How to explore two protein structures on the same screen?
Hi, I opened two protein structures, say 2JIT and 4WA9 and they were partially overlapped on the screen. How to move one protein so that they can be separated more? I can only move the two proteins as a whole but not individually. Further, I would like to highlight one residue for a particular protein and I could not find a way to first select a protein and then a residue. Thanks, Jing
Hi Jing, For an overview, you might want to try the “getting started” tutorial -- moving separately is mentioned in “models and model status,” and specifying individual residues is covered in “selection with the mouse” and “command/target”: <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> However, I’ll try to list the ways briefly in this message. There are many ways to move structures separately: (1) “freezing” (deactivating) some structure(s) and moving the others with the mouse <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> (2) superimposing similar structures <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> (3) using movement commands (move, turn, etc.) with “models” keyword to move only specific models <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> There are many ways to act on individual residues: (1) selecting them with Ctrl-click on the structure <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html#pickselect> (2) selecting them in the sequence window (menu: Favorites… Sequence) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html> (3) just specifying the residue(s) directly in a command, for example: color red #0:325.A … to color residue 325 in chain A of model 0 select #1:45.A,55.B … to select residues 45 in chain A and 55 in chain B of model 1 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierarchy> 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 Jul 28, 2015, at 1:29 AM, Jing Tang <jing.tang@helsinki.fi> wrote:
Hi, I opened two protein structures, say 2JIT and 4WA9 and they were partially overlapped on the screen. How to move one protein so that they can be separated more? I can only move the two proteins as a whole but not individually. Further, I would like to highlight one residue for a particular protein and I could not find a way to first select a protein and then a residue. Thanks, Jing
Thanks Elaine. These links are very helpful. Jing -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: 29. heinäkuuta 2015 20:21 To: Jing Tang Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] How to explore two protein structures on the same screen? Hi Jing, For an overview, you might want to try the getting started tutorial -- moving separately is mentioned in models and model status, and specifying individual residues is covered in selection with the mouse and command/target: <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> However, Ill try to list the ways briefly in this message. There are many ways to move structures separately: (1) freezing (deactivating) some structure(s) and moving the others with the mouse <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> (2) superimposing similar structures <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> (3) using movement commands (move, turn, etc.) with models keyword to move only specific models <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> There are many ways to act on individual residues: (1) selecting them with Ctrl-click on the structure <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html#pickselect> (2) selecting them in the sequence window (menu: Favorites Sequence) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f ramemav.html> (3) just specifying the residue(s) directly in a command, for example: color red #0:325.A to color residue 325 in chain A of model 0 select #1:45.A,55.B to select residues 45 in chain A and 55 in chain B of model 1 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hiera rchy> 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 Jul 28, 2015, at 1:29 AM, Jing Tang <jing.tang@helsinki.fi> wrote:
Hi, I opened two protein structures, say 2JIT and 4WA9 and they were partially overlapped on the screen. How to move one protein so that they can be separated more? I can only move the two proteins as a whole but not individually. Further, I would like to highlight one residue for a particular protein and I could not find a way to first select a protein and then a residue. Thanks, Jing
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Elaine Meng -
Jing Tang