successive minimizations: can we use a unique protein setup?
Hi everyone, I want to do the following: 1. minimize a region of a structure 2. change some part of the region by hand (like swap a residue) 3. minimize once more. and this 2 or three times. However, each time I want to minimize I have to pass through the all setup of the protein (add H, hist protonation, and so one). Couldn't we keep the information of the first setup and directly fo through the minimization? All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es ----- Missatge original ----- De: chimera-users-request@cgl.ucsf.edu Data: Dimecres, Novembre 5, 2008 2:00 am Assumpte: Chimera-users Digest, Vol 67, Issue 4
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Today's Topics:
1. Using match (Omar Davulcu) 2. Re: Using match (Eric Pettersen) 3. Re: Models or chain (Eric Pettersen) 4. removing side chains (Matthew Dougherty) 5. Re: removing side chains (Eric Pettersen) 6. Re: Using match (Elaine Meng)
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Message: 1 Date: Mon, 3 Nov 2008 14:53:19 -0800 From: "Omar Davulcu" <davulcuo@ohsu.edu> Subject: [Chimera-users] Using match To: chimera-users@cgl.ucsf.edu Message-ID: <001301c93e06$f7394020$e5abc060$@edu> Content-Type: text/plain; charset="us-ascii"
Hi,
I'm using the match command with a cutoff to align specific regions of related enzymes. It appears to work fine and remove residue pairs above the cutoff, but is there a way to list those residue pairs which were (or were not) removed?
Thanks for any help!
Omar Davulcu
Hi JD, As you have found, the Minimize Structure tool or minimize command has limitations and inconveniences. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.h... If you didn't change the set of atoms (by changing I mean adding atoms or swapping a side chain, not just modifying positions such as with bond rotation), I believe that when the "prep" dialog appears, you can just un-check all of the options (hydrogen addition, etc.) and they will not be run again. However, if you did change the set of atoms (adding, swapping), it is necessary to run at least the "add charge" step again because it also assigns AMBER atom types to the atoms. Depending on what you changed, it might be necessary to also run "add hydrogens" again; for example, if you swap a residue, the new sidechain doesn't include hydrogens yet. I hope this helps, ELaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Nov 6, 2008, at 1:13 AM, Jean Didier Pie Marechal wrote:
Hi everyone, I want to do the following:
1. minimize a region of a structure 2. change some part of the region by hand (like swap a residue) 3. minimize once more.
and this 2 or three times.
However, each time I want to minimize I have to pass through the all setup of the protein (add H, hist protonation, and so one). Couldn't we keep the information of the first setup and directly fo through the minimization? All the best, JD
participants (2)
-
Elaine Meng -
Jean Didier Pie Marechal