[Chimera-users] how to save distance to a file

Eric Pettersen pett at cgl.ucsf.edu
Mon May 5 16:11:49 PDT 2014


I should say that this assumes you've already superimposed the atoms with e.g. the "match" command.

--Eric

On May 5, 2014, at 4:10 PM, Eric Pettersen <pett at cgl.ucsf.EDU> wrote:

> On May 5, 2014, at 4:07 PM, chang YG <changyg2008 at gmail.com> wrote:
> 
>> Hi Eric,
>> 
>> Thank you very much for the quick response. I can't wait to try the script you provided.
>> 
>> For the RMSD, I have two conformers for the same sequence. If I encounter any problem, I will give it my best shot before posting questions.
> 
> In that case it should be easy:
> 
> from chimera import openModels, Molecule
> m1, m2 = openModels.list(modelTypes=[Molecule])
> import Midas
> rmsd = Midas.rmsd(m1.atoms, m2.atoms)
> etc.
> 
> --Eric
> 
>> 
>> Yonggang
>> 
>> 
>> On Mon, May 5, 2014 at 3:59 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>> On May 5, 2014, at 3:57 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>> 
>>> print>>f, a1, a2, diet
>> 
>> Stupid auto-correct spelling.  "diet" should be "dist".
>> 
>> --Eric
>> 
>> 
> 

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