[Chimera-users] Ramachandran plot for a selection

[Eric Pettersen]

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
> 
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