[Chimera-users] aligning PDB file

Eric Pettersen pett at cgl.ucsf.edu
Mon Oct 27 15:35:48 PDT 2014

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 Pettersen
                        UCSF Computer Graphics Lab

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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