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