSIG in mopro.inp section.

! SPACE GROUP P 21 : optional
CELL a b c alpha beta gamma lambda
Unit cell parameters and wavelength in Angstrom and degree
(free format).

ZERR sig_a sig_b sig_c sig_alpha sig_beta sig_gamma
Error on unit cell parameters in Angstrom and degree (free format, optional).

SYMM number_symmetry_cards lattice_mode (CENTRO)
The lattice mode can be A, B, C, P, I, R or F.
When the lattice mode is declared, the lattice mode symmetry cards
do not need to be included (e.g. X+1/2, Y+1/2, Z for mode C).
The CENTRO keyword indicates that the space group is centrosymmetric,The symmetry cards are read in the next lines.

SYMM 2 P ! Example of P21 space group:
X , Y , Z
-X , 1/2+Y, -Z

SYMM 2 P CENTRO
If the structure is CENTROsymmetric, just add on the line the keyword.
With the CENTRO option, inversion symmetry cards are automatically.
generated; therefore, do NOT add the (-X , -Y , -Z) symmetry card !

SCALE nb_scale SC1 SC2 ...
number of scale factors and their value(s).
With MoPro, the scale factor is applied to the calculated structure factors, and are defined as a polynomial function of the reciprocal
resolution :
scale factor = sum SCi * s^(i-1) where s= sinTHeta/lambda

UOVER uoverall ISO
UOVER U1 U2 U3 U12 U13 U23 ANI
value of the overall thermal U factor (B = 8.Pi^2 U).
It can be isotropic or anisotropic.
When refining UOV, the shifts are immediately applied to the whole structure.

SOLVT K B
values of solvent parameters K and B in the exponential scaling model. The calculated structure factors Fcalc are modified into Fmod according to :
Fmod = ( 1 - K exp (-B s^2 ) ) Fcalc
If no solvent correction is applied, both K and B must zero.

SOLVT ENV K B
values of solvent parameters K and B in the bulk solvent ENVelope correction.
The ENVelope structure factors are added to structure factors Fcalc of the molecule:
Fmod = Fcalc + K exp ( -B s2 ) Fenv
The Fenv amplitudes and phases are given in a reflection file (containing h k l F PHI°).
The file is specified by FILE SOLV .

FMULT eta
value of the f multiplier (anomalous scattering). Usually eta=1.
For wrong enantiomorph eta=-1. For twin crystals -1< eta <1.

EXTIN extinction_value GAUSS ISOT TYP1 ! G*10^4 specifies the value of the isotropic Gaussian extinction parameter default options are : ISOTropic, TYP1 & Gaussian.

extinction types available are: TYP1 TYP2
Type 1: primary extinction is due to Mosaic Spread (seconds)
Type 2: secondary extinction is linked to Domain Size (Centimeters)

distributions: GAUSS (Gaussian) or LOREN (Lorentzian)
(ANIS : anisotropic extinction is not tested yet).

Example:
EXTIN extinction_value LOREN ISOT TYP2
EXTIN extinction_value GAUSS ISOT TYP2

Tbar = 0.02 (cm) is the default optical path used for extinction correction.
TBAR tbar_value can be specified in the reflections file.

KAPPA nkap
next nkap lines : value of kappa1/kappa2 contraction/expansion coefficient of the spherical and multipolar valence respectively.
kappa1 applies to VAL, and kappa2 to P00 monopole and PLM multipoles.
Exemple of lines giving kappa1 & kappa2 values.
The text after ! is commentary.
1.000000 1.000000 ! OW HOH 1
1.160000 1.000000 ! H1 HOH 2

DUMMY ndum
next ndum lines : DUMY X Y Z DumAtomName 0
Dummy atoms may be useful to define the local atomic axes systems.
Their atom numbering starts from NA+1,
where NA is the number of atoms in the regular molecule.
The residue number is 0.

ATOMS number_atoms

Each atom description starts with keyword "ATOM"

Fist Line :
ATOM Atom_nb Atom_name Residue_name Residue_nb X Y Z Occ Mul Chem
XYZ: Fractional atomic coordinates
Occ: Occupancy factor. (See also Occupancy CONSTRAINT).
Mul: Site symmetry Multiplicity.

Second Line :
axis atom1 atom2 multipol_level kappa_nb Valence_Cons Multipol_Cons Occ_Cons

axis :
Coordinate system definition of atom among :
Standard : XY ZX bXY bZX 3ZX 3bZ 3Zb
Is also accepted: YX XZ YZ ZY, bYX bXZ bYZ bZY
-XY -YZ -ZX are left handed local axes systems
nXY nYZ nZX are left handed local axes systems using bisecting directions
(nXY is similar to bXY, except for Z which is reversed)

XY means X is the direction atom0-atom1
& XY plane is formed by atom0 atom1 atom2
bXY means X is the bisecting direction of atom2/atom0\atom1
& XY plane is formed by atoms atom0 atom1 atom2

atom1 atom2 : designation of atoms defining local axes of atom.
examples:
12 : atom number 12
CA : atom CA
3_C : atom C of residue number 3
Symmetry equivalent atoms may be used to define the second atom used for local axes definitions.
The Symmetry code is added to an atom as a string 'SYM' finished with proper symmetry card number or ORTEP code.
N_SYM65554 : atom N with symmetry relation 65554 (ORTEP)
2_C4A_SYM4 : atom C4A of residue 2 with symmetry #4
Dummy atoms may be used for atom1 & atom2 axes definitions.
Dummy atoms numbering start from Nat+1, where Nat is the number of real atoms in the structure.

multipol_level : among COR MON DIP QUA OCT HEX
Level of multipole function used in Fcalc.
COR : core electrons only, no valence
MON : core and spherical valence only

K##: The kappa1/kappa2 number corresponding to the current atom.
Valence_cons : atom to which the valence is constrained to be identical.
Valence constraint applies to Pval & Plm multipoles
V0 no constraint
V3 atom is constrained to atom no. 3
V5_CA atom is constrained to atom CA of residue no. 5

Multipole_cons : atom to which the multipoles are constrained to be identical this constraint applies only to Plm multipoles
M0 no constraint
M3 atom is constrained to atom nb 3
M5_CA atom is constrained to atom CA of residue nb 5

Occup_cons : atom to which the occupation is constrained to be identical (Q=Q') or complementary (Q+Q'=1.)
Examples:
Q0 no occupancy constraint
To constrain atoms C1a and C1b (residue number 1) to have a sum of occupancies equal to unity (Qa+Qb=1):
the occupancy flag of atom C1b is set to Q1_C1a.
To constrain atoms C1a and C2a to have same occupancy (Q1=Q2),
set the occupancy flag of atom C2a to Q-1_C1a or 1-Q1_C1a
Occupancy relations can also be declared in the Constraints file:
> CONOCC 1 C1a C2a CONOCC 1 C1b C2b
> SUMOCC 1 C1a C1b

When a minus sign '-' is used, the occupations are complementary (Q+Q'=1).
Else the occupation factors are constrained to be identical.
If the X-axis direction is negative, the coordinate system will be inverted (by Z-axis inversion) in order to obtain a left handed system.
Otherwise the coordinate system will be right handed.

* Line 3
UANI/UISO U11 U22 U33 U12 U13 U23
UANI keyword for anisotropic thermal motion
UISO keyword for isotropic thermal motion followed by 1 (UIso) or 6 (Uij) thermal motion parameters

* Line 4 (format * )
6.000 0. 0. 0. 0. 0. 0. 0. 0. 0.
Two Monopole populations: Pval & P00
Three Dipole populations. Plm: (1,1+) (1,1-) (1,0)
Five Quadrupole populations. Plm: (2,0) (2,1+) (2,1-) (2,2+) (2,2-)

* Line 5 (if atom has at least octupolar level)
0. 0. 0. 0. 0. 0. 0.
Seven Octupole populations.
Plm: (3,0) (3,1+) (3,1-) (3,2+) (3,2-) (3,3+) (3,3-)

* Line 6 (if atom has at least hexa-decapolar level)
0. 0. 0. 0. 0. 0. 0. 0. 0.
Nine Hexadecapoles.
Plm: (4,0) (4,1+) (4,1-) (4,2+) (4,2-) (4,3+) (4,3-) (4,4+) (4,4-)
Followed by the Charge Density Constraint which indicated to which atom the current atom is constrained.

For atoms with multipole order=6 : there are in adition Eleven 32-poles.
(5,0) (5,1+) (5,1-) (5,2+) (5,2-) (5,3+) (5,3-) (5,4+) (5,4-) (5,5+) (5,5-) (not implemented yet).

The spherical harmonics functions are defined in $ Multipoles.

For the application of Symmetry and Equivalency Constraints on the multipoles, see the SYMPLM, CONPLM, CONVAL, AVEPLM & AVEVAL keywords in $ CONSTRAIN.

ANHAR Nat MoxOrder
Kewword to define anharmonic thermal parameters.
Nat is the number of anharmonic atoms and MaxOrder the maximal order.
The following lines contain the atom numbers and the Gram Charlier coefficients.
In the following example atom #26 & #27 are anharmonic to order 3:
(Order 2 corresponds to anisotropic thermal tensor).

ANHAR 2 3
26
0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00
0.00E+00 0.00E+00
27
0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00
0.00E+00 0.00E+00

Other example, when max_order is 4.
ANHAR 1 4 ! number_of_anharmonic_atoms max_order
5 ! C 1 atom_number
> 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00
0.00E+00 0.00E+00
0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00
0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00 0.00E+00

STOP This keyword closes the molecular parameters file.

ATOMS in SPECIAL POSITION.
These atoms are located on a crystallographic symmetry site (mirror plane, inversion center or rotation axis).
The atom multiplicity is stored after the occupancy in the molecular file.
The valence and multipole populations in the file are given for an atom with full occupation.
(Occ=1. & Multiplicity=2) has the same effect as (Occ=0.5 & Mult=1).
The positions, thermal and multipolar parameters can be constrained using POINTS, SYMANH and SYMPLM keywords.
THE FILT (filter variables) option can be used to handle the parameters which should not be refined.

Example of an atom on a mirror plane with X=0 and therefore U12=U13=0 :
ATOM 1 OW HOH 1 0.00000 -0.18260 -0.06259 1.000 2 O
mZX H1 H2 OCT K1 V0 Q0
UANI 0.016464 0.019319 0.024018 0.000000 0.000000 0.011924
6.000 0. 0. 0. 0. 0. 0. 0. 0. 0.
0. 0. 0. 0. 0. 0. 0.
CONSTRAINTs to be applied :
POINTS X=0 OW 1
POINTS U12=0 1 OW
POINTS U13=0 OW 1
POINTS Y=X+0.5 H1 2
SYMANH mx H1 2
SYMPLM mx H1 2

Other examples:
POINTS Y=X O1 1 !atom on 3 fold axis in cubic system
POINTS Z=X O1 1
POINTS U22=U11 O1 1
POINTS U33=U11 O1 1
POINTS U13=U12 O1 1

POINTS U23=U12 O3 1
POINTS U23=-U12 O3 1

SYMPLM mymz OW 1 ! multipoles follow two mirrors
SYMPLM 2x OW 2 ! multipoles follow two fold axis

**********************************************************************
3.2 - REFLECTION DATA FILE
**********************************************************************

In the reflection data file, both intensities or structure factors moduli are allowed. The reflection lines contain the Miller indices followed by the Intensity or the Structure Factor Amplitude and its sigma:
! H K L Iobs SigIobs Free_flag
1 1 6 22351.400 1187.900
1 1 7 51.400 87.900 0
1 1 8 14351.400 1187.300 F ! free reflection
The Free reflection flag 'F' is optionally read after H K L Y sY.
'-1' is also accepted as free reflection flag.
Zero or blank Free Flag means the reflection belongs to working set.
'F' means the reflection is used as test only for R-free computation.
(Brunger, Nature, 1992)
Blank or commentary lines (!) are allowed in the reflection data file.
The general format (*,*,*, *,*,*) is accepted when the numbers are separated by spaces.
When necessary, a reading format can also be specified with the instruction HKLI FORMAT (see mopro.inp)

**********************************************************************
3.3 - THE COMMANDS FILE "mopro.inp"
**********************************************************************

The MoPro input commands file is read sequentially during the execution of MoPro. The default file name is "mopro.inp". The aim of such type of input file is to respect the notion of refinement strategy. A multipolar refinement is usually not straightforward : many strategies, tests and maybe errors can be made before reaching a correct convergence and a physically meaningful model.
Thus, the MoPro input file has been modified (when compared to the original MOLLY) in order to take into account several strategies during the same run.

Its especially convenient if you work on a supercomputer center.
In this case, you often have to submit a job, then to wait for the execution of the job and eventually for the result.
In MoPro, you can include in the mopro.inp file as many refinement strategies you want.
The only compulsory command in the mopro.inp file is FILE PARA.
Comments can be specified anywhere in the file with lines beginning with !.
Stereochemical analyses can be performed without specifying any reflection file.

FILE specifications

FILE PARA filename
input file describing the structure and charge density parameters.

FILE DATA filename
input reflection file name containing H K L F sigF
or H K L I sigI.

FILE SOLV filename
name of the optional reflection file containing the structure factors of the bulk solvent envelope in the case of protein crystals :
H K L Fcalc(solvent) PHIcalc(solvent)
see SOLVT ENV defined in the parameters file.

FILE TABL filename
name of file describing scattering factors of atoms or orbital populations. Default: "mopro.tab"

FILE CONS filename
name of optional CONSTRAINts file. Default: "CONSTRAIN"

FILE REST filename
name of optional RESTRAINts file name. Default: "RESTRAIN"

FILE WAVE filename
name of file describing wave functions of atoms. Default: "WAVEF"

FILE ANOM filename
name of anomalous scattering file. Default: "asf_Kissel.dat"

FILE SELE filename
or
SELE FILE filename
name of refinement file (manual selection of refined parameters).

In a mopro.inp commands file, a file declaration can appear several times, for example
FILE CONS Constraints1
...
FILE CONS Constraints2
...

Refinement specifications

AUTO REFI
The automatic refinement proposes a complete standard strategy for electron density refinement
of a small molecule at ultra high resolution
This can be applied for small molecules with very good diffraction data


REFI ALL ncycles
Refine all parameters SCA XYZ UIJ (ANH) VAL PLM KP1 KP2 successively.
XYZ UIJ parameters of non hydrogen atoms are refined at high order.
Examples:
REFI ALL 4 DAMP 0.5 ! damping factor applied to parameters shifts.
REFI ALL 6 CONV 0.1 ! refine each parameter type up to convergence criterion |max_shift|/sigma<0.1
REFI ALL 6 NOHO ! no high order refinement for XYZ UIJ NOH


REFI DENS ncycles
Refine all charge density parameters successively: VAL PLM KP1 KP2. This is useful for refinement
vs. theoretical structure factors.
DAMP and CONV keywords are also applicable: REFI DENS DAMP 0.8 CONV 0.1


Custom refinements.
Specific variables to be refined can be selected with keyword SELE.
SELE XYZ NOH selects coordinates of non-hydrogen atoms.
SELE UIJ HYD selects thermal parameters of hydrogen atoms.
The main variables are: SCA XYZ UIJ VAL PLM KP1 KP2

other type of variables are:
P00 DIP QUA OCT HEX : specific multipole populations
QZ2 : QZ2 quadripoles only
Notice for DIP and PLM keywords: on hydrogen atoms, only the non-zero dipoles and the main dipole along the H-X bond is refined.
DPH : forces all dipoles on hydrogen atoms to be refined
MNZ : refines only Non-Zero Multipoles

ANH : anharmonic thermal motion coefficients
EXT : extinction coefficient.
SC1 SC2 SC3 ~etc... : specific scale factor #1 #2 #3 ...
FMU : Eta coefficient, Eta=+1 for correct enantiomer, Eta=-1 for inverted molecule.
This parameters requires non merged Friedel pairs.

BOV or UOV : overall B-factor. at the end of refinement it is applied to all Uij's;
therefore BOVER=0 in resulting molecular file.

SWA SW1 SW2 : solvent correction coeffiecients (for macromolecules only).
KAP : combination of KP1 + KP2.
XYZ , X , Y , Z, XY , XZ , YZ , : atoms coordinates
OCC : occupancy factors (all parameters different from unity 1.0 in the molecular file ).

The variables keywords can be combined with atoms selection keywords.

The keywords available to select atoms are:
WAT : WATer atoms only (residue name HOH or WAT)
HYD : HYDrogen atoms only
DIS : DISordered atoms only
VIR : VIRtual atoms only (interactomic spherical charges, chemical type Q)
ISO : ISOtropic atoms only
ANI : ANIsotropic atoms only

NOW : NO Water atoms (residue name HOH or WAT)
NDI : NO Disordered atoms

NOH : NO Hydrogen atoms
NOQ : NO Virtual atoms
NOC : NO Carbon atoms
NOCa : No Calcium atoms, etc...
NO_C_c : No carbon core_only atoms
CHEM Br : only Bromine atoms, etc...
CHEM C O N : only carbon or oxygen or nitrogen atoms

NOZ : NO Zeroes : exclude parameters with a zero value (PLM, UIJ...)

B># : only atom with Beq > #
B<# : only atom with Beq < #

Examples :
SELE FILE ref.UX ! opens file ref.UX
SELE XYZ UIJ HYD NOW
SELE PLM B<11 NOW
SELE SCA SW1 SW2
SELE XYZ WAT
SELE UIJ ANI
SELE PLM NOH + DPH QZ2 HYD ! refine DX DY DZ QZ2 for hydrogen

REFI keywords
This is the most important keyword in MoPro.
Each REFI keyword does correspond to a refinement step as indicated in the output file.
When the program meets a REFI keyword, it checks if the instruction SELE is present before in the input file.

If yes, the program performs the refinement of the last selected parameters. If not, the program stops with an error message.

There are keywords associated with REFI (written on the same line, in any order), but only LS or CG is compulsory:

REFI LS number_cycles
REFI CG number_cycles :
refinement using matrix inversion (LS) or preconditioned conjugate gradients (CG) followed by the number of cycles.

REFI DAMP damping_factor
If you want to apply a damping factor to the parameter shifts.
Example : REFI LS 3 DAMP 0.7

REFI DIAG : keep only diagonal elements in normal matrix.

REFI SPARSE sparse_cutoff_distance (in Angstrom)
This keyword is useful in the case of large molecules (proteins) to select the inter-atomic distance cutoff for the inclusion in the normal matrix.
A cutoff of infinity means all the matrix elements will be computed and used in the refinement (this is the default!).
A 3 Angstrom cutoff means that only the correlation elements of the normal matrix which correspond to atoms separated by less than 3A will be used in the refinement.
Of course, a zero cutoff means the bloc diagonal approximation of the normal matrix will be used.
The "sparse" option is especially convenient in case of high resolution protein structures, as a 4A cutoff reduces the matrix size by c.a. 90% (and therefore the CPU time) without major altering the parameter shifts!

REFI LS 5 CONV conv_lim
The CONV keyword make the refinement stop when max(parameter_shift/sigma) is smaller than the value conv_lim.

REFI LAST
This keyword means that, at the end of the refinement step, a subsequent calculation of the structure factors and the agreement factors statistics will be performed.
The calculated Structure factors are therefore updated with the latest structure parameters.
The command WRIT RFAC has a similar effect.

Here are some examples of refinement steps :

REFI LS 1 DAMP 0.2 SPARSE 3. LAST
One cycle of least squares refinement, with a 0.2 damping factor, a Fcalc and R factors calculation at the end of the step, and using a 3A sparse distance cutoff.

REFI CG 10 SPARSE 3. LAST
10 cycles of conjugate gradients refinement, using the bloc diagonal approximation of the normal matrix and Fcalc and R factors calculation at the end of the step.

REFI CG 5 DAMP 0.8
5 cycles of conjugate gradients refinement, with a 0.8 damping factor.


Refinement options

SCAT GAUSS
Scattering factors are Gaussian, similar to SHELXL.
Multipolar refinement is not possible with this option.

> REFI DIAG CG 1
Refinement with diagonal matrix approximation (fast matrix calculation and inversion).

FILT sigma_cutoff :
Filter out parameters refined with a large standard deviation ( > cutoff ).
The FILT option eliminates the zero or low diagonal elements in the normal
matrix and helps to avoid matrix singularity.
It removes also strong binary correlations between variables ( |Corr| > 0.999 ).
FILT : FILTer using default sigma cutoff = 1.
FILT NO : do not filter out parameters (default, if no filter option specified)
Notice VALence population refinement of atoms like Li+, Na+, K+,
which are close to zero, might yield a sigma. Some core atoms might need
to be be displaced to VALence shell for proper refinement.

FILT EIGV cutoff (NORM)
Filter eigenvalues. Eigenvalues smaller than cutoff*max(eigenvalue) are filtered.
NORM is optional, the matrix A'ij of correlation coefficients is then
diagonalized, where A'ij = Aij / (Aii*Ajj)^0.5
The range of eigenvalues in A' matrix is more narrow than in initial normal matrix A.


GRID SOLV
GRID SOLV KSOLmin KSOLmax KSOLincr BSOLmin BSOLmax BSOLincr
2D Grid search of best solvent parameters.
Bulk Solvent correction in case of macromolecules as described in Jiang & Brunger J.Mol.Biol 1994,243,100-115
F = Fmol + Fsol * Ksol * exp(-Bsol*s^2)
Solvent Parameters Ksol Bsol parameters shall not refine well by least squares.
The limits and increments of the 2D grid shall be specifed.

Options Regarding Reflections

DELF cut-off
Delete during the refinement the disagreable reflections with |Io-Ic|/wsigIo > cut-off.
If the weigthing scheme is standardt (WSIG 1), wsigIo = sigma(Iobs) of the intensity.
The reflections deleted are updated at every refinement cycle.

FREE HKL N (Istart)
One reflection out of N is considered as Free reflection (Brunger, Nature, 1992). Free reflections are not used in the refinement, but a R-free value is computed on the subset.
If specified, Istart indicates the first free reflection (default N).
FREE HKL 20 1 ! every 20th reflection is free, the firt free being #1

HKLI F
HKLI I The input reflections file contains structure factors F
or diffraction intensities I (default).
The default format is read(input,*) : all the numbers should be separated by spaces.

HKLI F FORMAT (3I5, 10X, 2F9.2, 2X,A)
specifies the format of the reflections file
Here: 3 integer numbers of length 5, ignore 10 characters, 2 real numbers with 9 characters and 2 decimal digits, ignore 2 characters, free flag character.
The program can hence read a file containing e.g. H K L Icalc Iobs sigI, by ignoring the columns corresponding to Icalc.
The format is also useful when large numbers touch the precedent number in the reflections file.

HKLR F
HKLR I Indicates if the refinement is performed versus the structure factors F (default) or the diffraction intensities I.

OMIT h k l to omit reflection h k l.
Applies only to refinement instructions subsequent in 'mopro.inp'.

RADI XRAY
RADI NEUT ! specifies radiation type X-ray or Neutron.

RESO resolution1 resolution2
The resolution range is expressed in Angstrom.
It is applied during the refinements and can be changed during the refinement strategy. (see also SINT)
Default: 0.1 999. Example: RESO 0.7 20.

SCAT TABL ! scattering factors of atoms are computed from mopro.tab & WAVEF library files.
SCAT GAUSS ! scattering factors are stored inside from the program as a sum of Gaussian functions.
These are the same scattering factors as in program SHELXL.
Some charged of heavy atoms are not available for this option.
The SCAT GAUSS option is available only for spherical neutral atoms.
It is useful for faster computation of structure factors in the refinement of macromolecules.

SINT s1 s2
Reciprocal Resolution range s expressed in Angstrom^-1.
s = sin(Theta/Lambda) = 1 / 2d where d is the resolution.
It is applied during the subsequent refinements and can be changed anytime by another SINT/RESO command.
Default: 0. 2. Example: SINT 0. 0.7

SIGC sigma_cutoff
Reflections which are below a signal/noise ratio, are omitted.
The cutoff is applied on I/((I) or F/((F), depending on the reflection file content. Default & recommended values : 0.
Example: SIGC 0.

WSIG wS wI wD
Apply a weighting scheme on reflections:
WSIG = 1 / [ ( wS * SigIo^2 + wI * Io^2 ) * D^wD ]
Default : WSIG = 1/SigI^2 with wS=1 wI=0 wD=0
where D is the resolution of the reflection.

Special cases:
WSIG UNIT : unitary weight on structure factors WSIG(F)=1
(meaning WSIG(I)=2F if refinement is vs Intensities)

WSIG SHEL a a : Shelxl weighting scheme. W(Ihkl) = 1/(sigmaI + a*P^2 + b*P)^2
where P = (Fo^2 + 2*Fc^2)/3

WSIG B : Weighting scheme depending on the resolution:
W(Fhkl)=exp(-B*s**2)
where B is an isotropic thermal parameters. Typical value: B=1.
This option can be useful for refinement vs. theoretical structure factors.

WSIG GOF3 : computes and applies a new weighting scheme
WSIG(wS,WI,wD) at each cycle for goodness of fit equal to unity.

WSIG GOF2 : computes automatically and applies a new weighting scheme WSIG(wS,wI).

WSIG GOF1 : computes automatically and applies a new weighting scheme WSIG(wS).

WSIG GOF2 & WSIG GOF3 can diverge and should be used with care !
The weighting scheme is also written to the molecular parameters file.



CONSTRAINTS & RESTRAINTS COMMANDS

CONS kwd applies a constraint on demand.
CONS NO kwd removes constraints of type SYMP or CONP.

ANGL DIST URAT KAP constraints are applied on demand, while
SYMP CONP constraints are by default, applied automatically.

CONS ANGL
CONS DIST
CONS URAT
CONS PLAN
These keywords apply respectively the CONANG, CONDIS, CONURA and CONPLA constraints found in the CONSTRAIN file.
The changes applied are written to the file CONSTRAIN.log.
These 4 constraints are applied only on demand.

CONS PLAN HYD : moves only hydrogen to least squares plane
CONS PLAN : moves all atoms to least squares plane
CONS NO PLAN : do not apply planarity constraints present in Constraints file
CONS NO PLAN NOH : do not apply planarity constraints on non-hydrogen atoms

Constraints on the charge density:

CONS KAPP : Constrain chemically equivalent atoms to have same Kappa sets.
KAPP constraints are normally applied automatically before each refinement cycle (exception: see CONS NO KAPP).
CONS KAPP HYD : Constrain chemically equivalent HYDrogen atoms to have same Kappa sets.

CONS NO KAPP : Remove equivalence constraints on KAPPAs; as consequence, there is one (KP1,KP2) set per Atom.

CONS NO KAPP NOH : Remove equivalence constraints on KAPPAs, except for hydrogen atoms, which remain constraint.

CONS EQUI or CONS CONP
Apply chemical equivalence of atoms constraints on demand at any time in mopro.inp.
EQUI type includes CONPVM CONPLM CONVAL
AVEPVM AVEPLM & AVEVAL
EQUI constraints are normally applied automatically before each refinement cycle (exception: see CONS NO EQUI).

CONS EQUI HYD : Constrain chemically equivalent HYDrogen atoms to have same valence and multipole populations.

CONS NO EQUI : Remove atoms equivalence constraints on multipoles
In subsequent refinement cycles, these constraints are not applied anymore.

CONS NO EQUI NOH : Remove atoms equivalence constraints on multipoles, except for hydrogen atoms, which remain constrained.

CONS NO EQUI DIS : NO equivalence constraints for DISordered atoms.

CONS SYMP
Apply SYMPLM type constraints on demand at any time in mopro.inp.
Basic SYMPLM type constraints are i mx my mz mmm 2x 2y 2z 222 3m...
mirrors and axes may be appended: mxmy mymz 2x2y
SYMPLM constraints are normally applied automatically before each refinement cycle (exception: see CONS NO SYMP).

CONS NO SYMP : Remove Symmetry constraints on PLM multipoles

REST YES or NO
Decides if RESTRAIN file is to be used or not. Default: YES.

PREP REST DIST
PREP REST URAT
PREPares automatically DISTance and URATio RESTRAINts for a newly studied molecule and writes the RESTRAIN file.
This is based on the connectivity of hydrogen atoms.
The PREP functionalities should be applied only once at the beginning of the refinement.

PREP REST SIMD
PREPares automatically SIMDIS RESTRAINts and writes them in the RESTRAIN file.
This is based on the connectivity of hydrogen atoms.
For example for a X-CH3 groups, all X...H distances are restrained to be similar.
PREP REST SIMA
PREPares automatically SIMANG RESTRAINts and writes them in the RESTRAIN file.
This is based on the connectivity of hydrogen atoms.
For example for a X-CH3 groups, all X-C-H angles are restrained to be similar, the same applied to the three H-C-H angles.
SIMANG restarints are not recommended as they can generate singular normal matrices and unstable refinements. PREP REST SIMD is prefered.
PREP CONS DIST
PREP CONS URAT
PREPares automatically CONDIS (distance) and CONURA (Ueq ratio) CONSTRAINts.
This is useful in the case of macromolecules, where hydrogen atoms are not refined.

PREP CONS ANGL
PREPares automatically CONANG constraints.
Example, for a water molecule H1-OW-H2, it generates: CONANG AHH residue_number OW H1 H1

PREP CONS SYMP
Creates some suggested SYMPLM symmetries according to atom local symmetries.

PREP CONS EQUI
PREP CONS KAP
Creates some suggested CONPVM and CONKAP equivalence constraints between atoms in similar chemical functions.

PREP CONS FIXY
Prepares some POINT Symmetry constraints such as:
POINTS X=0. ATOM NR
POINTS Y=0.5 ATOM NR
POINTS Z=0.25 ATOM NR


ANALYSIS COMMANDS (INCLUDING STEREOCHEMISTRY)

After a refinement of coordinates with LS option, i.e. inversion of the full normal matrix, standard deviations are also given for stereochimical parameters (DIST, ANGL, RIGB).
WRIT ANGL : write all bond angles
WRIT ANGL at1 at2 at3 SYM #####

Writes a specific angle between 3 atoms in the mopro.out file.

The SYM ##### card if given , applies to the last atom.
Examples:
WRIT ANGL C 2 O 2 H0 4 SYM 55502
WRIT ANGL 1 C N H0
WRIT ANGL MET CG SD CE

WRIT AXES Displays the atomic local axes for multipoles definition

WRIT CONT distmax SYM #####
Show all contacts shorter than distmax with neighboring molecules.
Default distance cutoff: 3 Angstrom.

WRIT CONT 3.4 ! all contacts d> 3.4 A
WRIT CONT 3. SYM 55501 ! intramolecular contacts
WRIT CONT 3.7 SYM 55502 ! contacts with sym #2
WRIT CONT VDW -0.1 ! contacts closer than rvdw1+rvdw2-0.1 WRIT CONT ZON 2 4 ! contact involving residue numbers 2 to 4 WRIT CONT RES MET ! contacts involving MET residues only
WRIT DEVS
Calculates the deviations of the multipoles from the considered SYMPLM symmetry constrains
by computing the average ratio of the Plm populations over their sigma values:
< |Plm|/sigPlm >

The calculation is performed for the atoms with respect to the SYMPLM constrains stored in the CONSTRAIN file.
Both ratios for symmetry allowed and symmetry restricted multipoles are presented.
The CONS NO SYMP command must preceede the WRIT DEVS in the mopro.inp file.

WRIT DIHE
Write all dihedral angles in mopro.out file.

WRIT DIPO kwd
Computes the dipole moment of the molecule or of a subset of atoms.
Examples :
WRIT DIPO ! whole molecule
WRIT DIPO ZONE 3 5 ! dipole for residues # 3 to # 5
WRIT DIPO ATOM 3 5 8 ! dipole for atoms # 3, 5 and 8

WRIT DIST : write all bond distances

WRIT DIST at1 at2 SYM #####
Writes a specific bond distances in the mopro.out file.

Examples:
WRIT DIST N 1 C 2 ! distance between atoms N 1 and C 2
WRIT DIST N 1 C 2 SYM 55502 ! atom N 1 and symmetric atom C 2

For the definition of symmetry operations, which apply to the second atom, see$ DEFINITIONS.

WRIT DORB : analyze the orbitals of the d electron shell for transition metals Sc-Zn 21<=Z<=30.
WRIT DORB Chem : analyze the orbitals of the d electron shell for atoms of chemical type Chem.

WRIT HBON d
Write all Hydrogen bonds in structure with d(Acceptor,Donor) With all neighbour molecules, unless a symmetry card is specified.

Examples:
WRIT HBON atD atH atA SYM #####
prints geometry of Hydrogen BONd donor and acceptor atoms:
DH, DA, HA and angle DHA.
Ortep symmetry code applies to last atom, i.e.: atA.
atD, atH, atA refer to donor, hydrogen and acceptor atoms.
example: WRIT HBON N 1 H 1 O 2 SYM 55502

WRIT HBON DON atD
Writes only H-bonds involving the donors with atom name atD.

WRIT HBON ACC atA
Writes only H-bonds involving the acceptors with atom name atA.

WRIT HBON HYD atH
Writes only H-bonds involving the hydrogens with atom name atH.

DON, HYD, ACC keywords can be combined.
Example for a protein: WRIT HBON DON N HYD H0 ACC O
WRIT HBON 2.5 HYD HH DON N ! find all short H-bonds d(N,Acceptor)<2.5A involving atoms with names HH and N.

WRIT LIST filename
Write a summary of results at current state of the refinement, includes CIF and molecular parameter file and RESTRAINts used.

WRIT MATR
Write normal matrix Aij & normalized Aij/(Aii*Ajj)^1/2 elements.

WRIT PLAN n at1 at2 ... atn
Gives the equation the least square plane formed by the Nb atoms and the distances of the atoms to the plane. Hydrogen atoms are given a 0.2 weight in the geometrical centre and plane computation.
Example: WRIT PLAN 4 C 1 O 1 N 2 H0 2

WRIT PLAN n at1 at2 ... atn ### 1 at'
The distance to the plane of one supplementary atom is computed.
This atom is not taken into account for the plane definition.
Example: WRIT PLAN 4 C 1 O 1 N 2 H0 2 ### 1 CA 2

WRIT PLAN n at1 at2 ... atn ### 2 at1' at2'
The angle of the plane normal and the segment at1->at2 is computed.
Example: WRIT PLAN 4 C 1 O 1 N 2 H0 2 ### 2 CA 2 CA 1

WRIT PLAN n at1 at2 ... atn ### m at1' at2' at3' ... atm'
The angle between the two planes is computed.

WRIT ORTH
write a molecular parameters file in a cell with 90° angles.
By defaut the cell is cubic with length equal to max (a,b,c).
This can be useful to compute molecular properties in 3D and display them with programs which work only with orthogonal coordinates.

WRIT RFAC Write R-factor statistics in resolution shells.
Global statistics are written in a line starting with >>>

WRIT RFAC # Write R-factor statistics in resolution shells.
Global statistics are written in a line starting with #>>
This can be useful to grep statistics at a given step.
Notice, in usual refinement, after each cycle, statistics are also printed in a line starting with >>

WRIT RIGB
Print out all the values for the rigid bond test ().
dZ = Uij-Uij' value projected along the bond direction.
According to the Hirshfeld criterion, |dZ| should be lower than 0.001 Angstrom^2.

WRIT SYM (Xmax Ymax Zmax)
Prints out the list of symmetries contributing to the electron density in
the defined zone ( x between 0 and Xmax,...). XYZmin are equal to 0.
When XYZmax are not given, they are set to 1. The zone is then the unit cell.

WRIT UIJ
Analyses the thermal parameters ellipsoid Uij: eigenvalues of the tensor. Uij is expressed in (a*/a*, b*/b*, c*/c*).
The tensor and its eigenvalues in an orthogonal normed axes system is also given (a*/a*, b*'/b*', c*'). b*' // b*/b*-a*/a* cos(Gamma)


WRIT FLAK
Computes the Rfactor as a function of Flack parameter X=0. 0.05 0.1 ... 0.95 1.
For Flack parameter estimation, see also SELE ETA, refinement of eta parameter.
Rogers, Acta Cryst., A37, 734, 1981 defines eta that can be used in the determination of Absolute Configuration.
Flack takes values from 0 to 1, while eta takes values between -1. and +1.
Flack = 0. corresponds to eta=+1.
Flack = 1. corresponds to eta=-1.

WRITE OUTPUT FILES

WRIT CIF (filename)
Writes the Crystallographic Information File (CIF) for publication.
The output file name between is optional.
The default output fine name is the parameters_file with suffix ".CIF".

WRIT CIFM (filename) Writes also the multipoles to CIF file.

WRIT CIF SYM ##### Writes CIF applying the specified symmetry

WRIT CRYS Writes coordinates file .d12 for CRYSTAL quantum mechanics program.

WRIT VASP
Creates a coordinates file for VASP software
WRIT FCF3 (filename)
Write a reflection file with SHELXL fcf3 format:
H K L Fobs SigFobs Re(Fcalc) Im(Fcalc)

WRIT FCF6 (filename)
Write a reflection file with SHELXL fcf6 format:
H K L Iobs SigIobs Icalc PHASE(Fcalc)

WRIT FCNS (filename)
Write a reflection file in CNS & XPLOR format.

WRIT FOUR (filename)
This option is designed to print out a Fourier text file:
(h, k, l, Fobs, Fcalc, Phicalc ScaleFactor, sigmaF, WsigmaF Free)
The structure factors written are calculated with the current parameters, i.e. with the values corresponding to the last cycle of the refinement.
The file can be used directly with the display program VMoPro.
The scale factor may vary with the resolution if a solvent correction factor (1-Kexp(-Bs2)) is applied in case of proteins.

WRIT FOUR (filename) ANOM
The Phase is calculated including the anomalous scattering contribution. By default, PHIcalc does not include anomalous scattering.

WRIT FDEF (filename)
Computes Fcalc & PHIcalc for all reflections in the resolution range specified previously.
All reflections are generated, including those missing in the Fobs reflection file.
A resolution higher than the observed diffraction data can be specified.
Fcalc is decomposed in 3 terms:
- spherical deformation density
- multipolar deformation density
- core + neutral spherical valence
The .FDEF file is useful in VMoPro for calculation of the periodic deformation electrostatic potential by Fourier synthesis.
WRIT FDEF STAT (filename) : Fcalc of static electron density (Uij=0 & ANH=0)
WRIT FDEF DYNA (filename) : Fcalc of dynamic electron density (including Uij & ANH)

WRIT FCAL (filename)
Computes FAcalc & FBcalc for all reflections in the resolution range specified previously, similarly to WRIT FDEF.
WRIT FCAL STAT (finename) : static density
WRIT FCAL DYNA (filename) : dynamic density (default)
WRIT FCAL STAT BIN (filename) : output file in binary format. (WRITE NHKL ; WRITE IH, IK, IL, FA, FB)
The resolution limits must be specified before this command with RESO or SINT (in Refinement menu).
WRIT MERG (FRID)

Merge reflections according to crystal symmetry.
FRID: optional keyword, forces the merging Friedel pairs.
DIFF Computes the difference between two reflection files generated by WRIT FOUR.
DIFF FO-FC file1 file2 : {Fo1,Phi1} - {Fc2,Phi2} output file : FO-FC.Fhkl
DIFF FC-FC file1 file2 : {Fc1,Phi1} - {Fc2,Phi2} output file : FC-FC.Fhkl
DIFF PH-PH file1 file2 : Fo1, {Phi1} - {Phi2} output file : PH-PH.Fhkl
The resulting DIFFerence file contains: h k l s F(difference) 0. PHASE(difference)
This is useful to compute Dynamic Deformation Density Maps with VMoPro.
A dynamic deformation map can be computed in VMoPro with the FOUR command:
Use (m=1,n=0) coefficients for the map m*Fo-n*Fc
The two input files must have exactly the same reflections h k l.


DIFF FCAL file1 file2
Computes the difference between two reflection files generated by WRIT FCAL or WRIT
FDEF.
The output file is: DIFF.FCAL
The result is H K L S FA1-FA2 FB1-FB2
where FA and FB are real and imaginary part of structure factor.
The two input files must have exactly the same reflections h k l.

WRIT MOLL (filename)
Write coordinates & charge density file "molly.par" in "MOLLY" format.

WRIT PARA filename
This command is designed to save a molecular parameters file in MoPro format at any given step of a commands file with several instructions.
The output filename is optional.
When no filename is given, the program increments the version number (n->n+1)
of the molecular parameters file.

WRIT PDB filename.pdb
WRIT PDB filename.pdb SYM ##### ##### ....
Writes the orthonormal atomic coordinates in a Protein databank PDB
Format file.
When the SYM keyword is given along with the symmetry code, symmetry operations are also applied to the coordinates.
The symmetry definition is given in chapter 3.
WRIT PDB filename.pdb NOD ! atoms with no-disorder only
WRIT PDB filename.pdb DIS ! atoms with disorder only
WRIT PDB filename.pdb MAIN ! writes only one conformation for disordered atoms.
WRIT PDB filename.pdb DIS SYM 55501 55502

WRIT PDB filename.pdb CHARG
Writes the atomic charge (Nval-Pval) instead of equivalent thermal B factor.

WRIT PLMS (optional_filename)
Writes a list of charge density parameters for all atoms.
This can be useful for publication.

WRIT REFI filename
Write a refinement file (0/1) corresponding to the latest selection of variables
(SELE).

WRIT SHEL
Writes the molecular coordinates and thermal parameters in SHELXL
file format "shelx.ins".

WRIT XYZ
Writes the molecular coordinates in xyz file format.

VERBOSE OPTIONS

VERB keywords
The verbose option is convenient to choose what you want to be printed out in the "opro.out" file. They are few keywords, which have to be written on the same line as for the REFI keyword.

VERB CGC
With this option, the conjugate gradient iterations will be monitored in the mopro.out file. The values of the norm of the shift vector as well as the value of the residual will be written.
The default is no CGC. (The conjugate gradient cycles are not be
VERB CHECK do not delete file "mopro.check" for debuging purposes confounded with the minimization cycles !),
VERB CORR cutoff
Displays the parameters pairs that have a correlation coefficient larger than the cutoff.

VERB DELF |Fobs-Fcalc|/sig(Fobs) cutoff
When the absolute value of the structure factors disagreement is above the selected cutoff, the corresponding
{ h,k,l, Fobs, Fcalc, sig(Fobs), sin(Theta/Lamda) } will be written in the mopro.out file. The default is a 15.0 cutoff.

VERB EXT extinction_cutoff
Displays reflections with extinction factor lower than the extinction cutoff (default 0.8).

VERB SHELL number of resolution shells
This option is useful to select the number of resolution shells used in the agreement factors calculations (LAST keyword).
This value applies also to the variance and scale factor analysis by resolution shell. The default is 10 resolution shells.

VERB SHIFT |shift/s.u.|_cutoff
When the absolute value of the parameter shift over standard uncertainty ratio is above the selected cutoff, the corresponding shift will be printed out in the mopro.out file. The default is zero, i.e. all the shifts are written.

VERB WSIG
Proposes a reflection weighting scheme at each cycle for a goodness of fit equal to unity.


MODIFICATION of MOLECULAR STRUCTURE

ANIS keywords
Set some atoms anisotropic ( see also ISOT )
keywords among: DIS NOD HYD NOH VIR NOV
BBmin ( Bequiv limit )
Q Exemple: ANIS B<2 Q>0.9 NOH NOV

ASSB
Assembles the atoms spread in the crystal into a connected molecule. Useful after geometry
optimization with software CRYSTAL, as coordinates may be symmetry related.

ENAN
If written, the next refinement step will be performed with the enanthiomorph structure.
Anomalous scattering factors i*f" takes opposite sign in the structure calculation.
This keyword is meaningful only if the structure is non centrosymmetric!

ISOT keywords : set some atoms isotropic same keywords as for ANIS
Exemples :
ISOT DIS Set isotropic all DISordered atoms
ISOT HYD Set isotropic all HYDrogen atoms
ISOT VIR Set isotropic all VIRtual atoms
ISOT B>15.
factor
ISOT Q<0.7 Set isotropic atoms with occupancy < 0.7

NEUT : Electroneutrality of whole asymmetric unit content.
NEUT ZONE 1 2 : Global Electroneutrality of residue range [ 1 , 2 ]
NEUT RESI ALA : Electroneutrality of ALA residues
NEUT RESI ALA MET : Electroneutrality of the group ( ALA + MET) residues
NEUT CHARGE 1. : neutralize but leave a formal charge of +1 e.


SCAL Nsca Set number of scale factors : k = k0 + k1*S + k2*S^2 + ... + kn*S^n
with s = sinTheta / Lambda
SHAK XYZ 0.01 Shakes randomly the structure, here XYZ are varied by 1% on average.
SHAK UIJ NOH 0.002 Shakes UIj's except for hydrogen
Variables keywords : PLM VAL KP1 KP2 KAP P00 DIP QUA OCT HEX
Atoms selection keywords : HYD NOH VIR NOV
Notice only non-zero DIP, QUA, OCT, HEX, PLM multipoles are affected.

MOVE Atom NR Variable Shift
Changes a position or a thermal motion parameter of an atom.
Variables which can be "moved" are: X Y Z U11 U22 U33 U12 U13 U23.
Example: MOVE O2 1 X 0.001
MOVE O2 1 U11 -0.00012

SETM MON DIS DISordered atoms (Q<0.95) are set to monopolar level
SETM MON H Hydrogen atoms are set to monopolar level
SETM DIP H Hydrogen atoms are set to dipolar level
SETM QUA N Nitrogen atoms are set to quadripolar level
SETM OCT O Oxygen atoms are set to octapolar level
SETM HEX P Phosphorous atoms are set to hexadecapole level

SYMM ##### : apply symmetry to molecule (ORTEP code)
Example : SYMM 55601 : apply symmetry card #1 and translation +c

ROTA i angle : rotate molecule around axis no. i by specified angle.
Example : ROTA 3 20. : rotate around c axis by 20. degrees.

TRAN tx ty tz : translate molecule (default : fractional coordinates)
TRAN tx ty tz BOHR : translation in atomic units (1 Bohr = 0.52917706 A)
TRAN tx ty tz ANGS : translation in angstrom

TRAN SEQ N : for a protein, translate residue numbers: Nr -> Nr + N
This is useful when protein has several chains.

UIJP : Set Uij thermal ellipsoids positive definite.

ZERO To set atoms "free": neutral and spherical.
This is useful to compute dynamic deformation density maps
(FO,PHImult - FCsph,PHIsph) maps (see DIFF instruction)

ZERO Kappa & Kappa2 -> 1 PLM -> 0 PVAL -> NVAL

ZERO KAP kappa1 & kappa2 set to unity
ZERO KP1 kappa1 set to unity
ZERO KP2 kappa2 set to unity

ZERO VAL valence population PVAL -> NVAL
ZERO PLM multipoles PLM set to zero

ZERO UIJ Uij thermal parameters set to zero
ZERO ANH Anharmonic Thermal Parameters set to zero

HYD and NOH keywords may be added to (de)select hydrogen atoms.
A value different from unity may be specified after KP1 KP2 or KAP.

ZERO KP1 HYD 1.16 kappa1 of hydrogen atoms are set to 1.16
(good starting values of Stewart)
ZERO KP2 HYD 1.3 kappa2 of HYDrogen set to value 1.13
ZERO KP2 HYD kappa2 of HYDrogen set to unity
ZERO KP2 NOH 1. kappa2 of NOn Hydrogen atoms set to unity
ZERO NOH KP2 1. kappa2 of NOn Hydrogen atoms set to unity
ZERO VAL NOH Pval of NOn Hydrogen atoms set to Nval

COMMANDS HANDLING

ADDR address : specifies address in "mopro.inp" file for GOTO instruction
exemple : GOTO high_order_refinement
skipped instructions ....
ADDR high_order_refinement

GOTO address
go to a specified ADDRess in mopro.inp, to skip some lines

LOOP address number_cycles
loop over commands until specified address for several cycles

INCL macro_file_name
INCL is used to apply macros. The commands found in the specified file are included to those present in "mopro.inp".

STOP This keyword indicates the end of the instructions to be applied.
The rest of the 'opro.inp' file is ignored.

SYST command
The system executes the require command. e.g: SYST cp filea fileb

------------------------------------
Example 1 of minimal "mopro.inp" file.

FILE PARA peptide.01
WRIT DIST ! analyze all bond distances
STOP

------------------------------------
Example 2 of "mopro.inp" file.

FILE PARA peptide.01
FILE DATA peptide.Ihkl
HKLI I ! input Iobs
HKLR F ! refine vs. Fhkl
SINT 0. 1.1
SELE SCA
REFI LS 1
STOP

- To start, we read the MoPro molecular parameters file peptide.01, which includes the unit cell parameters, the symmetry cards, the coordinates and thermal parameters. - Then we read the reflections data file named peptide.Ihkl.
- The data file contain Diffraction Intensities I.
- The refinement is performed versus Structure factors F.
- We select the diffraction data 0. < s = sinTheta/Lambda) < 1.1 A-1.
- The variables selected are the scale factor(s).
- One refinement cycle is performed with full matrix inversion (LS).
A parameters selection file is created: "ref.template".

------------------------------------
Example 3.

The following mopro.inp file gives an example of charge density refinement strategy for a small compound.

FILE PARA peptide.par01
FILE DATA peptide.Ihkl
FILE WAVE C:/LibMoPro/WAVEF
FILE TABL C:/LibMoPro/mopro.tab
FILE ANOM C:/LibMoPro/asf_Kissel.dat

VERB CGC SHIFT 10. SHELL 10 DELF 30. AXES WSIG CORR 0.7
SIGC 0.
HKLI I
HKLR F

GOTO HIGHORDER
RESO 30. 0.4
SELE SCA XYZ UIJ
REFI CG 4 SPARSE 3.

ADDR HIGHORDER

RESO 0.7 0.4 ! high order refinement
SELE XYZ UIJ NOH
REFI LS 5 DAMP 0.8 LAST
WRIT DIST
WRIT ANGL

RESO 30. 0.7 ! low order refinement
SELE SCA XYZ UIJ HYD
REFI LS 2
SELE PLM
REFI LS 9 DAMP 0.7 CONV 0.1
WRIT RFAC

WRITE PARA ! save molecular parameters : version n+1

SELE VAL
REFI LS 2 DAMP 0.8
SELE KP1
REFI LS 2 DAMP 0.8
SELE PLM
REFI LS 2 DAMP 0.8
SELE KP2
REFI LS 2 DAMP 0.8

WRITE FOUR peptide02.mul.Fchkl
ZERO ! set atoms free : spherical & neutral
WRITE FOUR peptide02.sph.Fchkl

DIFF FO-FC peptide02.mul.Fchkl peptide02.sph.Fchkl
! computes a difference FOmul.exp(iPHImul) -FCsph.exp(iPHIsph)
! reflection file 'FO-FC.Fhkl'
! A dynamic deformation electron density map can then be obtained
! by Fourier transform in VMoPro

The "mopro.inp" file above describes an extract of a standard
charge density refinement strategy:
- a refinement versus all the reflections of structural parameters xyz Uij
- then a high order refinement (0.7 - followed by a multipoles Plm, Pval and kappa1 refinement against the low resolution range.
- this procedure should be recycled until convergence

As the "mopro.inp" file is sequentially read during the execution of MoPro, each REFI refinement instruction uses the last options encountered, including resolution range, variables selection and so on.
The atomic parameters used are the currently refined parameters, these may be saved with command WRIT PARA filename.
The parameters file or reflections file may be changed during the "mopro.inp" commands ( using FILE PARA & FILE DATA).

**********************************************************************
3.4 - THE RESTRAIN FILE
**********************************************************************

A restraint is applied by adding a quadratic function
[(Xcalc-Xtarget)/SigmaX]**2
to the total function minimized
sum [( Fobs-Fcalc)/SigmaF]**2.

A restraint gives a target to a structural or charge density parameter or a derived quantity. Restraints allow a standard deviation from the target while Constraints do not.

The restraints you want to apply during the refi-nement are specified in the RESTRAIN file. If the RESTRAIN file is found in the local directory, then they are applied. In this case, an analysis of restraints is written in the file RESTRAIN.log. The restraints implemented in MoPro are summarized in the table below.

The way to define atoms concerned by the restraints is given in the definitions section $4. An atom is always designated by an atom name and a residue number nres.

Keyword & Syntax examples of RESTRAINts

ANGLER Angle between three atoms
ANGLER 3x(atom nres) target_angle(deg) sigma (deg)

DISTAN Distance between two atoms
DISTAN 2x(atom nres) target_distance(A) sigma(A)

LINEAR 2_atoms 1_light_atom sigma(A)
A3 is on line (A1,A2)
A3 is Q virtual atom or H atom, while A1 and A2 are heavier

ISOTRO Limits the anisotropy of a thermal ellipsoid.
ISOTRO atom nres sigma
URATIO Biso of a hydrogen atom is proportional to Beq of bonded atom.
URATIO 2x(atom nres) target_ratio sigma

UIJRAT proportionality between Uij factors of two atoms (the second atom rides on the first)
UIJRAT 2x(atom nres) target_ratio sigma

RIGIDB Rigid bond restrain on Uijs between 2 bonded atoms
RIGIDB 2x(atom nres) sigma(A^2) (assumes target=0)
RIGIDB 2x(atom nres) target(A^2) sigma(A^2)
Possible sigma value for small compounds: ~0.0005 A^2.
RIGIDB ALL BON 0.001 ! automatic : all A1-A2 covalent bonds
RIGIDB ALL ANG 0.005 ! automatic : all A1-A3 atoms connected to a same atom A2

KAPVAL Kappa1 are restrained to be correlated with atomic charges q = Pval-Nval.
KAPVAL chemical1 chemical2 ... sigma

VALKAP Atomic charges q = Nval-Pval values are restrained to be correlated with Kappa1.
VALKAP chemical1 chemical2 ... sigma

PLANAR Planarity of N>3 atoms (target=0)
PLANAR N Natoms sigma

* Similarity restraints

SIMANG Similarity of angles
SIMANG 3N_atoms sigma (degree)

SIMDIS Similarity of distances
SIMDIS 2N_atoms sigma (A)

SIMKAP Similarity of kappa1 & kappa2 sets
SIMKAP atoms sigK1 sigK2 .

SIMKP1 Similarity of kappa1 set
SIMKP1 atoms sigK1

SIMKP2 Similarity of kappa2 set
SIMKP2 atoms sigK2

SIMK12 Similarity of kappa1 and Kappa2 for one atom.
SIMKP2 1atom sigK12

SIMUIJ Similarity of Thermal Parameters Uij of two atoms
SIMUIJ 2atoms sigma

SIMPLM Similarity of multipole populations Plm of atoms ( Multipoles, but not Pval P00 )
SIMPLM atoms sigma

SIMVAL Similarity of VALence populations of atoms
SIMVAL atoms sigma

SIMPVM Similarity of VALence & Multipole populations of atoms
SIMPVM atoms sigma

* Specify a target to parameters

XYZRES restrain coordinates XYZ of an atom
XYZRES atom nres x y z sigmaX sigmaY sigmaZ
or
XYZRES atom nres x y z sigma

UIJRES restrain anisotropic thermal parameters of an atom
UIJRES atom nres U11 U22 U33 U12 U13 U23 sigmaU
or
UIJRES atom nres U11 U22 U33 U12 U13 U23 sU11 sU22 sU33 sU12 sU13 sU23

for an isotropic atom, the syntax is:
UIJRES atom nres Uiso sigmaU

KAPPA1 Specifies an ideal Kappa1 value.
KAPPA1 atom nres target sigma
KAPPA1, RESKP1 & KP1RES keywords have the same meaning

KAPPA2 Specifies an ideal Kappa2 value.
KAPPA2 atom nres target sigma
KAPPA2, RESKP2 & KP2RES keywords have the same meaning

VALRES restrain valence population Pval an atom
VALRES atom nres Pval sigma(Pval)

RSYMUL symmetry 1atom sigma
restraints the antisymmetric multipoles to zero (cf constrain SYMPLM)

WEIGHT Weight to alleviate or reinforce restrains in subsequent lines (default 1.)
WEIGHT 1.

REMARK To include a commentary in RESTRAIN file
FINISH end of RESTRAIN instructions (following lines are ignored).

Remarks :

The targets for XYZRES restraint have to be given in fractional coordinates.
The URATIO restraint usually applies between an hydrogen and the bonded heavy atom. The ratio is calculated between equivalents B factors of the two bonded atoms. It is usually set to 1.5 for CH3, O-H, NH3+ groups (remaining rotation degree of freedom) and 1.2 for CH2-, Carom-H, C-H, NH2 , NH groups.

Fr the PLANAR restraint, do not forget to give the number of atoms included in the restraint just after the PLANAR keyword.
Restraints application may be restricted to atoms with high thermal motion only, using the keyword B>

These are applicable to: DISTAN ANGLER PLANAR URATIO UIJRAT ISOTRO RIGIDB SIMUIJ SIMVAL SIMPLM SIMPVM
B># command have to be placed at the beginning of the RESTRAIN file, as they apply only to subsequent restraints found in the file.

Example of RESTRAIN file:
DISTAN B>8 ! distance restraints apply only when Beq>8.
ANGLER B>9.5 ! angle restraints apply only when Beq>9.5
SIMUIJ B>13

ANGLER ++2 C N H0 120. ! last 2 atoms are of residue i+1.

REMARK Stereochemistry of CA-NH3 group
DISTAN H1 1 N 1 1.033 0.005
DISTAN H2 1 N 1 1.033 0.005
DISTAN H3 1 N 1 1.033 0.005
DISTAN MOL C1 C1 1.033 0.005 SYM 55502 ! sym applies to 2nd atom

PLANAR 4 ++2 C O N H0 0.02 ! peptide planes (last 2 atoms are residue N+1)
PLANAR 5 GLN CD OE1 NE2 HE2A HE2B 0.02

ISOTRO WAT OW 0.3 ! all water oxygen atoms

! limit anisotropy of all atoms in a protein with high B-factor :
ISOTRO B>8 ! ISOTRO subsequent restraints apply only on atoms with Beq>8A^2.
ISOTRO CHEM C ! all carbon atoms
ISOTRO CHEM O ! all oxygen atoms
ISOTRO CHEM N
ISOTRO CHEM S

KAPPA2 S1 1 1.00 0.01

KAPPA1 CHEM H 1.16 0.03 ! all hydrogen atoms

KAPPA2 CHEM H_C 1.18 0.02 ! all hydrogen atoms linked to carbon
KAPPA2 CHEM H_N 1.40 0.02
KAPPA2 CHEM H_O 1.5 0.02

KAPVAL 0.04 ! charge & kappa of all atoms correlated
KAPVAL C O N 0.04 ! applies to C O N atoms only
KAPVAL H 0.01 ! H atoms

! similarity restraints
SIMANG ALA H3 N H1 H3 N H2 1.
SIMANG 1 H1 NT H2 H2 NT H3 H1 NT H3 1. ! 3 angles
SIMANG HOH H1 OW H2 ! all H1 / OW \ H2 angles

SIMDIS 3 CB HB1 CB HB2 0.01 ! 2 distances
SIMDIS ALA CB HB1 CB HB2 0.01 ! 2 distances
SIMDIS ALA CB HB1 ALA CB HB2 ALA CB HB3 0.01 ! 3 distances

SIMKAP ALA HB1 HB2 HB3 0.02 0.01
SIMKP1 ALA HB1 HB2 HB3 0.02
SIMKP2 ALA HB1 HB2 HB3 0.01
SIMK12 3 HA 0.01 ! KP1~KP2 for atom HA 3
>
SIMUIJ MET CB CG 0.02
SIMUIJ ALL BOND 0.05 NOH ! all covalent bonds, excluding hydrogen
SIMUIJ ALL ANGL 0.5 NOH ! all i - i+2 atom neighbours

SIMPVM ALL HA 0.03 ! all HA atoms
SIMPVM 1 HT1 HT2 HT3 0.03 ! NH3 terminus
SIMPVM MET HB2 MET HB2 0.03

SIMVAL MET HE1 HE2 HE3 0.03

SIMPLM MET HB1 LYS HB1 0.03

RSYMUL 3m MET CE 0.01 ! multipoles follow 3-fold symmetry

SIMVAL MET TRP CD1 CZ2 0.03 ! similar charge, different Plm geometry

WEIGHT 0.01 ! down weight subsequent restraints

RIGIDB MET CA CB 0.001
RIGIDB N 1 CA 1 0.001
RIGIDB C1 1 C1 1 0.001 SYM 55502 ! sym applies to 2nd atom

URATIO ALA CB H1 1.5 0.1
URATIO ALA N H0 1.2 0.1
FINISH

**********************************************************************
3.5 - THE CONSTRAIN FILE
**********************************************************************

The CONSTRAIN file is build similarly to the RESTRAIN file.
The atoms specifications are described in DEFINITION chapter.

The keywords recognized in the CONSTRAIN file are :
CONDIS CONANG CONPLA : stereochemistry
CONURA : thermal motion
CONANH : anharmonic thermal motion CONKAP : atoms have same KAPPA coefficients
CONPVM CONPLM CONVAL AVEPVM AVEPLM AVEVAL : charge density equivalence of atoms
SYMPLM : symmetry applying on multipoles
SYMANH : symmetry applying on anharmonic parameters
POINTS : point symmetry, for an atom in special positions, to fix X, Y, Z, Uij's to special values.

The Constraints CONKAP CONDIS CONANG CONURA are only applied on demand by the CONS command in mopro.inp.
CONS DIST
CONS ANGL
CONS PLAN
CONS URAT
CONS KAP

POINTS SYMPLM & CON/AVE / PVM/PLM/VAL constraints are automatically applied before each refinement cycle.
See also "CONS NO" command in "mopro.inp" which cancels these constraints.

CONPVM CONPLM CONVAL AVEPVM AVEPLM AVEVAL
These instructions define the charge density constraints: chemically similar atoms are set equivalent (e.g. all N H0 C CA or HA atoms of polypeptides).
CONVAL & AVEVAL apply to valence monopole populations only (VAL & P00).
CONPLM & AVEPLM apply to multipole populations only (PLM,l>0) .
CONPVM & AVEPVM apply to monopole & multipole populations (PVAL, P00 & PLM) .

CONP constraints are applied automatically after the parameters file is read.

AVEPVM, AVEVAL & AVEPLM set the multipole values to the average calculated over the atoms.
Therefore, discrepancies in Plm's in the input parameters file are tolerated and suppressed by averaging.

CONPVM, CONVAL & CONPLM check if all the multipole values are identical for all the concerned the atoms.
When there are discrepancies in Pval or Plm's of constrained atoms, all values are set to those of the reference atom.

SYMPLM sym atomname
Applies local or crystallographic symmetry constraints on the multipoles of an atom
Only one symmetry keyword can be specified by line, but some keywords shall be appended,
e.g.: mxmy

The symmetry keywords currently available are :
mx my mz mirrors
2x 2y 2z 2-fold axes
i in -1 inversion
3z 3 fold axis along z
3m 3-fold axis along z and three mirrors // z (one mirror my is the plane xz)
3x 3y 3-fold axis and three mirrors parallel to x or y (not recommended: use rather 3m)
mmm three mirrors mx my & mz
222 three 2-fold axes 2x 2y 2z
mxmy mymz mxmz ... mirrors may be appended
2x2y 2y2z 2x2z two 2 fold axes
-43m tetrahedral symmetry (with bZX local axes system)
4m 4z four fold axis along z
cy cylindical symmetry along z

SYMPLM mz atom nr ! multipoles obey a symmetry mirror _|_ axis Z
! multipoles antisymmetric with respect to z are zero

SYMPLM my atom nr ! multipoles obey a symmetry mirror _|_ axis Y
SYMPLM mymz atom nr ! multipoles obey 2 symmetry mirrors _|_ axes ZY

SYMPLM 3m atom ! multipoles obey a 3m symmetry around Z axis
! to be used when atom axes are defined by ZX only
! => multipoles obey a symmetry mirror _|_ axis Y
! => multipoles Z**K * X are zero
! => multipoles Z**K * XX-YY are zero
! => multipoles X**4+Y**4-6(XY)**2 is zero
! where K is a positive or zero integer number


SYMANH mx atom nr ! anharmonic parameters obey a mx mirror symmetry
avalable symmetries: mx, my, mz and combinations (mxmymz), i (inversion)

CONKAP
This instruction constrains atoms to have same kappa1 & kappa2 values.
It is applied automatically after parameters file reading.
If the concerned atoms have a different kappa number, the total number of kappas is reduced by 1 in the parameters file.
The first atom is the reference atom to which all other atoms appearing in the line are constrained.
When only some of the atoms sharing the same kappa1 or kappa2 values are desired to be constrained to another atom, the CONS NO KAP command should be applied to deconstrain all tied kappa parameters.

Examples :
CONKAP 1 H1 H2 H3
CONKAP ALA HB1 HB2 HB3
CONKAP SER HG ! HG atoms of all SER residues
CONKAP C1 2 C2 2
CONKAP C1 2 C2 2 C3 3 C4 3
CONKAP ALL HA ! all HA atoms
CONKAP ALL IDEN ! all atoms with same atom name and residue name

CONOCC & SUMOCC Occupations CONSTRAINTS.
Examples:
CONOCC C1a 1 C2a 1 C3a 1 ! atoms have same occupation Q1=Q2=Q3
SUMOCC C1a 1 C1b 1 ! sum of occupations of the 2 atoms is Q1+Q2=1

Example of a disorded moiety: H1a-C1a-C2a=O2a H1b-C1b-C2b=O2b
CONOCC C1a H1a C2a O2a
CONOCC C1b H1b C2b O2b
SUMOCC C1a C1b

POINTS : point symmetry
Applies to an atom located on a crystallographic special position.
Nomenclature : POINTS point_symmetry 1atom
The unique atom must be specified by "AtomName Nresidue" or "Nresidue AtomName".
These constraints apply on coordinates and on thermal parameters (Uij=0):
X=cst Y=cst Z=cst X=Y X=Z Y=Z
U12=cst U13=cst U23=cst U11=U22 U22=U33 U11=U33
Examples :
POINTS X=0. C1 1
POINTS Y=0.5 2 C2
POINTS U12=0 2 C2
POINTS U11=U22 MG1 1
POINTS U12=U11:2 O1 1 ! case of hexagonal crystal

CONURA: Biso of a hydrogen atom is proportional to Beq of the bonded atom.
syntax: CONURA 2atoms target_ratio
CONURA may also be used to contrain two atoms to have identical anisotropic thermal motion.
Example: CONURA I1v 1 I1c 1.0

CONDIS is a stereochemical constraint which translates hydrogen atoms along the X-H bond, it is useful to set the HX distance to standard values obtained from neutron diffraction.
syntax : CONDIS 2atoms target

Ideal distances for a multipolar atom model are from neutron diffraction sterochemical dictionary:
1.059 C-CH3 (in Angstrom)
1.066 X-CH3
1.092 >CH2
1.099 ->CH
1.083 >CH aromatic
1.077 C=CNH2+ -> NH+
1.009 -NH2 >NH

CONANG is a stereochemical constraint applying on angles to generate ideal geometries for chemical groups containing hydrogen atoms.
Examples
CONANG AXHHH 5_atoms
CONANG AXYHH 5_atoms
CONANG AXYZH 5_atoms
CONANG AXYHH 5_atoms (optional H/A\H angle, default 109.47deg)
CONANG AXHH 4_atoms (optional H/A\H angle, default 120deg)
CONANG AXYH 4_atoms
CONANG AXH 3_atoms (optional H/A\H angle, default 109.47deg)
CONANG AHH 3_atoms (optional H/A\H angle, default 104.5deg)

In CONANG instructions A X Y Z refer to non hydrogen atoms.
The central atom A, connected to all other atoms, has to be specified in first position.

The other atoms X Y Z H may be given in any order. For example, CONANG AXYHH ARG CB CG CD HB1 HB2
AXYHH has the following (tetraedral) geometry :

X CA
| |
Y - A - H1 ARG CG - CB - HB1
| |
H2 HB2

CONLIN is a stereochemical constraint applying on hydrogen and virtual atoms to be on a line formed by two atoms.
Examle: CONLIN 1 C1 N1 H1 ! H1 of HCN molecule is on the C-N line.

CONPLA is a stereochemical constraint applying on hydrogen atoms to be in a plane formed by non-H atoms.
CONPLA np np_atoms , where np is the total number of atoms forming the plane

Fixing values of some charge density parameters.
FIXKAP 1atom : kappa1 & kappa2 values are not refined for this atom
FIXPLM 1atom : multipoles fixed
FIXVAL 1atom : valence population fixed
FIXPVM 1atom : valence and multipole populations are fixed

FIXUIJ 1atom : Uij parameters of atom are fixed (not refined)
FIXUIJ 1atom a b c d e f : Uij parameters of atom are fixed to given value and are not further refined.
This constrain is useful to fix Uij values of Hydrogen atoms to values found by program SHADE (Madsen et al.).

Examples of CONSTRAINts:

CONURA 1 NT H1 1.5 ! ratio 1.5 for Biso(H1) / Beq(NT)
CONURA SER CA HA 1.2 ! all CA-HA bonds in SERine residues
CONURA SER OG HG 1.5
CONURA ALA CB HB1 1.5

CONANH 1 I1v I1c ! anh_params of I1v ride on those of I1c

CONDIS ALA H0 N 1.009
CONDIS ALA HB1 CB 1.059
CONDIS ALA HA CA 1.099

CONANG AXHHH ALA CB CA HB1 HB2 HB3
CONANG AXYHH ARG CB CA CG HB1 HB2
CONANG AXYZH ARG CA N C CB HA
CONANG AXHH ARG NH1 CZ HH1A HH1B
CONANG AXYH --- N CA H0 C
CONANG AXH SER OG CB HG
CONANG AHH HOH OW H1 H2
CONPLA 11 PHE CG CD1 CD2 CE1 CE2 CZ HD1 HD2 HE1 HE2 HZ
CONPLA 4 ++2 C O N H0 ! peptide bond
CONPLA 4 C1 1 C2 1 C3 1 H1 1

CONPVM ALL CA ! CA atom of all residues have same Plm & Pval
CONPVM SER OG ! all OG atoms of SER residues have same Plm & Pval
CONPVM GLU OE1 OE2
CONPVM THR HB1 HB2
CONPVM MET HE1 HE2 HE3
AVEPVM GLU OE1 GLU OE2

AVEPLM MET CB MET CG ! CB atom of MET residues have same Plm
CONPLM MET HB1 MET HE1

CONVAL TRP CG CD2 ! CG and CD2 atoms of TRP residues have same monopole Pval
AVEVAL MET SD ! SD atoms of MET residues have same monopoles Pval & P00

CONKAP ALL CA ! ALL CA ATOMS HAVE EQUIVALENT KAPPAs
CONKAP SER OG
CONKAP GLU OE1 OE2
CONKAP 1 H1 H2 H3

SYMPLM mzmy PHE CD1 ! 2 mirrors
SYMPLM 3m NT 1 ! 3m axis of -NH3+
SYMPLM 3m ALA CB ! 3m axis of -CH3
SYMPLM 3m BI3 B ! 3m axis of BI3 molecule
SYMPLM mz BI3 B ! mirror _|_ to z (BI3 planar)

POINTS X=0 C 1 ! points symmetry
POINTS Y=X+0.5 2 CA ! atom is on a symmetry point in tetragonal
POINTS Y=0.5 NT 1
POINTS Z=0.25 C2 1
POINTS U12=0 C2 1
POINTS U13=0 C2 1
POINTS U23=0 MOL ZN1

FIXKAP C1 1
FIXPLM H1 2
FIXVAL H2 2
FIXPVM C2 2


Information on Constraints application

Some constraints are "true constraints", i.e., they are applied during the refinement: the number of variables is reduced and the normal matrix is affected.
Currently the true constraints are:
CONDIS, CONKAP, CONPLM, AVEPLM, CONVAL, AVEVAL, CONPVM, AVEPVM, POINTS X=Y, POINTS U11=U22.

Some constraints fix some variables to a given value and these variables are not refined:
FIXUIJ, FIWVAL, SYMPLM (fixed value = 0), SYMANH, POINTS X=0, POINTS U12=0.

Some constraints leave the variable free to refine and after refinement, they are set to the asked value:
CONANG, CONPLA, CONLIN, CONURA, CONUIJ, MIDUIJ
For these types of constraints, it can be pertinent to apply the equivalent Restraints to stabilize the refinement.
Exemple CONURA 1 C1 H1 1.2 & URATIO 1 C1 H1 1.2 0.01
Another possibility is not to refine the concerned variables.
For example, when using CONANG constraints to fix hydrogen atom positions,
do not refine the position of H atoms (use SELE XYZ NOH command).


**********************************************************************
3.6 - THE PARAMETERS SELECTION FILE
**********************************************************************

The parameters to be refined in a cycle can be defined using keywords like XYZ UIJ HYD ... (see SELE option in mopro.inp file description)
Refering to a parameters selection file is a "manual way" of doing that.

In the multipolar model, there is a maximum of 38 parameters per atoms :
- 3 coordinates
- 6 anisotropic or 1 isotropic thermal motion parameters
- the occupancy factor
- 2 contraction/expansion coefficients kappa1 & kappa2
- 2 spherical valence populations Pval & P00
- multipole populations Plm (3 dipoles, 5 quadrupoles, 7 octapoles, 9 hexadecapoles).
This file is just like a condensed version of the molecular parameters file, where the variables you can refine are replaced by digits :
0 refers to a non refined parameter
1 refers to a refined parameter.

In the framework, in the following example, the 2 scale factors, the valence and multipole populations of the atoms are refined.

SCALE
11
FMULT
0
UOVER
0
SOLVT
00
EXTIN
0
KAPPA
00 00 00 00 00 00 00
00 00 00 00 00 00 00
ATOMS
000 000000 10 111 11111 1111111 000000000 OW WAT 1
000 0 10 100 H1 WAT 1
000 0 10 100 H2 WAT 1
STOP

You dont have to create yourself such files from scratch. By doing a refinement with a keyword selections like SELE SCA the program creates two parameters selection file named "ref.template" (with only zero values) and & "ref.current".
Then, one of these file can be used to create a new refinement file, by replacing some 0 by 1.
WRIT REFI filename enables to save the current refinement file.
Extinction can currently only be refined alone or with scale factors.

The format of one atom line is :
(3I1,I1,6I1,1X,2I1,1X,3I1,1X,5I1,1X,7I1,1X,9I1,A) correspondingto:
XYZ Occ 6_Uij 2 monopoles 3dipoles 5quadrupoles 7octapoles 9hexadecapoles.
The text on the right describing the atom names is commentary.

The kappa1/kappa2 integers are indicated by 00 for each set.
The number of 00 per lines has no importance. You just have to be sure that they are separated by one spacing character, and that there are as many 00 as kappa1/kappa2 sets defined in the atomic parameters file.

You can insert comments in those files with lines beginning by ! like in the atomic parameters file.

The integer numbers corresponding to the multipoles are indicated up to the maximum level of multipoles defined in the atomic parameters file. In the example above, as hydrogen atoms level is 2, integer numbers are indicated up to the dipoles.

**********************************************************************
3.7 - THE SCATTERING FACTORS TABLE FILE (default name: "mopro.tab")
**********************************************************************

This file describe the CORE and VALEnce scattering factors of the atoms.

With option W (Wave Functions) the orbital populations of atoms are given.

CHEM refers to the chemical atom type.

CORE refers to CORE electrons.

VALE Nval N00
VALE refers to VALEnce electrons. The reference numbers of electrons Nval and N00 are given for a neutral atom.
For light atoms Nval is the number of valence electrons while N00 is set 0.
For metals with d electrons, N00 might be set >0.

SLAT describes the multipoles: monopole P00, dipoles, quadrupoles, octapoles, hexadecapoles as Slater type functions.

Slater Radial Density function :
Rl(r) = zeta^(nl+3) r^nl exp(-zeta*r) / (nl+2)!

The SLAT line contains :
W or F : orbital populations description of valence
Alpha : in Bohr-1
nl zetal ( for l = 0, 1 2 3 4 )

l=0 monopole P00
l=1 dipoles
l=2 quadrupoles
l=3 octapoles
l=4 hexadecapoles

ANOM f' f" indicates the anomalous scattering factors.
When not specified, the program can compute f' & f" automatically from library asf_Kissel.dat (FILE ANOM asf_Kissel.dat)
Anomalous scattering should not be applied when refining vs. theoretical Fhkl data.

Exemple of mopro.tab file.
!----------------- Hydrogen --------------------------------------------
CHEM H
ANOM 0. 0.
CORE WAVE 1s0

VALE 1. WAVE 1s1
MONO 0. SLAT 1 1.
DIPO SLAT 2 2.26
QUAD SLAT 2 2.26
OCTA SLAT 2 2.26
HEXA SLAT 2 2.26
!----------------- Carbon ---------------------------------------------
CHEM C
!ANOM use asf_Kissel.dat
CORE WAVE 1s2
VALE 4. WAVE 1s0 2s2 2p2
MONO 0. SLAT 2 3.

DIPO SLAT 2 3.
QUAD SLAT 2 3.
OCTA SLAT 3 3.
HEXA SLAT 4 3.
!----------------- Nitrogen --------------------------------------------
CHEM N
! ANOM ! use asf_Kissel.dat
CORE WAVE 1s2
VALE 5. WAVE 2s2 2p3
MONO 0. SLAT 2 3.8

DIPO SLAT 2 3.8
QUAD SLAT 2 3.8
OCTA SLAT 3 3.8
HEXA SLAT 4 3.8
!----------------- Oxygen ----------------------------------------------
CHEM O
! ANOM use asf_Kissel.dat
CORE WAVE 1s2
VALE 6. WAVE 1s0 2s2 2p4
MONO 0. SLAT 2 4.5

DIPO SLAT 2 4.5
QUAD SLAT 2 4.5
OCTA SLAT 3 4.5
HEXA SLAT 4 4.5


Refinement of kappa_core
An atom may be decomposed in several atoms, for example K_c K_v
where K_c K_v represent (adjustable) core and valence parts of the K atom.
The atom has to be duplicated in the molecular parameters file with a same position
using a zero distance constraint between the two atoms.
This way, it is possible to refine a kappa1 (and Pval) coefficient for the core atoms.
Kappa_core refinement may be useful for ultra high resolution d=0.3A, for metals or for theoretical Fhkl data.
See mopro.tab for examples of core & valence replications of an atom.
Notice chemical types such as K_c, K_v, K_c1, K_c2, k_v1 are recognized as "K" for
for wavefunctions calculations. Therefore the WAVEF* file does not need any modification


FORM FACTORS in mopro.tab.
It is possible to use formfactors in MoPro to describe an atom.
The formfactor represents the scattering factor of the free atom
as a function of s=sin(Theta)/lambda, given by intervals of 0.05 A^-1
The FORM FACTOR replaces the computation of f(s) derived from the WAVE FUNCTIONS file.
Notice: the FORM FACTOR option is not yet implemented in VMoPro,
Therefore properties like rho(r) and lapl(rho(r)) cannot be computed in VMoPro.
However the calculation of the deformation electron density alone is possible.

Exemple for a carbon atom. f(s) with intervals of 0.05 A^-1.

CHEM C2

CORE FORM
2.00000 1.99634 1.98543 1.96748 1.94280 1.91183 1.87507 1.83309
1.78651 1.73597 1.68214 1.62566 1.56717 1.50727 1.44651 1.38542
1.32447 1.26405 1.20453 1.14621 1.08935 1.03414 0.98075 0.92931
0.87989 0.83255 0.78732 0.74420 0.70318 0.66421 0.62727 0.59228
0.55919 0.52793 0.49842 0.47058 0.44435 0.41964 0.39637 0.37446
0.35385 0.33447 0.31623 0.29908 0.28294 0.26777 0.25350 0.24008
0.22745 0.21557 0.20439 0.19386 0.18395 0.17462 0.16583 0.15755
0.14974 0.14237 0.13543 0.12887 0.12269 0.11685 0.11133 0.10612
0.10119 0.09653 0.09212 0.08795 0.08400 0.08026 0.07671 0.07335
0.07017 0.06715 0.06428 0.06156 0.05897 0.05651 0.05418 0.05196

VALE 4. FORM
1.00000 0.93988 0.78535 0.59244 0.41011 0.26336 0.15706 0.08579
0.04104 0.01478 0.00069 -.00578 -.00772 -.00715 -.00533 -.00302
-.00067 0.00150 0.00337 0.00490 0.00612 0.00703 0.00769 0.00812
0.00838 0.00848 0.00848 0.00838 0.00821 0.00799 0.00774 0.00746
0.00717 0.00686 0.00656 0.00625 0.00595 0.00566 0.00537 0.00510
0.00484 0.00459 0.00435 0.00412 0.00390 0.00370 0.00350 0.00332
0.00314 0.00298 0.00282 0.00268 0.00254 0.00241 0.00229 0.00217
0.00206 0.00196 0.00186 0.00177 0.00168 0.00160 0.00153 0.00145
0.00138 0.00132 0.00126 0.00120 0.00114 0.00109 0.00104 0.00100
0.00095 0.00091 0.00087 0.00083 0.00080 0.00076 0.00073 0.00070

MONO 0. SLAT 2 3.1762
DIPO SLAT 2 3.1762
QUAD SLAT 2 3.1762
OCTA SLAT 3 3.1762
HEXA SLAT 4 3.1762
!----- end mopro.tab file --------------


**********************************************************************
3.8 - THE WAVE FUNCTIONS FILE (default "WAVEF")
**********************************************************************

WAVEF contains the coefficients of the Slater functions of the Clementi Wave Functions. Example for a carbon atom:

CARBON
ATOM C s Clementi & Roetti
0 6 2 1s 2s
1 5.43599 .93262 -.20814
1 9.48256 .06931 -.01071
2 1.05749 .00083 .08099
2 1.52427 -.00176 .75045
2 2.68435 .00559 .33549
2 4.20096 .00382 -.14765
ATOM C p Clementi & Roetti
1 4 1 2p
2 0.98073 .28241
2 1.44361 .54697
2 2.60051 .23195
2 6.51003 .01025

First line : After 'ATOM:' the chemical species is defined (A4).

Second line: 3 integer numbers.
1rst : 0 refers to s electron shell, 1 to p, 2 to d, 3 to f
2nd : number of lines to read Slater functions
3rd : number of column to read coefficients of Slater functions

Next lines
Nl zeta coef0 coef1 ...
Nl & zeta define the Slater functions
coef0 , coef1 ... represent the factors of the Slater functions for electron shells s, p, d, f.

**********************************************************************
3.9 - THE "mopro.ini" FILE
**********************************************************************

This file is useful to save the path of the working directory and of several libraryfiles.
The "mopro.ini" seen by the graphical interface MoProGUI.jar is the same directory.
If the programs are run directly without the Graphical Interface, the 'mopro.ini' file may be in the same directory as the MoPro, IMoPro & VMoPro executable files, or alternatively in the working directory.

FILE DIR path ! working directory. Information used by VMoPro, IMoPro & VMoPro
All the input and output files are in the working directory, unless otherwise specified ( FILE TABL ... ).

VMoPro is an interactive program which reads also the following information in "mopro.ini":

FILE TABL D:/LibMoPro/mopro.tab ! TABL file, information used by VMoPro
FILE WAVE D:/LibMoPro/WAVEFtab ! WAVE file, information used by VMoPro
FILE DISP D:/Progs/xnview.exe ! 2D maps Display, information used by VMoPro

FILE VDWD:/LibMoPro/VDWcoef.dat ! Contains coefficients for van der Waals Energy. and is not read in the file mopro.ini anymore. This way, several mopro jobs can be run simultaneouly.
Example:
MoPro.exe /home/user/directory1/mopro.inp &
MoPro.exe /home/user/directory2/mopro2.inp &

**********************************************************************
4 - DEFINITIONS
**********************************************************************

*Atoms definition
There are several ways to define the atoms concerned in RESTRAIN, CONSTRAIN and mopro.inp file:

numresidue atom1 atom2 ...
atom1 numresidue1 atom2 numresidue2 ...
residuename atom1 atom2 ...
ALL atom1 atom2 ...
+++ atom1 atom2 ...(last atom belongs to next residue)
--- atom1 atom2 ...(last atom belong to precedent residue)
++N atom1 atom2 ...(last N atoms belong to next residue)
--N atom1 atom2 ...(last N atoms belong to precedent residue)

Example of different atoms definition:

DISTAN 15 CB OG 1.417 0.01
DISTAN CB 15 OG 15 1.417 0.01

DISTAN ALL CA HA 1.099 0.005
! concerns all CA-HA atom pairs of any residue

DISTAN SER CB OG 1.417 0.01
! concerns all CB-OG atom pairs of SER (serine) residues

DISTAN +++ C N 1.329 0.01
! all peptide bonds C(i) N(i+1)

WRIT DIST N 1 D1 0
! a dummy atom is refered to by its atom_name and residue_number, which is 0.

ANGLER --- H0 N C 120. 1.
CONANG AXH ++2 C N H0 120.

PLANAR 4 ++2 C O N H0 0.01
! all PEPTIDES C O (i) N H0 (i+1)

PLANAR 5 --2 N H0 CA C O 0.02
! all PEPTIDES N H0 CA (1) C O (i-1)

For the CONPLM CONVAL AVEPLM AVEVAL Constraints the following syntax is recognized:

CONPLM ALL atom
CONPLM residuename atom
CONPLM residuename1 atom1 residuename2 atom2

Examples:
CONPLM ALL CB ! ALL CB ATOMS ARE CONSTRAINT TO BE EQUIVALENT
CONPLM ALA CB ! CB ATOMS OF ALA RESIDUES ARE EQUIVALENT
CONPLM ALA CB MET CE ! ALA-CB and MET-CE (CH3) ATOMS ARE EQUIVALENT

*Symmetry Definition
When the SYM keyword is given, symmetry operations are also applied to the coordinates. This codification is used for writing PDB coordinates, for analysing stereochemistry:
(WRIT DIST WRIT ANGL WRIT CONT .... )

The symmetry is given along with the 5 digits.
The first 3 digits describe the translations along a b & c.
The fourth digit equal to 5 or more, means inversion is applied.
The fifth digit refers to the symmetry card number.

Exemples:
55501 : symmetry card #1 (X,Y,Z) & no translation,
46501 : symmetry card #1 (X,Y,Z) then translation X-1 Y+1
56551 : inversion symmetry (-X,-Y,-Z), then translation Y+1
55551 : inversion symmetry (-X,-Y,-Z)
65552 : inversion, then symmetry card #2, then translation X+1.
55502+C : symmetry card #2 & add translation (a+b)/2
55501+I : symmetry card #1 & add translation (a+b+c)/2

+A add a translation of (b+c)/2
+B add a translation of (a+c)/2
+C add a translation of (a+b)/2
+I add a translation of (a+b+c)/2
*DISORDER
Disordered atoms may have two alternative positions.
More than two positions is not recommended.
Atoms names are changed by addition of "a" and "b" at the end.
Exemple: CAa & CAb

Occupations of two atoms may be constrained to have sum equal to unity.
Exemple: To have Q(CAa_3) + Q(CAb_3) = 1.
The occupation constrains of atom CAb should be: Q-3_CA or 1-Q3_CA
Stereochemical & Thermal motion Restraints or Constraints take into account disorder.

For example DISTANCE MET CA HA restrains the CAa-HAa and CAb-HAb bond distances automatically.

Charge density Constraints ignore disorder:
CONPLM MET CA : includes all MET atoms with name CA CAa & CAb.

*Multipoles

(l,m)

Angular Function not normalized

Abreviation in mopro.out

multipole level

1

MONOP 1

Pval

(0, 0)

1

MONOP 2

P00

(1, 1)

x

DIPOL X

Dipoles

(1,-1)

y

DIPOL Y

(1, 0)

z

DIPOL Z

(2, 0)

2z2 - (x2 + y2)

4P 3ZZ-1

Quadrupoles

(2, 1)

zx

4P XZ

(2,-1)

zy

4P YZ

[2, 2)

(x2 - y2)/2

4P XX-YY

(2,-2)

xy

4P XY

(3, 0)

2z3 - 3z(x2 + y2)

(5Z2-3)Z

Octapoles

(3, 1)

x [4z2 - (x2 + y2)]

(5Z2-1)X

(3,-1)

y [4z2 - (x2 + y2)]

(5Z2-1)Y

(3, 2)

z (x - y) (x + y)

Z(XX-YY)

(3,-2)

2xyz

8P 2XYZ

(3, 3)

x3 - 3xy2

X3-3XYY

(3,-3)

y3 - 3yx2

Y3-3XXY

(4, 0)

8z4 - 24z2(x2 + y2) + 3(x2 + y2)2

16P Z4

HexaDecaPoles

(4, 1)

x [4z3 - 3z(x2 + y2)]

16P XZ3

(4,-1)

y [4z3 - 3z(x2 + y2)]

16P YZ3

(4, 2)

(x2 - y2) [6z2 - (x2 + y2)]

Z2*X2-Y2

(4,-2)

2xy [6z2 - (x2 + y2)]

16P XYZ2

(4, 3)

z (x3 - 3xy2)

16P X3Z

(4,-3)

z (y3 - 3yx2)

16P Y3Z

(4, 4)

x4 - 6x2y2 + y4

16PX4+Y4

(4,-4)

4x3y-4xy3

16P X3Y


> *Planes in VMoPro
Properties can be plot in a plane with VMoPro.
The plane definition is derived from 3 atoms, or more generally from 3 positions.
The VMoPro menu asks to define 3 atoms: A0, A1 & A2.
The first atom, A0, is the origin.
The OXY plane is always defined by these 3 atoms.
The user can choose different orientations of planes: XY YZ ZX bXY bYZ bZX.
In the case of planes of type XY, YZ, ZX, the OX direction is defined by AO & A1.
In the case of bXY, bYZ, bZX, the OX direction is bisecting the (AO,A1) & (AO,A2) directions.

For example, the YZ type enables to display a plane perpendicular to a bond.
The plane bZX of a water molecule H1-OW-H2 selects the bisecting mirror plane where the electron lone pairs are located.


> *ORTEP symmetry code
The ORTEP symmetry code is a short way to designate symmetry operator.
The first 3 numbers refer to the translation along a, b and c.
5 means no translation.
The numbers 4 to 5 refer to the symmetry number. Examples:
55501 refers to symmetry #1 with no translation, i.e. X, Y, Z
65401 refers to symmetry #1 with translation (6-5)a+(5-5)b+(4-5)c = a-c
55502 refers to symmetry #2 with no translation.
57503 refers to symmetry #3 with an additional translation of +2b.
55551 refers to the inversion -X, -Y, -Z
35551 refers to the inversion followed by a translation -2a
55552 referes to the inversion follwoed by symmetry #2.
55501+A refers to a translation of lattice mode A, i.e. (b+c)/2
55501+B refers to a translation of lattice mode B, i.e. (a+c)/2
55501+C refers to a translation of lattice mode C, i.e. (a+b)/2
55501+I refers to a translation of lattice mode I, i.e. (a+b+c)/2
55502+A refers to symmetry #2 followed by translation (b+c)/2


*List of space groups

P 1 # 1

P -1 # 2

P 2 # 3

P 21 # 4

C 2 # 5

P m # 6

P c # 7

C m # 8

C c # 9

P 2/m # 10

P 21/m # 11

C 2/m # 12

P 2/c # 13

P 21/c # 14

C 2/c # 15

P 2 2 2 # 16

P 2 2 21 # 17

P 21 21 2 # 18

P 21 21 21 # 19

C 2 2 21 # 20

C 2 2 2 # 21

F 2 2 2 # 22

I 2 2 2 # 23

I 21 21 21 # 24

P m m 2 # 25

P m c 21 # 26

P c c 2 # 27

P m a 2 # 28

P c a 21 # 29

P n c 2 # 30

P m n 21 # 31

P b a 2 # 32

P n a 21 # 33

P n n 2 # 34

C m m 2 # 35

C m c 21 # 36

C c c 2 # 37

A m m 2 # 38

A e m 2 # 39

A m a 2 # 40

A e a 2 # 41

F m m 2 # 42

F d d 2 # 43

I m m 2 # 44

I b a 2 # 45

I m a 2 # 46

P m m m # 47

P n n n # 48

P c c m # 49

P b a n # 50

P m m a # 51

P n n a # 52

P m n a # 53

P c c a # 54

P b a m # 55

P c c n # 56

P b c m # 57

P n n m # 58

P m m n # 59

P b c n # 60

P b c a # 61

P n m a # 62

C m c m # 63

C m c e # 64

C m m m # 65

C c c m # 66

C m m e # 67

C c c e # 68

F m m m # 69

F d d d # 70

I m m m # 71

I b a m # 72

I b c a # 73

I m m a # 74

P 4 # 75

P 41 # 76

P 42 # 77

P 43 # 78

I 4 # 79

I 41 # 80

P -4 # 81

I -4 # 82

P 4/m # 83

P 42/m # 84

P 4/n # 85

P 42/n # 86

I 4/m # 87

I 41/a # 88

P 4 2 2 # 89

P 4 21 2 # 90

P 41 2 2 # 91

P 41 21 2 # 92

P 42 2 2 # 93

P 42 21 2 # 94

P 43 2 2 # 95

P 43 21 2 # 96

I 4 2 2 # 97

I 41 2 2 # 98

P 4 m m # 99

P 4 b m #100

P 42 c m #101

P 42 n m #102

P 4 c c #103

P 4 n c #104

P 42 m c #105

P 42 b c #106

I 4 m m #107

I 4 c m #108

I 41 m d #109

I 41 c d #110

P -4 2 m #111

P -4 2 c #112

P -4 21 m #113

P -4 21 c #114

P -4 m 2 #115

P -4 c 2 #116

P -4 b 2 #117

P -4 n 2 #118

I -4 m 2 #119

I -4 c 2 #120

I -4 2 m #121

I -4 2 d #122

P 4/m m m #123

P 4/m c c #124

P 4/n b m #125

P 4/n n c #126

P 4/m b m #127

P 4/m n c #128

P 4/n m m #129

P 4/n c c #130

P 42/m m c #131

P 42/m c m #132

P 42/n b c #133

P 42/n n m #134

P 42/m b c #135

P 42/m n m #136

P 42/n m c #137

P 42/n c m #138

I 4/m m m #139

I 4/m c m #140

I 41/a m d #141

I 41/a c d #142

P 3 #143

P 31 #144

P 32 #145

R 3 #146

P -3 #147

R -3 #148

P 3 1 2 #149

P 3 2 1 #150

P 31 1 2 #151

P 31 2 1 #152

P 32 1 2 #153

P 32 2 1 #154

R 3 2 #155

P 3 m 1 #156

P 3 1 m #157

P 3 c 1 #158

P 3 1 c #159

R 3 m #160

R 3 c #161

P -3 1 m #162

P -3 1 c #163

P -3 m 1 #164

P -3 c 1 #165

R -3 m #166

R -3 c #167

P 6 #168

P 61 #169

P 65 #170

P 62 #171

P 64 #172

P 63 #173

P -6 #174

P 6/m #175

P 63/m #176

P 6 2 2 #177

P 61 2 2 #178

P 65 2 2 #179

P 62 2 2 #180

P 64 2 2 #181

P 63 2 2 #182

P 6 m m #183

P 6 c c #184

P 63 c m #185

P 63 m c #186

P -6 m 2 #187

P -6 c 2 #188

P -6 2 m #189

P -6 2 c #190

P 6/m m m #191

P 6/m c c #192

P 63/m c m #193

P 63/m m c #194

P 2 3 #195

F 2 3 #196

I 2 3 #197

P 21 3 #198

I 21 3 #199

P m -3 #200

P n -3 #201

F m -3 #202

F d -3 #203

I m -3 #204

P a -3 #205

I a -3 #206

P 4 3 2 #207

P 42 3 2 #208

F 4 3 2 #209

F 41 3 2 #210

I 4 3 2 #211

P 43 3 2 #212

P 41 3 2 #213

I 41 3 2 #214

P -4 3 m #215

F -4 3 m #216

I -4 3 m #217

P -4 3 n #218

F -4 3 c #219

I -4 3 d #220

P m -3 m #221

P n -3 n #222

P m -3 n #223

P n -3 m #224

F m -3 m #225

F m -3 c #226

-3 m #227

F d -3 c #228

I m -3 m #229

I a -3 d #230

**********************************************************************
5 - VMoPro (Computation and Visualization of propreties
**********************************************************************

VMoPro can be run interactively and displays the following main menu.

vmopro > VMoPro Possible commands:
INIT : initialize VMoPro Library & Graphics Display

STAT : STATic (deformation) electron density
ELEC : ELECtrostatic potential map
FOUR : FOURier m*Fo-n*Fc electron density
LAPL : LAPLacian of total electron density
GRAN : GRAdient NORM of electron density or electrostatic potential
CRIT : find CRITical points
ENER : interaction ENERgy computations
INTE : INTEgration of properties: topological charges

SELE : define atoms SELEction for property calculation
PARA : read new MoPro molecular parameters file
PLOT : create & PLOT postscript image from 2D grid
GRID : GRIDs handling
CONT : set Gradient / Basin / IsoCONTour lines options

SYST command : call system to apply a command e.g.: SYST ls SYST dir
HELP ? : help, list of commands
QUIT EXIT STOP END

GRID enable to add, substract, multiply two 2D or 3D grids.
It can also multiply a grid by a scaling factor.
GRID STAT gives statistics on one or two grids (rms values, average, correlation...).

CONT menu if for setting Contour Options to display 2D grid.
I : Isocontour lines
G : Gradient lines (of electrostatic potential or of electron density).
B : Basin lines

LAPL and GRAN menues propose to compute the critical points, which are then added to the 2D grid file and displayed in the postscript file.

CRIT finds the critical points of the electron density, of the electrostatic potential
or of the electron density Laplacian.
For intermolecular CPs, the symmetry codes need to be specified.

Postscript files generated can be edited and merged to combine lines on a same image, for example:
-critical points generated by LAPL can be added to the total electron density map.
-gradient lines (CONT G) can be combuined with isocontour lines (CONT I).

For topological integration of atomic charges and volumes, the program WinXPro can also be used.

**********************************************************************
6 - VMoProViewer
**********************************************************************

* MoProViewer is a Graphical User Interface to display molecules and properties.
It reads MoPro molecular files and propose menus to compute with VMoPro derived properties.
Avalable currently only on Windows.

VMoProViewer can display the bond paths using the file 'cp.dat' generated by VMoPro during calculation of critical points.

**********************************************************************
7 - SOME USEFUL DISPLAY PROGRAMS
**********************************************************************

Jmol is integrated in the MoProGUI. It can dispaly molecules and proposes menus for quick computations of properties.
It reads cube files and can generate:
- 2D isocontour maps
- 3D isosurfaces

* PYMOL (version 0.9 or 1.1) to display 3D XPLOR/CNS isocontour electron density maps.
xplor maps can be generated by VMoPro.
PYMOL is a molecule display program, which can be downloaded at :
http://pymol.sourceforge.net/
To display the molecule "mol.pdb" and the map "gridmap.xplor" at 2.5 sigma level:
File open mol.pdb
File open gridmap.xplor
type : "isomesh m1 , gridmap , 2.5 " or type : "isosurface m1 , gridmap , 2.5 "
for a second surface with different a level, type : "isosurface m2 , gridmap , -2.5 "

* program Pymol version 1.1 or more only
To color a solvent accessible or van der Waals molecular surface according to a property, like electrostatic potential.
- open PDB coordinates file, (called here mol.pdb)
- open 3D xplor grid file with property to map on van der Waals surface, (called here pot.xplor)
- create a ramp for colors (called here ramp_pot)
ramp_new ramp_pot , pot , [-1.,0.,1.]
- create the van der Waals surface of molecule mol:
show surface , mol
- set the solvent probe radius (default=1.4)
set solvent_radius, 1.4
- color the surface according to the property:
set surface_color, ramp_pot, mol
- change ramp of colors if necessary:
ramp_new ramp_pot , pot , [-0.5,0.,0.5]
- you can set surface transparency with menu Setting / Transparency / Surface

To color an isosurface of property #1 (like total electron density) according to property #2, (like electrostatic potential).
- open PDB coordinates file, (called here mol.pdb)
- open 3D xplor grid files #1 and #2, (called here dens.xplor and pot.xplor)
- create isosurface for property #1:
isosurface prop1 , dens, 0.7
- create a ramp for colors (called here ramp_pot)
ramp_new ramp_pot , pot , [-1.,0.,1.]
- color the surface according to the property #2:
set surface_color, ramp_pot, prop1
- change ramp of colors if necessary:
ramp_new ramp_pot , pot , [-0.5,0.,0.5]
- you can set surface transparency with menu Setting / Transparency / Surface
- more colors can be defined :
ramp_new ramp_pot , pot , [-0.4 , -0.2, 0.,0.2,0.4], [red,orange, white,blue, cyan]

* gsview32 version 3.6 of GhostView to display postscript files generated by VmoPro from 2D grids.
http://www.cs.wisc.edu/~ghost/gsview/get36.htm
http://www.ghostgum.com.au/ installer : gsv45w32.exe
More recent versions of gsview do not read postscript files generated by VmoPro.
gsview32 requires to install at first ghostscript (the installer gs811w32.exe can be downloaded on sourceforge).

* xnview.exe to display 2D maps, postscript files generated by VMoPro.
http://www.xnview.com/
XnView needs ghostscript to display postscript files
(the installer gs811w32.exe can be downloaded on sourceforge).

* kghostview to display 2D postscript figures on Linux.

* molekel (version 4.3 ) http://www.cscs.ch/molekel/
(1) load coordinates file ( cube format )
(2) To display electron density isocontour cube maps generated by VMoPro:
Surface menu : load cube file
adjust cutoff & create surface
(3) To display electrostatic potential on molecular surface
Compute menu : Fast surface
Surface menu : grid value & pick surface

* molekel (version 5.0.3) www.bioinformatics.org/molekel/wiki/Main/HomePage>
(1) Load coordinates file ( pdb, cube ... format )
(2) Display the Workspace View (see Menu : View ) in order to keep a list of the files opened
(3) To visualize isovalue surfaces from grid data in Gaussian cube format generated by VMoPro:
Select and click on the file choosen in the Workspace View;
then go in Menu Surfaces: select : Grid Data
You can adjust the cutoff (Value in the dialog box), color, rendering style, iteration, ...
then press the Generate button.
The selection of the Real-time update option will cause a surface to be re-generated without having to press the Generate button each time any value in the dialog box changes
(4) To display color on a molecular surface according to property stored in a cube file
(e.g. electrostatic potential) :
In Menu Surfaces, select:
. Solvent Accessible Surface : click box for Map MEP (From Grid Data).

Notice : orthogonal cube file can be generated, using an orthogonalized molecular file.
Such a file is generated with MoPro command : WRIT ORTH
The molecular_file.ORTH can be used as input for VMoPro to compute the properties in a cube file.

* vmd to display cube maps generated by VMoPro.
http://www.ks.uiuc.edu/Research/vmd/
FILE NEW_MOLECULE LOAD cube file
GRAPHICS REPRESENTATIONS create_representation
Drawing_method : isosurface
adjust isovalue

* MOLISO : to display a property on an iso-contour surface.
Needs to 2 .cube grid files.
http://userpage.chemie.fu-berlin.de/~chuebsch/moliso/download.html

* mapslice, is a home made (Dr Guillot) program to generate 2D grids in VMoPro format.
The program projects the values written in a cube or a xplor 3D grid file in a plane.
VMoPro can then create a postcript file from the projected grid.

* WINXPRO is a program to compute properties from the molecular charge density:
notably topology, critical points, basin integration, bond path.
It is available from Pr Tsirelson at http://xray.nifhi.ac.ru/wxp.

**********************************************************************
8 - DATABASE TRANSFER
**********************************************************************

Import2MoPro : is an interactive program to import SHELXL, PDB, CIF & MOLLY coordinates files.

For proteins and peptides, there is the possibility to transfer multipoles from the Protein Multipolar Database.

For proteins, the imported structures should be fully refined and contain all hydrogen atoms (whether they are visible or not in electron density).

In the case of a multipolar parameter transfer from the database, the exact atom and residue name nomenclature must be respected.

Nevertheless, MoPro performs some checkings during the transfer to avoid atom/residue names mismatch.

The database contains the following residues with the given atom names:

DATABANK.oct2002

ALA : C O N CA CB H0 HA HB1 HB2 HB3
ARG : C O N CA CB CG CD NE CZ NH1 NH2 H0 HA HB1 HB2 HG1 HG2 HD1 HD2 HE HH1A HH1B HH2A HH2B
ASH : C O N CA CB CG OD1 OD2 H0 HA HB1 HB2 HOD
ASN : C O N CA CB CG OD1 ND2 H0 HA HB1 HB2 HD2A
HD2B

CYH : C O N CA CB SG H0 HA HB1 HB2 HG (cysteine)
CYS : C O N CA CB SG H0 HA HB1 HB2 (cystine)

GLN : C O N CA CB CG CD OE1 NE2 H0 HA HB1 HB2 HG1 HG2 HE2A HE2B
GLH : C O N CA CB CG CD OE1 OE2 H0 HA HB1 HB2 HG1 HG2 HOE ( protonated glutamate )
GLU : C O N CA CB CG CD OE1 OE2 H0 HA HB1 HB2 HG1 HG2
GLY : C O N CA H0 HA1 HA2

HID : C O N CA CB CG ND1 CD2 CE1 NE2 H0 HA HB1 HB2 HD2 HE1 HD1 ( Hydrogen on ND1 )
HIP : C O N CA CB CG ND1 CD2 CE1 NE2 H0 HA HB1 HB2 HD1 HD2 HE1 HE2 ( Protonated histidine )
HIS : C O N CA CB CG ND1 CD2 CE1 NE2 H0 HA HB1 HB2 HD2 HE1 HE2 ( Hydrogen on NE2 )

ILE : C O N CA CB CG1 CG2 CD1 H0 HA HB HG1A HG1B HG2A HG2B HG2C HD1A HD1B HD1C
LEU : C O N CA CB CG CD1 CD2 H0 HA HB1 HB2 HG HD1A HD1B HD1C HD2A HD2B HD2C

LYS : C O N CA CB CG CD CE NZ H0 HA HB1 HB2 HG1 HG2 HD1 HD2 HE1 HE2 HZ1 HZ2 HZ3
MET : C O N CA CB CG SD CE H0 HA HB1 HB2 HG1 HG2 HE1 HE2 HE3
PHE : C O N CA CB CG CD1 CD2 CE1 CE2 CZ H0 HA HB1 HB2 HD1 HD2 HE1 HE2 HZ
PRO : C O N CA CB CG CD HA HB1 HB2 HD1 HD2 HG1 HG2

SER : C O N CA CB OG H0 HA HB1 HB2 HG
THR : C O N CA CB OG1 CG2 H0 HA HB HG1 HG2A HG2B HG2C

TRP : C O N CA CB CG CD1 NE1 CD2 CE2 CE3 CZ2 CZ3 CH2 H0 HA HB1 HB2 HD1 HE1 HE3 HZ2 HZ3 HH2
TYR : C O N CA CB CG CD1 CD2 CE1 CE2 CZ OH H0 HA HB1 HB2 HD1 HD2 HE1 HE2 HH
VAL : C O N CA CB CG1 CG2 H0 HA HB HG1A HG1B HG1C HG2A HG2B HG2C

CO2 : CT OT1 OT2 ! C terminus
NH3 : NT H1 H2 H3 ! N terminus
HOH : O H1 H2

CYH = cysteine
CYS = cystine CYT SG_local_axis: CB & SG'
HIS = histidine NE2-HE2 HIP = HIS protonated HID = histidine ND1-HD1
ASH = ASP aspartic acid protonated
GLH = GLU glutamic acid protonated

WAT = WATER MOLECULE WITHOUT H
HOH = WATER MOLECULE WITH HYDROGENS O H1 H2

**********************************************************************
9 - CHECKLIST TO GET STARTED
**********************************************************************

1) run MoProGUI.jar the graphical interface. It requires JAVA version 5 on your computer.

2) Import2MoPro.exe : importation & database transfer program.
This is an interactive program to transform a shelxl, molly, mopro, cif or pdb file to MoPro format.
The multipoles databank can be used to transfer parameters for proteins .

3) Prepare a H K L Iobs sigI (Free) reflections file (free format)

4) The LibMopro directory should contain
- a mopro.tab file with all chemical atom types present in the structure.
- a WAVEF file containing description of atoms wafefunctions.
- asf_Kissel.dat file to compute automatically the anomalous scattering values according to wavelength used

5) Apply AUTO REFI, for an automatic charge density refinement of a small molecule.
The RESTRAIN & CONSTRAIN files are build automatically (with PREP commands).

6) Visualize & Check maps with VMoPro:
deformation electron density, electrostatic potential, Fourier residual ...
A program to display postscript file (gsview32.exe) shouldbe declared in MoProGUI.

**********************************************************************
10 - HOW TO ...
**********************************************************************

**********************************************************************
10.1 - HOW TO Compute a Fourier Residual Electron Density Map
**********************************************************************

The residual Fourier Difference map is obtained from the summation over reflections :
( Fobs - Fcalc ) . exp (i.PHI_calc)

At first with MoPro, generate a FOURier file (command 'WRIT FOUR')
The file contains h k l s Fo Fc PHIc sigFo

Then, with VMoPro, compute the FOURier map with command 'FOUR' and answer questions:
- enter the reflections Fourier file name *.FOUR
- use default coefficients (1., 1.) for m.F1-n.F2 difference Fourier.

Simple Fourier Transform enables to compute a custom grid in 2D or 3D.
Fast Fourier Transform enables to compute a 3D grid on whole unit cell only.

VMoPro generates a postscript file from the 2D grid.
3D grids are available in Xplor/CNs format (for program Pymol) or cube.

**********************************************************************
10.2 - HOW TO Compute a Dynamic Deformation Electron Density Map
**********************************************************************

The Dynamic Deformation is a Fourier Difference map obtained from:
Fobs . exp(i.PHI_mul) - Fcalc_sph . exp (i.PHI_sph)

At first with MoPro
- from the multipolar atom model, generate a FOURier file (WRIT FOUR mul.FOUR)
- Zero the deformation electron density of the molecule, (ZERO) all atoms are set spherical and neutral
- from the spherical atom model, generate a FOURier file (WRIT FOUR sph.FOUR)
- Compute the difference Fourier map ( DIFF FO-FC mul.FOUR sph.FOUR
The output file name will be called FO-FC.Fhkl

The typical script is :
WRIT FOUR mul.FOUR
ZERO
WRIT FOUR sph.FOUR
DIFF FO-FC mul.FOUR sph.FOUR

Other options are available at this step:
for a "model deformation electron density map", choose option FC-FC
for a "phase deformation electron density map", choose option PH-PH

Then, with VMoPro, compute the FOURier map with command FOUR
using input reflections Fourier file "FO-FC.Fhkl"
and default coefficients (1., 1.) for m.F1-n.F2 difference Fourier.

**********************************************************************
10.3 - HOW TO Refine Electron Density vs. Theoretical Data
**********************************************************************

Prepare a reflections file containing: H K L F sigmaF
sigmaF can be set to unity for example.
To avoid anomalous scattering calculation (f' = f" = 0), do not declare the FILE ANOM ask_Kissel.dat.
For structure factors computed from the whole electron density (core+valence), the standard ‘mopro.tab’ file can be used.
If the structure factors are computed from the valence electron density only,
(programme VASP), a new atomic tables file (mopro.tab) needs to be created, with core electrons removed.
Example for carbon:
CHEM C_v
CORE WAVE 1s0
VALE 4. WAVE 1s0 2s2 2p2
MONO 0. SLAT 2 3.1
DIPO SLAT 2 3.1
QUAD SLAT 2 3.1
OCTA SLAT 3 3.1
HEXA SLAT 4 3.1

Set the thermal parameters of atoms to zero : ZERO UIJ

The atomic positions XYZ and the thermal parameters UIJ do not need to be refined.
As Uij's are known, there is no need to do a High Order refinement.
Refine only the parameters: VAL PLM KP1 KP2.
The scale factor is equal to unity in general, or SCA=0.5 in special cases when the
molecule is on a special position (mirror, multiplicity, internal symmetry).
Some people refine the SCAle factor for theoretical data.


**********************************************************************
10.4 - HOW TO get min and max residual density
**********************************************************************

- Compute with MoPro a Fourier file .FOUR
- With VMoPro, apply FOUR in the main menu.
Compute a Fo-Fc Fast Fourier Transform on whole unit cell.
(reply F to question: Do you want Simple or Fast Fourier Transform ? F/[S])
This creates a 3D grid for the electron density (format cube or XPLOR).
- With VMoPro, analyse the 3D grid with option STAT.
this gives the rms min and max values in the 3D grid.

A Fast Fourier Transform can also be computed from MoProViewer (3Dmaps)
Open the resulting Fo-Fc xplor map with MoProViewer
which will give information on the min, max and rms values.

The min and max residual densities have to be entered manually in the final cif file.

**********************************************************************
10.5 - HOW TO compute average free R-factors
**********************************************************************

A syntax (WRIT FREE) is available to compute simply average free rfactors.
A loop with refinements using different test sets has to appear at first.
In the following example, 20 different refinements are performed to get 20 free R-factors, using 5%=1/20 reflections as test sets.
WRIT FREE computes the average free R-factor from the 20 test sets.

LOOP lp1 20
FREE HKL 20 LOOP# lp1

SHAK UIJ 0.003
SHAK XYZ 0.003
REFI ALL 9 DAMP 0.8
WRIT RFAC #
ADDR lp1

WRIT FREE

The free R-factor calculation is useful to get the ideal weights of restraints applying
on the charge density: SIMKAP, SIMPVM, SIMPLM, SIMVAL and RSYMUL.
The weight of these restraints can be modified with the commands:
REST WGHT SIMKAP/SIMPVM/SIMPLM/SIMVAL/RSYMUL weight
Example: REST WGHT SIMPVM 10.0

**********************************************************************
10.6 - HOW TO obtain a map with Gradient Vector Field or Basin lines
**********************************************************************

The gradient lines of the total electron density permit to visualize the atomic basins.
The gradient lines of the total electrostatic potential show the electric field.
At first compute a 2D grid of the property (STAT TOT or ELEC TOT).
Use CONT option in main interactive menu of VMoPro.
The CONT options C/G/B enables to choose between Contour, Gradient and Basin lines.

Type PLOT, from the VMoPro main menu, to draw the postscript file.
Notice: the same grid can be used to obtain the different pictures.


**********************************************************************
10.6 - HOW TO refine the Pval charges of only the water molecule
**********************************************************************

Your asymmetric unit contains an organic molecule with a water molecule.
You may want to keep the water molecule electrically neutral (qO+2qH=0.).
You can name the water atoms with residue name 'HOH' or 'WAT'.
Example: ATOM 1 OW HOH 1 0.427409 0.050013 0.613826 1.0000 1 O Then, the valence populations of the water atoms only can be refined
in the Mopro/Refinement menu of MoProGUI.
Alternatively, water atoms can be excluded from the Pval refinement.



**********************************************************************
11 - REFERENCES
**********************************************************************

Domagala, S. & Jelsch, C. (2008). J. Applied Cryst. 41, 1140-1149.
Optimal local axes and symmetry assignment for charge-density refinement.

Guillot B., Viry L., Guillot R., Lecomte C. & Jelsch C.
J. Applied Crystallography (2001). 34, 214-223.
Refinement of proteins at subatomic resolution with MoPro.

Hansen, N.K. & Coppens, P., (1978) Acta Cryst., A34, 909-921.
Testing aspherical atom refinements on small-molecule data sets.

Jelsch C. Acta Cryst. (2001). A57. 558-570.
Sparsity of the normal matrix in the refinement of proteins at atomicand subatomic resolution.

Jelsch C., Pichon-Pesme V. & Lecomte C. & Aubry A.
Acta Cryst. (1998). D54, 1306-1318.
Transferability of multipole charge density parameters: Application to very high resolution oligopeptide and protein structures.

Jelsch C., Teeter M.M. Lamzin V., Pichon-Pesme V., Blessing R.H. & Lecomte C. Proc. Natl. Acad. Sci. USA. (2000) 97, 3171-3176
Accurate protein crystallography at ultra-high resolution:
valence electron distribution in crambin.

Jelsch, C., Guillot B., Lagoutte, A. & Lecomte C.
J. Applied Crystallography (2005). 38. 38-54.
Advances in protein and small-molecules charge-density refinement methods using MoPro.

Kuhs W.F. Acta Cryst. (1992). A48, 80-98 (anharmonicity, Gram-Charlier parameters)
Generalized atomic displacements in crystallographic structure analysis

Pichon-Pesme, V., Lecomte, C. & Lachekar, H. (1995)
J. Phys. Chem., 99, 6242-6250.
On building a databank of transferable experimental electron density parameters: application to polypeptides.

Pichon-Pesme, V., Jelsch, C., Guillot, B. & Lecomte, C. (2004)
Acta Cryst. A60.
A comparison between experimental and theoretical aspherical atom scattering factors for charge density refinement of large molecules

**********************************************************************
12 - INDEX
**********************************************************************

ADDR mopro.inp see also GOTO : ::
ANGL mopro.inp WRIT CONS : ::
ALL mopro.inp REFI : ::
ALL RESTRAIN residue_name : ::
ANGLER RESTRAIN : ::
ANH mopro.inp SELE : ::
ANHAR molecular parameters file : ::
ANI mopro.inp SELE : ::
ANIS mopro.inp : modification ::
ANOM mopro.inp mopro.ini FILE : mopro.tab
ASSB mopro.inp : modification ::
ATOMS molecular parameters file : ::
AVEPLM CONSTRAIN : ::
AVEPVM CONSTRAIN : ::
AVEVAL CONSTRAIN : ::
AUTO mopro.inp REFI : ::
AXES mopro.inp VERB : ::

BASIN LINES VMoPro CONT : ::
B> B< mopro.inp SELE & ISOT : RESTRAIN file ::
BIN mopro.inp WRIT FCAL : ::
BOND PATH VMoPro CRIT & MoProViewer : ::
BOV mopro.inp same as UOV : ::

CHECK mopro.inp VERB : ::
CELL molecular parameters file : ::
CENTRO molecular parameters file : ::
CHEM : mopro.tab ::
CG mopro.inp REFI : ::
CIF mopro.inp WRIT : IMPORT2MoPro ::
CIFM mopro.inp WRIT : ::
CONANH CONSTRAIN : ::
CONANG CONSTRAIN : ::
CONDIS CONSTRAIN : ::
CONLIN CONSTRAIN : ::
CONPLM CONSTRAIN : ::
CONPLA CONSTRAIN : ::
CONPVM CONSTRAIN : ::
CONVAL CONSTRAIN : ::
CONURA CONSTRAIN : ::
CONP mopro.inp CONS : ::
CONS mopro.inp : ::
CONS mopro.inp FILE : ::
CONSTRAIN : default input file ::
CONSTRAIN.log output file : ::
CONT mopro.inp WRIT : ::
CONV mopro.inp REFI : ::
CONVAL CONSTRAIN : ::
CORE mopro.tab : ::
CORR mopro.inp VERB : ::

DAMP mopro.inp REFI : ::
DATA mopro.inp FILE : ::
DATABASE : IMPORT2MoPro ::
DELF mopro.inp VERB : ::
DELF mopro.inp : ::
DIFF mopro.inp : ::
DIHE mopro.inp WRIT : ::
DIP mopro.inp SELE : ::
DPH mopro.inp SELE SETM : ::
DIPO mopro.inp WRIT : mopro.tab ::
DIR mopro.ini FILE : ::
DIS mopro.inp SELE : ::
DIST mopro.inp WRIT CONS : ::
DIST mopro.inp PREP REST : ::
DISTAN RESTRAIN : ::
DUMMY molecular parameters file : ::
DYNA mopro.inp WRIT FDEF/FCAL : ::

EBS2 mopro.inp : ::
ELEC : VMoPro ::
ENAN mopro.inp : modification ::
ENV parameters file SOLV : ::
EQUI mopro.inp : ::
EQUIV parameters file : ::
EXTIN parameters file : ::
EXT mopro.inp SELE : ::

FCAL mopro.inp WRIT & DIFF : ::
FC-FC mopro.inp DIFF : ::
FCNS mopro.inp WRIT : ::
FCF mopro.inp WRIT : ::
FDEF mopro.inp WRIT : ::
FILT mopro.inp : ::
FINISH RESTRAIN CONSTRAIN : ::
FIXKAP CONSTRAIN : ::
FIXPLM CONSTRAIN : ::
FIXPVM CONSTRAIN : ::
FIXVAL CONSTRAIN : ::
FIXY CONSTRAIN : ::
FLAK mopro.inp WRIT : ::
FMU mopro.inp SELE : ::
FMULT mopro.inp : ::
FO-FC mopro.inp DIFF : ::
FORMAT mopro.inp HKLI : ::
FORMFACTOR mopro.tab : ::
FOUR mopro.inp WRIT : ::
FREE mopro.inp HKL : ::

GOTO mopro.inp
GRAN vmopro
GRAD vmopro
GRID vmopro

mopro.inp see also ADDR : ::
VMoPro : ::

mopro.inp SOLV : ::

HBON mopro.inp WRIT : ::
HEX mopro.inp SELE SETM : ::
HEXA mopro.tab : ::
HKL mopro.inp FREE : ::
HKLI mopro.inp F I : ::
HKLR mopro.inp F I : ::
HYD mopro.inp SELE & ISOT ZERO ::

IMPORT $ 5 : ::
INCL mopro.inp : ::
ISOTRO RESTRAIN : ::
ISO mopro.inp SELE : ::
ISOT mopro.inp : ::

KAP mopro.inp CONS SELE : ::
KAPPA molecular parameters file : ::
KAPPA1 RESTRAIN : ::
KAPPA2 RESTRAIN : ::
KP1 mopro.inp SELE : ::
KP2 mopro.inp SELE : ::
KP1RES RESTRAIN : = KAPPA1 ::
KP2RES RESTRAIN : = KAPPA2 ::

LAST mopro.inp REFI : ::
LINEAR RESTRAIN : ::
LIST mopro.inp WRIT : ::
LS mopro.inp REFI : ::
LOOP mopro.inp : ::

MERG mopro.inp WRIT : output file ::
MOLLY mopro.inp WRIT : IMPORT2MoPro ::
mopro.check : output file ::
mopro.inp : input file ::
mopro.out : output file ::
mopro.tab : default input file ::
MOVE : mopro.inp ::
NEUT mopro.inp : modification ::
NEUTron mopro.inp RADI : ::
NO mopro.inp CONS : ::
NOD mopro.inp SELE : ::
NOH mopro.inp SELE ZERO : ::
NOHO mopro.inp REFI : ::
NOV mopro.inp SELE : ::
NOW mopro.inp SELE : ::
NOZ mopro.inp SELE : ::

MON mopro.inp SELE SETM : ::
MNZ mopro.inp SELE : ::

OCT mopro.inp SELE SETM : ::
OCTA mopro.tab : ::
OMIT mopro.inp : ::
ORTH mopro.inp WRIT : ::

P00 mopro.inp SELE : ::
PARA mopro.inp FILE WRIT : ::
PDB mopro.inp WRIT : IMPORT2MoPro ::
PH-PH mopro.inp DIFF : ::
PLAN mopro.inp WRIT : ::
PLANAR RESTRAIN : ::
PLM mopro.inp SELE : ::
POINTS CONNSTRAIN : ::
PREP mopro.inp REST DIST & URAT ::

QUA mopro.inp SELE SETM : ::
QUAD mopro.tab : ::
QZ2 mopro.inp SELE : ::

RADI mopro.inp XRAY/NEUT : ::
ref.current : output file ::
ref.template : output file ::
RESI mopro.inp DIPO : ::
REFI mopro.inp AUTO : ::
RESKP1 RESTRAIN : = KAPPA1 ::
RESKP2 RESTRAIN : = KAPPA2 ::
RESO mopro.inp (cf SINT) : ::
REST mopro.inp : ::
REST mopro.inp FILE : ::
REST mopro.inp PREP : ::
RESTRAIN : default input file ::
RESTRAIN.log : output file ::
RFAC mopro.inp WRIT :
RIGB mopro.inp : ::
RIGIDB RESTRAIN : ::
ROTA mopro.inp : ::
RSYMUL RESTRAIN : ::

SCA mopro.inp SELE : ::
SCAL mopro.inp : modification ::
SCALE parameters file : ::
SCAT mopro.inp TABL GAUSS : ::
SELE mopro.inp : ::
SETM mopro.inp : modification ::
SHAK mopro.inp : modification ::
SHELX mopro.inp WRIT : IMPORT2MoPro ::
SHELL mopro.inp VERB : ::
SHIFT mopro.inp VERB : ::
SINT mopro.inp (cf RESO) : ::
SIGC mopro.inp : ::
SIMANG RESTRAIN : ::
SIMDIS RESTRAIN : ::
SIMKAP RESTRAIN : ::
SIMKP1 RESTRAIN : ::
SIMKP2 RESTRAIN : ::
SIMK12 RESTRAIN : ::
SIMPLM RESTRAIN : ::
SIMPVM RESTRAIN : ::
SIMUIJ RESTRAIN : ::
SIMVAL RESTRAIN : ::
SLAT mopro.tab : ::
SOLV mopro.inp FILE GRID : ::
SOLVT molecular parameters file : ::
SPARSE mopro.inp : ::
SPACE GROUP molecular parameters file : ::
STAT mopro.inp WRIT FDEF/FCAL : ::
STOP mopro.inp parameter file : ::
SW1 mopro.inp SELE : ::
SW2 mopro.inp SELE : ::
SYM mopro.inp : RESTRAIN file ::
SYMANH CONSTRAIN : ::
SYMM molecular parameters file : ::
SYMM mopro.inp : modification ::
SYMMETRY definitions : ::
SYMPLM CONSTRAIN : ::
SYST mopro.inp : ::

TABL mopro.inp mopro.ini FILE : ::
TRAN mopro.inp : modification ::
TRDB mopro.inp : transfer database ::

UIJ mopro.inp SELE : ::
UIJP mopro.inp : modification ::
UIJRAT RESTRAIN : ::
UIJRES RESTRAIN : ::
UOV mopro.inp SELE : ::
UOVER molecular parameters file : ::
URAT mopro.inp CONS : ::
URAT mopro.inp PREP REST : ::
URATIO RESTRAIN : ::

VAL mopro.inp SELE : ::
VALE mopro.tab : ::
VALRES RESTRAIN : ::
VERB mopro.inp : ::
VIR mopro.inp SELE : ::

WAVE mopro.inp mopro.ini FILE : ::
WAVEF : default input file ::
WEIGHT RESTRAIN : ::
WILS mopro.inp WRIT : ::
WRIT mopro.inp : output ::

XRAY mopro.inp RADI : ::
XYZ mopro.inp SELE WRIT : ::
XYZRES RESTRAIN : ::
ZERO mopro.inp : reset ::
ZERR molecular parameters file : ::

**********************************************************************
13 - HOW TO GET MoPro ?
**********************************************************************

The Software if freely distributed to the scientific community.

Connect to the WeB Site :
http://www.crystallography.fr/crm2/fr/labo/equipes/biomod/mopro-download.html
(Group Biocristallography & Modelling of CRM2 )

Under Logiciel MoPro / Software MoPro fill out the User Registration Form.

MoPro DOCUMENTATION THE END