[Chimera-users] aligning PDB file

Sanjeev Sariya s.sariya_work at ymail.com
Mon Oct 27 16:31:11 PDT 2014


*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 at 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 at 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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