[Chimera-users] aligning PDB file

[Eric Pettersen]

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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