Hi everyone, Coot has an easily implemented way of "walking" through a peptide chain. It works like this:
From the drop down menu, choose "go to atom", pick the first residue. The view zooms to the first residue. Now hit the space bar, and the view smoothly advances to the next residue in the chain. Hold shift-space, and it smoothly moves back.
Having an easy way to smoothly transition the view from one residue to the next would would be useful in Chimera. From my perspective it would be great for teaching, but I would think a simple way of walking along the backbone would be generally appreciated. I imagine this feature would be easy to construct with a Python script, maybe using the "fly" or "focus" commands. I'm not sure how to tie this to a keystroke, but an alternative is to give the function a toolbar button. If this capability doesn't already exist, could someone provide some advice on writing the script? I'm only just learning Python. Thanks for the help Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon@depauw.edu
Hi Dan, Well there's probably a few ways to approach this, but one possibility is to define a saved position for each residue and fly between them. Here's some code that flies through the non-HET residues of the first open model in Chimera: import chimera residues = [r for r in chimera.openModels.list()[0].residues if not r.isHet] for i, r in enumerate(residues): chimera.runCommand("focus " + r.oslIdent()) chimera.runCommand("savepos p%d" % i) chimera.runCommand("fly 10 " + " ".join(["p%d" % i for i in range(len(residues))])) It's somewhat nausea inducing. You could use the above as a jumping off point and then define some keyboard accelerators to fly back and forth between positions (it would need to remember what the "current" position is). Defining keyboard accelerators is described here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/accele... Good luck! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Sep 10, 2010, at 11:51 AM, Daniel Gurnon wrote:
Hi everyone, Coot has an easily implemented way of "walking" through a peptide chain. It works like this: From the drop down menu, choose "go to atom", pick the first residue. The view zooms to the first residue. Now hit the space bar, and the view smoothly advances to the next residue in the chain. Hold shift-space, and it smoothly moves back.
Having an easy way to smoothly transition the view from one residue to the next would would be useful in Chimera. From my perspective it would be great for teaching, but I would think a simple way of walking along the backbone would be generally appreciated. I imagine this feature would be easy to construct with a Python script, maybe using the "fly" or "focus" commands. I'm not sure how to tie this to a keystroke, but an alternative is to give the function a toolbar button.
If this capability doesn't already exist, could someone provide some advice on writing the script? I'm only just learning Python. Thanks for the help Dan
-- ____________________________
Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135
p: 765-658-6279 e: danielgurnon@depauw.edu _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Daniel Gurnon -
Eric Pettersen