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.
(Win)Coot
reference,
citation and further information
The official reference for WinCoot is published now:
You can use this BibTeX database entry
(which can be imported into EndNote or directly download the file for
import in your citation manager to your citation manager)...
format as you please:
@Article{emsley10:coot, author = {Emsley P, Lohkamp B, Scott W, Cowtan K}, title = {Features and Development of Coot}, journal = {Acta Crystallographica Section D - Biological Crystallography}, year = 2010, volume = 66, pages = 486-501 }
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
you.
Lohkamp, B., Emsley, P. & Cowtan, K. (2005) Coot News. CCP4
Newsletter, 42, Contribution 7.
Installation and Windows problems
Which Windows
version does WinCoot run on?
WinCoot has been successfully tested on Windows 11, Windows 10,
Windows 8(.1), Windows 7, Windows Vista, Windows XP, Win2000, and
WinNT . There may be some specific problems...
WinCoot with CCP4
Starting from CCP4-8.0.011, WinCoot is a compulsory component of
CCP4.
To use a newer (or older) WinCoot
in CCP4 Cloud: define it in the CCP4Cloud Config app.
in CCP4i2: define it in Edit->Preferences or (if this does not work) replace the CCP4-8\WinCoot directory with the
version you like (no guarantees, and will need to replace again
after applying ccp4 updates). NB: good to make a backup of the
CCP4 supplied version e.g. by renaming the original directory.
Coot has been part of the CCP4 Windows package (since 6.0.x) and
is identical to one of the latest versions (not always the very
latest or pre-release) you can download from my pages.
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.
Problem
resizing/maximizing or updating the WinCoot window.
WinCoot may not update the graphics window upon resize/maximize
(something like this)
or in general not update (like this). The
reason is most likely a graphics card driver issue. It usually can
be fixed by installing an updated and appropriate graphics card
driver from the manufacturer. E.g. if you have a "proper"/dedicated
graphics card (i.e. NVIDIA, ATI etc; not a build-in Intel) it is
recommended to install the drivers from the manufacturer rather than
the ones supplied by Windows.
Dll errors such as
"Can't find entry point bla in xyz.dll":
This is related to Windows picking up wrong dll versions. Either
download a new installer (after WinCoot 0.8.8) or do the following:
Copy (or move) everything (files and folders) from:
C:\YourWinCootDirectory\libexec
to
C:\YourWinCootDirectory\bin
Downloading of
pdbs does not work/Python errors
This is related to Windows picking up the wrong version of Python.
Either download a new installer (after WinCoot 0.8.1) or do the
following:
Copy (or move) the file python27.dll from:
C:\YourWinCootDirectory\bin
to
C:\YourWinCootDirectory\libexec
Installer hangs
In the end of the installation the Installer may become unresponsive
(only seen on Windows 8 and above so far). It appears that (usually)
WinCoot is installed correctly though and there is no reason for
concern. Just kill the Installer. Working on a fix is in progress.
Display is 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
Ligand icon)
"Manage Buttons"
Select "Full Screen" under Display
(De)Activate full screen mode using the new button
WinCoot hangs
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.
WinCoot crashes
upon Save coordinates...
This is most likely cause by another software interfering with
WinCoot. Bluestack is known to cause these issues. Uninstalling the
offending software solves the issue. Possibly, deactivation of
background processes connected to bluestack will help as well
(untested). [Thanks to Amy Chu]
This is most likely cause by other software interfering with
WinCoot. The best known (to me) is the English-Chinese dictionary
software called "youdao". So, either close the offending program
or in the case of "youdao" just close the function of automatic
translation when select or mouse move. In this way you can even
use WinCoot and "youdao" together. [Thanks to Shoude Zhang]
WinCoot does not
start/crashes immediately
This could be caused by other software interfering with WinCoot; one
know example is "Duet Display" (thanks André Graça). Uninstalling
the offending software will of course help, but may not be desired.
Maybe temporarily disabling running services of the other software
may help.
If this is not the case and/or solving the problem, please get in
touch.
Problems with
virtual desktops (e.g. Dexpot, VirtuaWin)
Nothing which can be done from WinCoot side (*). However, you can
fix this by showing WinCoot on all Desktops. Here
a thread about this topic on the bb.
(*) For the more interested. It appears that gtkglext does not work
well with newer versions of GTK which causes this to be problematic
recently now.
Ramachandran plot
(or sequence view) crashes
Fixed in 0.8.9 pre-releases (from 7109 onward), so please download
the latest installer.
This is caused by some underlying graphics libraries and usually
happens with larger files. There is a fix in the pipeline but sadly
no news as to when it will be available. In the meantime I can only
suggest to split your larger structure into smaller ones (e.g.
chains) and/or use this
script to get at least a clickable list of outliers. [Then run
the script file (Calculate->Run script), which will give a new
menu under validate to give you outliers in a button list form. NB
if you put the file in your .coot-preference directory it will
always be loaded.]
Bizarre
connectivity of coordinate files
I guess you see something like this.
This should finally, really not happen any more (from 0.9.6.1),
however there is rare cases on Windows 7+ where it occurs. It is
related to the fact that you have a 'non-english speaking' computer.
Well, what you need is a "." (dot) and not a "," (comma) as a
decimal symbol.
FIX 1: Change some locale/language settings on your computer will
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.
FIX2: In a more permanent fix (without messing with your usual
setting) you can try the following:
Edit your wincoot.bat (runwincoot.bat prior to 0.8.8) file the
following way:
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:
PAUSE
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
see this
MS site).
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 wincoot.bat (e.g. in C:\WinCoot; prior to
0.8.8 runwincoot.bat). [Right-Click
coot-real(.exe)->Properties->Compatibility->Disable
desktop composition]
set the theme to Windows Classic. [Control
Panel->Appearance and
Personalization->Pernsonalization/Change Theme->Windows
Classic]
in your graphics card Control Panel switch off any threading
option.
WARNING:: There may be other problems on Vista.
WinCoot installer
warnings
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
(stable, development).
I only get a 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.
Does stereo work
with WinCoot?
Yes, it works fine. All of it, hardware, side-by-side, Zalman, 120Hz
LCD, ... IF you have the right hardware!!
WinCoot with
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
and XP.
WinCoot with
NVIDIA and Win 10?
If you run into problems with stereo on Windows 10 (using an NVIDA
card), you can try the following (thanks to Jose Brito):
Open NVIDIA Control Panel --> Manage 3D settings.
Go to Program Settings tab.
Add the file you launch the program from by clicking on Add
button.
In the setting window, change the 'Power Management Mode' to
'Prefer Maximum Performance'. Also below settings as well:
Vertical sync - off
Threaded optimization - off
Triple buffering - off
Stereo enable on
Run the program and check.
Others (Kent Rossman) have reported that some XBOX servive (GameDVR) may intefer with the stereo.
Disabling and uninstalling this may help.
There may be other issues though which are related to the fact
that pre-0.9 WinCoot is 32bit and some graphics card drivers don't
seem work well with 32bit applications. This should be fixed in
64bit WinCoot (i.e. starting 0.9), certainly from 0.9.4.1 onwards.
Text missing in
some widgets when using Scheme/Guile scripting
Currently Scheme/Guile is not available, so no problem there...
Using WinCoot
Where is the
startup file? How do I manually customise WinCoot?
WinCoot's "HOME" directory is C:\YourWinCootDirectory. So
you can have a .coot.py file with python instructions in
there to be executed on startup. Alternative, any other python file
(.py extension) in C:\YourWinCootDirectory\.coot-preferences
will be executed on startup as well. [Thanks FvD]
How do I change
the font size of the labels?
You can edit your cootrc file (found in C:\YourWinCootDirectory\share\coot).
Please replace the line (under style "defaultfont"; line ~26)
font =
"-adobe-helvetica-medium-r-normal--*-75-*-*-*-*-*-*,*"
with (e.g.)
font_name = "tahoma 12"
You can choose other (available) font names there too as well as
further increase (or decrease) the size of the label (default size
is 8).
What are these
'Generic objects'?
Generic objects are other displayed objects than models or maps,
e.g. probe dots.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?
Now you can get probe and reduce together with
WinCoot (select during the installation). Or you can use the
programs which come with CCP4 (if they are found in the PATH).
For older WinCoot versions without probe and reduce,
depending on your WinCoot version follow these steps:
copy/move probe.exe into YourWinCootDirectory\bin
(or
somewhere
else
in
your
PATH ; for an
alternative see 5)
for reduce:
extract reduce*.zip
rename/copy reduce*.exe to reduce.exe
copy/move reduce.exe into YourWinCootDirectory\bin
(or
somewhere
else
in
your
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)
so
that
probe_command
and
reduce_command
describe the location of your files (e.g. probe_command =
"C:\\Mydirectory\\probe.exe") OR add the following lines to e.g.
YourWinCootDirectory\.coot.py:
probe_command = "C:\\Mydirectory\\probe.exe"
reduce_command = "C:\\Mydirectory\\reduce.exe"
WinCoot 0.5:
as for WinCoot 0.5.1 BUT observe that the 'Molprobity Probe
Clash Gaps' GUI is not working properly!
Older version that 0.5:
download probe.
(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)
so
that
probe_command
and
reduce_command
describe the location of your files (e.g. probe_command =
"C:\Mydirectory\probe.exe")
[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
to
your
correct
name
or
put a line in your YourWinCootDirectory\.coot.py
which
reads
something
like
reduce_command_name = "my_reduce_filename". OBS: no .exe in the
end for the filenames!!!!]
Done!
How do I get
raster3d and/or povray working with WinCoot?
Raster3d is provided with WinCoot now (from 0.9.6), so no separate
installation is required for this.
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.
How do I handle
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
(wincoot.bat; runwincoot.bat prior to 0.8.8) 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 information can be found on the installation page.
How does Python
scripting work?
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:
Some more information on Scheme/Guile and Python scripting can be
found on the Coot
WIKI page.
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:
global refmac_extra_params
refmac_extra_params = ['NCYC 3', 'WEIGHT 0.3']
Other WinCoot
information
Coot in a Cage
Olga asks:
draw a picture of coot in a cage
ChatGPT:
I'm sorry, but as a text-based AI language model, I cannot create
visual content such as pictures or drawings. However, I can
describe a coot in a cage for you!
A coot is a small water bird with a distinctive white beak and a
black body. If it were in a cage, it would likely be pacing back
and forth on the cage floor, trying to find a way out. Its
feathers might be ruffled and its eyes might be darting around
nervously, as it is not used to being confined. The cage itself
might be made of metal bars, with a small door that can be locked
to prevent the coot from escaping.
.. maybe it looks like this:
Old FAQs
(deprecated, pre-0.3, etc.)
GTK/GDK/Pango
warnings
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
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.
Hardware-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.
Others
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...
