On Fri, May 14, 2010 at 2:06 PM, William G. Scott <
wgsc...@chemistry.ucsc.edu> wrote:
> Check /usr/local/xtal/coot64/bin/coot
>
> to see if I set $PYTHONPATH right.
>
> It should have /usr/local/xtal/coot64/lib/python2.6/site-packages/gtk-2.0
It does (and that path appears in sys.path). And I
When I use the 0.6.1 package from Bill's web site, I get this error when I
try to start the Python scripting GUI:
COOT_PYTHON_DIR was defined to be /usr/local/xtal/coot64/share/coot/python
but no PyGtk and hence no coot_gui.
Not sure what to do about this, because it appears to have the module
On Tue, Mar 16, 2010 at 12:56 PM, Paul Emsley wrote:
> Coot is distributed with a copy of the refmac library, which has PDB
> version 2.3 atom names.
>
> You can override that dictionary by setting up CCP4 in the normal way.
> You can further override the dictionary by setting the environment vari
On Fri, Feb 5, 2010 at 12:34 PM, subh wrote:
> Hi,
> I am trying to open the .cif file (in coot) that I downloaded from PDB, in
> my Mac OS X.
> Coot cannot open the map. Could you suggest how I can see the map that is
> downloaded form the PDB-RCSB web site.
>
What does Coot print out on the co
2010/1/11 Sara Züger
> Thanks Miguel,
>
> but is there another way to do this sphere refinement? I'm working on a
> shared computer and have no administrator rights and also no experience
> with
> python/file handling of coot.
>
> Or else, if there is no other way, can somebody explain me exactly
On Mon, Jan 4, 2010 at 12:43 PM, Huw Jenkins wrote:
> I guess this means something to do with the scheme scripting isn't getting
> properly defined in the coot script but I can't work out what from
> comparisons of the old and new coots.
>
The package distributed by CCP4 was not compiled with sup
Is there a way to open map files from a script with the actual column labels
alone, instead of /crystal/dataset/F, etc.? I tried /*/*/F, but this
doesn't work in 0.6. One of my coworkers claims that MTZ files don't allow
duplicate column names regardless of which crystal or dataset ID they're
ass
On Mon, Aug 17, 2009 at 9:50 AM, Ben Eisenbraun wrote:
> > The Phenix GUI will modify this file (only if you launch Coot from it) to
> > ensure that Coot can find Probe, which could be causing the problem - I
> > didn't take into account the possibility of a home directory being shared
> > across
On Mon, Aug 17, 2009 at 8:32 AM, Ben Eisenbraun wrote:
> I have a very odd issue. I have two builds of Coot, one for OS X Intel and
> one for OS X PPC. On each of those platforms, I have a standalone
> probe/reduce in the shell PATH. When I run either of these Coots, they
> manage to find and t
On Fri, Jun 5, 2009 at 9:54 AM, Jason Greenwald <
jason.greenw...@phys.chem.ethz.ch> wrote:
> In the meantime I am using the COOT.app package from the CCP4 download
> site, so if anyone knows how to save more than one session using this
> installation, I would be happy to hear it.
>
I couldn't fi
On Tue, Apr 28, 2009 at 3:52 PM, Oliver Clarke wrote:
> Is it possible in coot to script a way to colour residues by their position
> on the ramachandran plot? This would be really handy, particularly for large
> structures, in order to visually see where problem areas of the structure
> are. I'm
>
> I'm looking for a script that automatically loads a PDB file when it has
>> changed on disk in order to display the changes with a previous version of
>> that file.
>>
>
Here is a Python version. I prefer to overwrite the old molecule - but this
will work either way. (I think - it is untested
Is this even possible? Either Python or Scheme would be okay. I figured
out how to hide everything (in Python), but I'm trying to reload files via a
button, and they always have the same name, so the display manager becomes
confusing quickly.
thanks,
Nat
There is an open-source implementation of the dssp method called
ksdssp, written by the UCSF group that distributes Chimera. I haven't
had reason to use it yet but the source definitely has functions for
writing out the pdb records. I suspect that one of the BioPython/perl/
etc. modules ha
This has been a problem on and off with recent OS X binary builds too. The
interpreter is actually supposed to be coot itself - I don't think
/sw/bin/python is going to do you any good, since it doesn't have access to
the memory of the running coot process. I don't know what the source of the
var
Hey Bill, this has the correct and complete Python module search paths too
(although /usr/local/xtal/coot/share/coot/python is repeated four times, but
this doesn't appear to break anything). What's the difference between this
and the coot-0.5-pre1 build you sent out on Thursday?
thanks,
Nat
(sti
On Thu, Dec 11, 2008 at 3:05 AM, William Scott
wrote:
> I need a couple of people to volunteer to test this on 10.4 and 10.5 intel
> machines:
>
> http://sage.ucsc.edu/xtal/coot/coot-0.5-pre1-intel_10.4_10.5.tgz
>
This build appears to have python embedded more or less correctly, so it now
uses t
This may not be required any more, but I remember having to explicitly add
the GLX module to the list of extensions to get NVidia cards to work. I'm
not sure exactly what the syntax is, but I know the module is just called
"glx", so maybe try putting 'Options "glx" "Enabled"' in the 'Extensions'
s
The problem with the iPhone is that the OpenGL library it uses is only a
subset of the OpenGL used on real computers, so porting any existing
molecular graphics application would be non-trivial, aside from the many
other issues with developing for iPhone. I do like the idea of using the
touch-scre
19 matches
Mail list logo
