*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:

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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