Hi Greg, It’s reasonable if you realize the limitations: minimization is just minimization... it doesn’t explore the energy “landscape” by going over any humps. Even a short MD doesn’t do that much to explore the landscape. Then again, you may not want to do longer MD anyway, especially if you haven’t added a box of solvent, lest the structure get messed up overall (shrink, expand, or get stuck in some unlikely conformation). After virtual mutation, if you are fully aware that it may just be cleaning the structure up a bit locally rather than doing some kind of detailed prediction of mutation effects, perfectly reasonable. The minimization done with that tab of the Molecular Dynamics Simulation tool is the same as with the Minimize Structure tool, as far as I know (so stick with what you prefer). <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 26, 2019, at 12:20 PM, Gregory Babbitt <gabsbi@rit.edu> wrote:
I am not sure if anyone else does this, but sometimes I will use swapaa to change rotamer(s), then go to MD/ensemble analysis and run just the dock/structure prep (i.e. add H) and then energy minimization tab under 'molecular dynamic simulation'. I usually increase the default values to several thousand steps of steepest descent. If you check the options box for 'live run' you can watch the structure morphing and stabilizing..then resave as new PDB file.
Anybody have any thoughts as to if this is a reasonable combination of steps in Chimera?
Greg at RIT
________________________________________ From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, July 26, 2019 10:54 AM To: Joshua Plank Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Editing sequences within Chimera
Hi Josh, I guess you mean actually changing the 3D structure. Yes, you can “swap” amino acids by replacing side chains with the Rotamers tool (menu: Tools.. Structure Editing… Rotamers) or the “swapaa” command. This only does a simple replacement; it does not predict any large/overall changes in the structure.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>
There is an example of using Rotamers in the Structure Analysis and Comparison tutorial. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 25, 2019, at 2:00 PM, Joshua Plank <jplan002@ucr.edu> wrote:
Hi, I am wondering if it is possible to edit the amino acid sequence somehow? I have a .pdb file of the protein I'm interested in, but would like to change two of the amino acids to something else. Is this possible? thanks, Josh
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