[Chimera-users] Ramachandran plot for a selection

Eric Pettersen pett at cgl.ucsf.edu
Wed May 27 11:11:52 PDT 2015


Yeah, the Ramachadran plotting in Chimera doesn't really work with trajectories in the way you want (it can only plot all the residues of the current frame).

The Ramaplot plugin of VMD does pretty much exactly what you want:  http://www.ks.uiuc.edu/Research/vmd/plugins/ramaplot/

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On May 26, 2015, at 11:51 AM, "Elena Lilkova" <elilkova at phys.uni-sofia.bg> wrote:

> Dear Chimera community,
> 
> First I would like to just say that I am new to Chimera. I made a MD
> simulation of a protein using NAMD. Now I am interested in generating a
> Ramachandran plot for the whole trajectory, but only for a specific
> selection of my protein, namely three specific residues. I fail to
> succeed. Could anyone probably suggest a solution?
> 
> Elena Lilkova
> 
> elilkova at phys.uni-sofia.bg
> 
> PhD student,
> Atomic Physics Department,
> Faculty of Physics,
> University of Sofia "St. Kliment Ohridski"
> 
> 5 James Bourchier Blvd.
> 1164 Sofia,
> Bulgaria
> 
> Elena Lilkova
> 
> elilkova at phys.uni-sofia.bg
> 
> PhD student,
> Atomic Physics Department,
> Faculty of Physics,
> University of Sofia "St. Kliment Ohridski"
> 
> 5 James Bourchier Blvd.
> 1164 Sofia,
> Bulgaria
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users






More information about the Chimera-users mailing list