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 Post subject: CIF handling
PostPosted: Mon Feb 04, 2013 10:23 am 
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Hello,

As a small-molecule crystallographer, I use maya for rendering pictures. I came accross your ePMV plugin and saw it was able to "Fetch" CIF files. Is there any possibilities to load a local CIF file through the ePMV GUI ?

Best Regards,


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 Post subject: Re: CIF handling
PostPosted: Mon Mar 11, 2013 5:50 pm 
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Hi
sorry for the late answer. If you want to read a cif file, simply click browse or Load PDB and select your cif file.

Ludo


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 Post subject: Re: CIF handling
PostPosted: Tue Mar 12, 2013 8:07 am 
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Hi Ludo,

I was proceeding this way but I get the following error :

ERROR *********************************************
# Traceback (most recent call last):
# File "C:\Users\jeanneau\Documents\maya\2013-x64\plug-ins\/MGLToolsPckgs\ViewerFramework\VF.py", line 898, in tryto
# result = command( *args, **kw )
# File "C:\Users\jeanneau\Documents\maya\2013-x64\plug-ins\/MGLToolsPckgs\ePMV\pmv_dev\secondaryStructureCommands.py", line 182, in doit
# mol.secondaryStructureFromFile()
# File "C:\Users\jeanneau\Documents\maya\2013-x64\plug-ins\/MGLToolsPckgs\MolKit\protein.py", line 1188, in secondaryStructureFromFile
# self.secondaryStructure(ssBuilder)
# File "C:\Users\jeanneau\Documents\maya\2013-x64\plug-ins\/MGLToolsPckgs\MolKit\protein.py", line 1178, in secondaryStructure
# c.secondaryStructure(ssBuilder)
# File "C:\Users\jeanneau\Documents\maya\2013-x64\plug-ins\/MGLToolsPckgs\MolKit\protein.py", line 949, in secondaryStructure
# ssBuilder.createSSNodesForChain(self)
# File "C:\Users\jeanneau\Documents\maya\2013-x64\plug-ins\/MGLToolsPckgs\MolKit\getsecondarystructure.py", line 323, in createSSNodesForChain
# turnData, coilData)
# File "C:\Users\jeanneau\Documents\maya\2013-x64\plug-ins\/MGLToolsPckgs\MolKit\getsecondarystructure.py", line 60, in createSSstructures
# self.getCoils(chain)
# File "C:\Users\jeanneau\Documents\maya\2013-x64\plug-ins\/MGLToolsPckgs\MolKit\getsecondarystructure.py", line 174, in getCoils
# if not r.hasCA: # we hit residue that breaks coil
# AttributeError: Residue instance has no attribute 'hasCA'
ERROR *********************************************
# Traceback (most recent call last):
# File "C:\Users\jeanneau\Documents\maya\2013-x64\plug-ins\/MGLToolsPckgs\ViewerFramework\VF.py", line 898, in tryto
# result = command( *args, **kw )
# File "C:\Users\jeanneau\Documents\maya\2013-x64\plug-ins\/MGLToolsPckgs\ePMV\pmv_dev\secondaryStructureCommands.py", line 727, in doit
# if SS.sheet2D is None:
# AttributeError: Helix instance has no attribute 'sheet2D'


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 Post subject: Re: CIF handling
PostPosted: Tue Mar 12, 2013 4:40 pm 
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Hi,

is it a custom cif file, is it a small molecule. If it is a small molecule there is no secondary structure obviously.
Before loading your CIF file, try to go to the ePMV preference and change the start up representation to None, or Atoms.
You can also send me the file, so I can look into it (autin_@_scripps.edu)
Let me know if it help.

Ludo


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 Post subject: Re: CIF handling
PostPosted: Wed Mar 13, 2013 11:33 am 
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Hi,

Thanks for these tips but it does not seem to solve the issue with the CIF files I use (I generate them with Crystals refinement software for submission to the CCDC). I can however convert them to pdb and open them with ePMV.
However I was interested in opening CIF files directly in order to gather the symmetry information contained in the CIF file and thus be able to generate symmetry related molecules, unit-cell contents or packing diagrams (basically to use maya as a molecular builder similar to the soft I actually use : Diamond from www.crystalimpact.com).

Best Regards,

ps. I sent you a typical CIF file I use by email.


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