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@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@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
Dear Elena, Welcome to Chimera! Instead of “Ramachandran” plot, you could use the plotting functions in the MD Movie tool (Chimera’s trajectory viewer). This would not show psi versus phi, you would have to plot each dihedral (psi and phi for each residue of interest) versus trajectory frame. You can show them all on the same plot, however. Documentation here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> Start the tool (Chimera menu: Tools… MD/Ensemble Analysis… MD Movie). I don’t know what type of files you have from NAMD, but it can read PSF + DCD or prmtop + DCD files. Then when MD Movie is showing your trajectory, from its dialog choose Analysis…Plot and then specify the dihedrals you want to plot. See the link above for details. Although Chimera has a Ramachandran Plot feature, it doesn’t sound appropriate for what you want to do. It just shows the plot for the whole structure, and only a single structure at a time, not multiple frames of a trajectory. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ramachandran/ramachandran.html> 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 May 26, 2015, at 11:51 AM, Elena Lilkova <elilkova@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
Dear Elaine, thank you for your response! Best regards,Elena Lilkova On Wednesday, May 27, 2015 8:47 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Elena, Welcome to Chimera! Instead of “Ramachandran” plot, you could use the plotting functions in the MD Movie tool (Chimera’s trajectory viewer). This would not show psi versus phi, you would have to plot each dihedral (psi and phi for each residue of interest) versus trajectory frame. You can show them all on the same plot, however. Documentation here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> Start the tool (Chimera menu: Tools… MD/Ensemble Analysis… MD Movie). I don’t know what type of files you have from NAMD, but it can read PSF + DCD or prmtop + DCD files. Then when MD Movie is showing your trajectory, from its dialog choose Analysis…Plot and then specify the dihedrals you want to plot. See the link above for details. Although Chimera has a Ramachandran Plot feature, it doesn’t sound appropriate for what you want to do. It just shows the plot for the whole structure, and only a single structure at a time, not multiple frames of a trajectory. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ramachandran/ramachandran.html> 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 May 26, 2015, at 11:51 AM, Elena Lilkova <elilkova@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
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@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@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@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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participants (3)
-
Elaine Meng -
Elena Lilkova -
Eric Pettersen