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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