chimera visualization
Dear Elaine, I would like to produce images from chimera showing an NMR bundle structure (backbone only) with stick-represented residues each one belonging to different single structures. I know it´s possible to do it with pymol but unfortunately the structures superimposition is not as good as in chimera. Would it be possible? Thank you in advance, Valerio
Dear Valerio, It should be no problem. Just superimpose the structures and show their backbones as sticks, in the same way as for crystal structures. You could superimpose with MatchMaker (in menu under Tools… Structure Comparison) or with Ensemble Match (in menu under Tools… MD/Ensemble Analysis). <www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> There are examples of using these tools in various tutorials: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html> You can show backbone sticks with the Actions menu or with commands, for example: open 1g1p ~ribbon disp @n,ca,c,o 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 31, 2015, at 5:19 AM, Valerio Chiarini <valerio.chiarini@helsinki.fi> wrote:
Dear Elaine, I would like to produce images from chimera showing an NMR bundle structure (backbone only) with stick-represented residues each one belonging to different single structures. I know it´s possible to do it with pymol but unfortunately the structures superimposition is not as good as in chimera. Would it be possible? Thank you in advance, Valerio
Hi Elaine, the problem is that the structures I superimpose with matchmaker belong to the same pdb file, which means that I can select one chain but when I am about to show a residue (eg. ser) in stick the previous selection disappears and the serines of all structures are shown. Valerio Quoting Elaine Meng <meng@cgl.ucsf.edu>:
Dear Valerio, It should be no problem. Just superimpose the structures and show their backbones as sticks, in the same way as for crystal structures.
You could superimpose with MatchMaker (in menu under Tools… Structure Comparison) or with Ensemble Match (in menu under Tools… MD/Ensemble Analysis). <www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
There are examples of using these tools in various tutorials: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html>
You can show backbone sticks with the Actions menu or with commands, for example:
open 1g1p ~ribbon disp @n,ca,c,o
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 31, 2015, at 5:19 AM, Valerio Chiarini <valerio.chiarini@helsinki.fi> wrote:
Dear Elaine, I would like to produce images from chimera showing an NMR bundle structure (backbone only) with stick-represented residues each one belonging to different single structures. I know it´s possible to do it with pymol but unfortunately the structures superimposition is not as good as in chimera. Would it be possible? Thank you in advance, Valerio
Dear Valerio, It should not matter, each is still a separate model. If you open the PDB as model #0 but it contains an NMR ensemble, the members are models #0.1, #0.2, … etc. I don’t know what steps you are using, but you can control exactly which structure(s) in which to show a particular residue in several ways. Here are just two ways: Ctrl-click to select the ribbon segment of just one residue in one structure (this mainly works for where they are not too close together), menu: Actions… Atoms/Bonds… show Use a command, for example to show residue 45 of chain A in the 5th ensemble member of model 0 only: display #0.5:45.A You can use the balloon information that pops up when you hold the mouse cursor over some part a of a structure to tell you which model number and which residue it is. Again, it is just the same as if you have multiple non-NMR structures open. 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 Sep 2, 2015, at 1:04 AM, Valerio Chiarini <valerio.chiarini@helsinki.fi> wrote:
Hi Elaine, the problem is that the structures I superimpose with matchmaker belong to the same pdb file, which means that I can select one chain but when I am about to show a residue (eg. ser) in stick the previous selection disappears and the serines of all structures are shown. Valerio
Quoting Elaine Meng <meng@cgl.ucsf.edu>:
Dear Valerio, It should be no problem. Just superimpose the structures and show their backbones as sticks, in the same way as for crystal structures.
You could superimpose with MatchMaker (in menu under Tools… Structure Comparison) or with Ensemble Match (in menu under Tools… MD/Ensemble Analysis). <www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
There are examples of using these tools in various tutorials: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html>
You can show backbone sticks with the Actions menu or with commands, for example:
open 1g1p ~ribbon disp @n,ca,c,o
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 31, 2015, at 5:19 AM, Valerio Chiarini <valerio.chiarini@helsinki.fi> wrote:
Dear Elaine, I would like to produce images from chimera showing an NMR bundle structure (backbone only) with stick-represented residues each one belonging to different single structures. I know it´s possible to do it with pymol but unfortunately the structures superimposition is not as good as in chimera. Would it be possible? Thank you in advance, Valerio
participants (2)
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Elaine Meng -
Valerio Chiarini