[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 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:
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?

Chimera-users mailing list
Chimera-users at cgl.ucsf.edu

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20141027/76cb7467/attachment.html>

More information about the Chimera-users mailing list