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WinCoot FAQ

WinCoot FAQs and problems page

Known bugs and problems?

For the usual coot problems and bugs have a look at Paul's FAQ page. Often RTFM helps too, therefore coot documentation, tutorial etc. is provided for your comfort. Unfortunately there is a few further minor bugs which I'm currently about to fix. So, WinCoot might crash on you unexpectedly (like a lot of other Windows programs...). Please let me know if there is any further bugs rather than the following and please don't tell me about these ones again:

WinCoot on Vista

WinCoot currently doesn't work with the Desktop Compositing on Vista. However, here are some ideas to overcome this problem:
  1. set the theme to Windows Classic
  2. disable the desktop-styling in the properties of coot-real.exe (in C:\WinCoot\bin) or maybe the runwincoot.bat (in C:\WinCoot)
  3. disable the desktop compositing (guess that is what is done - amongst other things - when you use Windows Classic).
WARNING:: There may be other problems on Vista.
In the future there may be a special Vista version without the compositing problem...

Bizarre connectivity of coordinate files

I guess you see something like this. This should not happen any more (from 0.3.3.1)! If it still does please let me know and try the following:

It may be that you have a 'non-english speaking' computer and changing some settings on your computer may fix this.
Go to Start -> Settings -> Control Panel ->  Regional and Language Options. Then Customise your settings and change your Decimal symbol to "." (dot) [was a "," comma I guess]. In turn you might want to change you Digit grouping symbol from "." (dot) to "," (comma) to avoid possible confusions. This is the procedure for 'British' Windows XP, but should be similar on other Windows systems and/or languages.

Grey display window

Turning down your graphics card acceleration should solve this. To do so go to Start->Settings->Control Panel->Display->Settings->Advanced->Troubleshoot. Then move the slider to towards None (usually one bar above None is still acceptable). This is most likely due to graphics card/drivers. Currently I don't know how to fix it otherwise.

Stereo

There has been several reports that stereo is fairly unstable. However this should be fixed now and no extra version needs to be downloaded.

Side-by-side stereo

Once side-by-side stereo is invoked resizing the WinCoot window only resizes one of the panels. We currently have no fix for this and tend to blame Mr. Gates for the problem. However if you resize the window before switching to side-by-side stereo everything seems to be fine.

GTK/GDK/Pango warnings

Some computers occasionally seem to give some GTK, GDK and/or Pango warnings in the Command Prompt Windows (although I haven't seen it for a while). Please ignore these warnings as long as WinCoot doesn't crash. If it does, please let me know.

Missing Buttons

If you are used to 'normal' Coot you might miss some buttons/functions, these are disabled on purpose due to missing functionality, e.g. 'Filter' in file selection dialogs. WinCoot should get more and more complete though...

Crash on reading mtz files

On some computers WinCoot crashes when opening mtz files. However, this should be fixed now, I hope!
If it happens too often and is too painful then the easiest way to avoid it is to read in map files. Otherwise try reading in the mtz file again (and again...). Sometimes using a script or state file seems to help as well.

Others


So, it's not that much and should work ok for model building...I hope.

WinCoot is tested successfully on Win2000, WinNT and Windows XP.

FAQ

What about WinCoot and CCP4?

Coot is part of the CCP4 Windows package (6.0.x) now. This is CCP4's version and currently doesn't seem to be fully functional. It is not done by me, hence I might not be able to answer questions with regards to the 'official' CCP4 Coot release.
I don't know when updates for the CCP4 packages will be made available and for my support (whatever it's worth it) I recommend to use my releases!

What are these 'Generic objects'?

These are (dot) objects generated by the programs probe and reduce from the Richardson Lab. The generic objects will show you intra-molecular interactions. You will need to install these programs to use this function in (Win)Coot. You can download them from here. Ideally put the executables (probe.exe and reduceV2.13.2.win.exe) somewhere in you PATH  ([or] e.g. in C:\YourWinCootDirectory\bin) and off you go.

How do I get raster3d and/or povray working with WinCoot?

Just download and install the appropriate program (raster3d, povray) and WinCoot should find them. However it might be better (faster) to put them somewhere in your PATH.

Hints on running WinCoot

Different projects

When working on different projects you might like to go back to these different ones when running WinCoot, i.e. reading in a 0-coot-state.py file for each project. Since the coot state file is always loaded from the directory which WinCoot is started from you have to change this. You can do this by having different WinCoot shortcuts running in different directories or by starting WinCoot (runwincoot.bat) from the Command Prompt in the appropriate directory. Alternatively make a copy the 0-coot-state.py files and read it in as a python script file. Some additional informations can be found on the installation page.

Python scripting

Python scripting is different to (default) guile scripting which is mainly described in Paul's instructions (although it's mentioned somewhere, fairly hidden). You have to change the commands in the following way:
GUILE scripting:	(guile-command argument1 argument2)

PYTHON scripting:	python_command(argument1,argument2)

Refmac interface

If you have CCP4 installed on your computer you should be able to run REFMAC5 on your build structure from WinCoot. Be aware that there is some slight changes to the handling and filenames for extra refmac parameters in comparison to 'normal' Coot. First the file which give refmac extra parameters is called refmac-extra-params.txt for easy text editing (see an example here). It is a simple text file which can include all your refmac extra parameters in a new line (for an example see here). WinCoot will search for the file in the directory from where WinCoot is started from. Refmac extra parameters can be given in 3 different locations (the highest priority first), in your .coot.py file, in the refmac.py and in the refmac-extra-params.txt file (in $COOT_PYTHON_DIR). The first 2 require 2 lines in the code like:
global refmac_extra_params
refmac_extra_params = ['NCYC 3', 'WEIGHT 0.3']

(Win)Coot reference, citation and further information

The official reference for Coot has now been published:

You can use this BibTeX database entry (which can be imported into EndNote)... format as you please:

@Article{emsley04:coot,
  author =    {Paul Emsley and Kevin Cowtan},
  title =     {Coot: Model-Building Tools for Molecular Graphics},
  journal =   {Acta Crystallographica Section D - Biological Crystallography},
  year =      2004,
  volume =    60,
  pages  =    2126-2132
}

Additional  information on Coot especially WinCoot can be found in thee CCP4 Newsletter (Number 42, Summer 2005). Feel free to cite it as well as the 'official' Coot reference in case WinCoot was useful for you.

Lohkamp, B., Emsley, P. & Cowtan, K. (2005) Coot News. CCP4 Newsletter, 42, Contribution 7.
Last modified 09/01/2008