Re: [Chimera-users] Mirror image proteins

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@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@cgl.ucsf.edu> An: "Sarko, Dikran" <dikran.sarko@yahoo.com> CC: Mailing List <chimera-users@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@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
participants (1)
-
Elaine Meng