[Chimera-users] ConSurf script on ChimeraX

[Eric Pettersen]

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> 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
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180409/fe6615ad/attachment.html>