For the usual Coot problems and bugs have a look at Paul's FAQ page.
Often RTFM helps too, therefore the Coot documentation, tutorial
etc. is provided for your comfort. Nevertheless, 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.
Additional information on Coot especially WinCoot can be found
in the CCP4
Newsletter (Number 42, Summer 2005). Feel free to cite it as
well as the 'official' Coot reference in case WinCoot was useful for
Lohkamp, B., Emsley, P. & Cowtan, K. (2005) Coot News. CCP4
Newsletter, 42, Contribution 7.
Installation and Windows problems
version does WinCoot run on?
WinCoot has been successfully tested on Windows 7, Windows Vista,
Windows XP, Win2000, and WinNT . There may be some specific
WinCoot on Vista
WinCoot in general works on Vista. As of 0.5-pre-1 (1339)
WinCoot should work properly with Desktop Compositing (Vista Theme)
as you can see here.
However, if you have problems with compositing, here are some
solutions to overcome this problem:
disable the desktop compositing of coot-real.exe (e.g. in
C:\WinCoot\bin) or runwincoot.bat (e.g. in C:\WinCoot).
set the theme to Windows Classic. [Control
in your graphics card Control Panel switch off any threading
WARNING:: There may be other problems on Vista.
WinCoot on Windows
7 (and later)
Initial reports suggest that WinCoot works fine on Windows 7 and 8.
If you have problems please report to me (incl. details such as
graphics card, processor, etc) and try the suggestions for Vista.
More news once I tested more myself.
not responsive in full screen mode
This may be caused by the auto-hide function of the Windows Taskbar.
If you disable the auto-hide Taskbar WinCoot should work fine.
[Thanks to Jack Sadowsky]. On other occasions it was actually the
other way around (enabling the auto-hide function) which works.
Another possible fix (untested) may be to use WinCoot's full screen
mode (feedback appreciated...):
right mouse click on main toolbar (besides the Go To
Select "Full Screen" under Display
(De)Activate full screen mode using the new button
opening and/or saving files
This may be caused by the modern file chooser. So, either revert to
the classic one (Edit->Preferences...->General/File
Selection tab; top pane change to Classic File Selector)
or avoid using the GUI for file selections by using e.g. drag'n'drop
to open files and Quick Save (Ctrl s) for saving files.
connectivity of coordinate files
I guess you see something like this.
This should not happen any more (from 0.3.3.1), however there is
rare cases on Windows 7 where it occurs again (this is progress for
you!). So if it does please let me know about your system and try
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.
In a more permanent fix (without messing with your usual setting)
you can try the following:
place the following after set COOT_PREFIX=C:\WinCoot
control intl.cpl,, /f:"%COOT_PREFIX%\lang_on.xml"
place the following at the end of the file:
control intl.cpl,, /f:"%COOT_PREFIX%\lang_off.xml"
N.B. the lang_xxx.xml files are for Swedish Swedish (sv-SV)
and you have to change them to your regional setting (for codes
You may get a Windows warning that the installation of WinCoot could
not be completed for some reason. In most cases this is caused by an
incomplete download of the installer. Please make sure that the
WinCoot installer is downloaded completely. If not, try again. A
brief check about the size can help (something above 70Mb
currently). The correct way is to varify the download via the md5sum
I inly get a grey
Turning down your graphics card acceleration should solve this. To
do so go to Start->Settings->Control
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.
Does stereo work
Yes, it works fine. All of it, hardware, side-by-side, Zalman, 120Hz
LCD, ... IF you have the right hardware!!
NVIDIA 3D Vision/120Hz LCDs?
This works if you have the high end Quadro
graphics cards which enable OpenGL. To set the graphics card up,
please follow the instructions e.g. given by the PyMOL community.
You find general information here
and here are specific instruction for Vista
Text missing in
some widgets when using Scheme/Guile scripting
Currently Scheme/Guile is not available, so no problem there...
What about WinCoot
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
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. More
detailed instructions below.
How do I get
molprobity (probe and reduce) working in WinCoot?
Depending on your WinCoot version follow the following steps:
copy/move probe.exe into YourWinCootDirectory\bin
PATH ; for an
alternative see 5)
rename/copy reduce*.exe to reduce.exe
copy/move reduce.exe into YourWinCootDirectory\bin
PATH ; for an
alternative see 5)
Optionally: copy/move reduce_wwPDB_het_dict.txt to the same
directory where you moved reduce.exe to
OPTIONAL ALTERNATIVE: if the executables are NOT in PATH (e.g. YourWinCootDirectory\bin):
edit either group_settings.py
(found in YourWinCootDirectory\share\coot\python)
describe the location of your files (e.g. probe_command =
"C:\\Mydirectory\\probe.exe") OR add the following lines to e.g.
probe_command = "C:\\Mydirectory\\probe.exe"
reduce_command = "C:\\Mydirectory\\reduce.exe"
as for WinCoot 0.5.1 BUT observe that the 'Molprobity Probe
Clash Gaps' GUI is not working properly!
Older version that 0.5:
(or look here
BUT DO NOT INSTALL PROBE NEWER THAN 2.11 - for now)
run probe*.exe and extract into YourWinCootDirectory\bin (or somewhere else in
your PATH ; for
an alternative see 5)
extract the content of reduce*.exe.zip and move the files from
reduce4win into YourWinCootDirectory\bin
(or somewhere else in your PATH ;
for an alternative see 5)
if the executables are not in PATH : edit group_settings.py (found in YourWinCootDirectory\share\coot\python)
describe the location of your files (e.g. probe_command =
[N.B. if you have a different
reduce version to "reduceV2.13.2.win" or changed the name you have
either to change reduce_command_name = "reduceV2.13.2.win" in YourWinCootDirectory\share\coot\python\generic_objects.py
put a line in your YourWinCootDirectory\.coot.py
reduce_command_name = "my_reduce_filename". OBS: no .exe in the
end for the filenames!!!!]
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
How do I handle
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.
How does Python
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
Some more information on Scheme/Guile and Python scripting can be
found on the Coot
How do I use extra
parameters in the 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:
refmac_extra_params = ['NCYC 3', 'WEIGHT 0.3']
Other WinCoot information
(deprecated, pre-0.3, etc.)
You may see some GTK, GDK and/or Pango warnings in the Command
Prompt Windows (some will be there on start-up, but otherwise 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.
Crash on reading
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.
There has been several reports that stereo is fairly unstable.
However this should be fixed now and no extra version needs to be
On some computers there seem to be a conflict of WinCoot with
CCP4i due to the SYMINFO variable (only beta2). This should not
occur any more since we use a .bat file to run WinCoot now...