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
Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu
To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu
You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..."
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)
-------------------------------------------------------------------- --
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