[chimerax-users] [Chimera-users] ConSurf script on ChimeraX

Eric Pettersen pett at cgl.ucsf.edu
Tue Apr 10 13:18:00 PDT 2018 

Hi Fabian,
	As a stopgap, you can color by bfactor by using a script I’ve attached.  I’m attaching two scripts, one a generic color-by-bfactor that can be used for anything in the bfactor column.  You would edit the values at the top of the script to choose low-high coloring or low-mid-high coloring, and what values to associate to what colors.  The other script is tailored to ConSurf output in that it knows the nine ConSurf colors and colors only those residues whose bfactors are all equal and are integers in the range 1-9.  You just open the ConSurf-generated PDB and then open the script (which runs it).  I’ve attached an example output image (2gbp).

—Eric




> On Apr 10, 2018, at 12:26 AM, Fabian Glaser <fabian.glaser at gmail.com> wrote:
> 
> Dear Eric,
> 
> Thanks for your detail answer, so maybe the only thing it will be really useful now is to be able to color the residues with consurf colors in ChimeraX, with that I will be able to make figures for a paper, which is what I am after at this point. 
> 
> Of course we would be very happy to get a script for ChimeraX at some point that could be included in our output pages.
> 
> Best,
> 
> Fabian
> 
> Fabian Glaser PhD
> 
> Head of the Structural  Bioinformatics section 
> Bioinformatics Knowledge Unit - BKU
> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
> Technion - Israel Institute of Technology, Haifa, Israel
> Web http://bku.technion.ac.il/ <http://bku.technion.ac.il/>
> Tel +972 (0) 4 8293701
> 
> 
>> On 10 Apr 2018, at 1:59, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
>> 
>> Hi Fabian,
>> 	ChimeraX is not backwards compatible with Chimera, so a Chimera session file cannot be opened in ChimeraX — such as what you tried to do below.  We want to add a tool to Chimera that will write out a file that ChimeraX can read to restore the Chimera session as best it can, but we haven’t gotten there yet.
>> 	Furthermore, although ChimeraX can display sequence alignments, its capabilities in that regard are currently much less than what Chimera offers.  The features it lacks that ConSurf uses are:
>> 
>> 	1) Read Clustal ALN alignments
>> 	2) Show alignment headers
>> 		2b) Make header values available as residue attributes
>> 	3) Show Phylogeny trees
>> 	4) Color alignment/structures from coloring file
>> 
>> To show ConSurf results in even bare bones form would require #1 and #4, and obviously #2 and #3 add a lot of value.  So I’d say ChimeraX is not “ConSurf ready” yet.  What I will do is open an “enhancement request” ticket in our bug database with you on the recipient list.  As the above features get added I will update the ticket and at whatever point you feel it’s worthwhile you could work on getting ConSurf to deliver ChimeraX results.  I would help with any questions or issues that popped up.  Sorry I don’t have better news.
>> 
>> —Eric
>> 
>> 	Eric Pettersen
>> 	UCSF Computer Graphics Lab
>> 
>>> On Apr 8, 2018, at 7:56 AM, Fabian Glaser <fabian.glaser at gmail.com <mailto:fabian.glaser at gmail.com>> wrote:
>>> 
>>> Hi, 
>>> 
>>> I would like to use Chimera ConSurf scripts in ChimeraX, but I get the following error when I try to run the script on ChimeraX
>>> 
>>> ModuleNotFoundError: No module named 'cPickle'
>>> 
>>> File "consurf_final_zn.py", line 1, in 
>>> 
>>> See log for complete Python traceback.
>>> 
>>> If you wish to report this error, send mail to chimerax-bugs at cgl.ucsf.edu <mailto:chimerax-bugs at cgl.ucsf.edu> and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created.
>>> 
>>> Is this something that can be fixed or updated?
>>> 
>>> More generally I would like to update ConSurf with a version of the script for ChimeraX, can you help me with that?
>>> 
>>> Here is the beginning of the original chimera script
>>> 
>>> import cPickle, base64
>>> try:
>>> 	from SimpleSession.versions.v65 import beginRestore,\
>>> 	    registerAfterModelsCB, reportRestoreError, checkVersion
>>> except ImportError:
>>> 	from chimera import UserError
>>> 	raise UserError('Cannot open session that was saved in a'
>>> 	    ' newer version of Chimera; update your version')
>>> checkVersion([1, 12, 41623])
>>> import chimera
>>> from chimera import replyobj
>>> replyobj.status('Restoring session...', \
>>>     blankAfter=0)
>>> replyobj.status('Beginning session restore...', \
>>>     blankAfter=0, secondary=True)
>>> beginRestore()
>>> 
>>> def restoreCoreModels():
>>> 	from SimpleSession.versions.v65 import init, restoreViewer, \
>>> 	     restoreMolecules, restoreColors, restoreSurfaces, \
>>> 	     restoreVRML, restorePseudoBondGroups, restoreModelAssociations
>>> 	molInfo = 
>>> 
>>> Thanks a lot,
>>> 
>>> Best,
>>> 
>>> Fabian
>>> 
>>> Fabian Glaser PhD
>>> 
>>> Head of the Structural  Bioinformatics section 
>>> Bioinformatics Knowledge Unit - BKU
>>> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
>>> Technion - Israel Institute of Technology, Haifa, Israel
>>> Web http://bku.technion.ac.il/ <http://bku.technion.ac.il/>
>>> Tel +972 (0) 4 8293701
>>> _______________________________________________
>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>>> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>
>> 
> 

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