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
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 7, Windows Vista,
Windows XP, Win2000, and WinNT . There may be some specific problems...
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).
[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 on Windows 7
Initial reports suggest that WinCoot works fine on Windows 7. 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.
WinCoot display not
responsive in full screen mode
This is 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].
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 inly 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.
Text missing in some
widgets when using Scheme/Guile
scripting
Currently Scheme/Guile is not available, so no problem there...
Using
WinCoot
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.
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
(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
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") or add the
following lines to 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?
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 (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
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
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.
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.
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...