[Chimera-users] Mirror image proteins

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 4 12:33:36 PDT 2015


Dear Dikran,
You would need to open the structure before running the script, otherwise the script has nothing to work on.
Elaine

> On Aug 4, 2015, at 12:22 PM, Sarko, Dikran <dikran.sarko at yahoo.com> wrote:
> 
> Dear Elaine,
> 
> Thank you very much for your reply.
> I am not familiar with programing, however, I did exactly as described in the page you had refered to.
> 
> import chimera
> m = chimera.openModels.list()[0]
> for a in m.atoms:
> 	crd = a.coord()
> 	crd.x = 0 - crd.x
> 	a.setCoord(crd)
> 
> then I opened the 4LLZ pdb file as a test, however when I saved the structure and tried to combare it with the original one. Chimera opened only one structure (not tow as I expected).
> 
> Is there anything wrong, ore any additional advice.
> 
> PS: I suggest to incorporate an additional function in the next release of Cheimera that consider the generation of mirror image protein of pdb file as a function within the tools, or other appropriate function. Such function will attract a lot of attention, and Cheimera will be (to my knowledge), the 1st modeling program that offer such a function.
> 
> Thank you very much
> Dikran
> 
> Von: Elaine Meng <meng at cgl.ucsf.edu>
> An: "Sarko, Dikran" <dikran.sarko at yahoo.com> 
> CC: Mailing List <chimera-users at cgl.ucsf.edu> 
> Gesendet: 19:54 Montag, 3.August 2015
> Betreff: Re: [Chimera-users] Mirror image proteins
> 
> Hello Dikran,
> Only with a little scripting, but somebody asked the same thing a few years ago and a simple python script was posted to the list.  Please see:
> 
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005882.html>
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005883.html>
> 
> Remember that in python the indentation is important.
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> 
> 
> > On Aug 2, 2015, at 1:11 PM, Sarko, Dikran <dikran.sarko at yahoo.com> wrote:
> > 
> > Hello,
> > is there any way to generate mirror image proteins (All AA in D-form) from an already exsist pdb file.
> > Thank you in advance
> > Dikran
> 
> 




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