Hi Chimera Developers, I've used chimera mostly by GUI inerface [click]. How do I get the match-align work from command line in a python script?I read a good description at: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007934.html work flow of the script is:take in 2 pdb files and match->align them. I think, I will have to open them before running 'mols = openModels.list(modelTypes=[Molecule])' ? How do I get the output saved in a FASTA file without MAV interface?
Hi Sanjeev, Take a look at this chimera-users message: [Chimera-users] easy way to make alignments in chimera . I think it answers most of your questions. The only change you would need to make is that where it uses "saveStockholm" you would instead use "saveFASTA". --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 27, 2014, at 2:25 PM, Sanjeev Sariya <s.sariya_work@ymail.com> wrote:
Hi Chimera Developers,
I've used chimera mostly by GUI inerface [click]. How do I get the match-align work from command line in a python script? I read a good description at: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007934.html
work flow of the script is: take in 2 pdb files and match->align them.
I think, I will have to open them before running 'mols = openModels.list(modelTypes=[Molecule])' ?
How do I get the output saved in a FASTA file without MAV interface?
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*Sorry, I missed reply to all. Thank you Eric for the URL. Could you please help me understand what is going on here? from chimera import openModels, Molecule # import models = openModels.list(modelTypes=[Molecule]) # array for model- different PDBs if models[0].id == 0: # what does this do? m0, m1 = models else: # m1, m0 = models # why interchanged the m1, mo? chains = [m0.sequence('A'), m1.sequence('B')] # how do I know how many chains are present in PDB file? Thank you. On Monday, October 27, 2014 6:35 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote: Hi Sanjeev, Take a look at this chimera-users message: [Chimera-users] easy way to make alignments in chimera . I think it answers most of your questions. The only change you would need to make is that where it uses "saveStockholm" you would instead use "saveFASTA". --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 27, 2014, at 2:25 PM, Sanjeev Sariya <s.sariya_work@ymail.com> wrote: Hi Chimera Developers, I've used chimera mostly by GUI inerface [click]. How do I get the match-align work from command line in a python script?I read a good description at: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007934.html work flow of the script is:take in 2 pdb files and match->align them. I think, I will have to open them before running 'mols = openModels.list(modelTypes=[Molecule])' ? How do I get the output saved in a FASTA file without MAV interface? _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Sanjeev Sariya