a request again...adjust torsion for pseudo bonds
Dear all, sorry to bother you again. I want to perform a conformational search rotating residues around their chelation bond with a metal. With the adjust torsion tool, I can't rotate around pseudo bond, and I actually need to transform the different pseudo bonds in bonds. Could you authorize pseudo bonds to be rotated around? (in the contrary I'll continue with transforming pseudo bonds in bonds, but I thought that remaining with pseudo bonds is better especially when you do "add hydrogens" or other stuffs afterwards ) All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological 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-dev-request@cgl.ucsf.edu Data: Dimecres, Maig 13, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 64, Issue 5
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Today's Topics:
1. [Chimera-dev] Compiling chimera from source code (christopher lau) 2. Re: [Chimera-dev] Compiling chimera from source code (Greg Couch)
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Message: 1 Date: Tue, 12 May 2009 21:15:56 -0700 From: christopher lau <chris.d.lau@gmail.com> Subject: [chimera-dev] [Chimera-dev] Compiling chimera from source code To: chimera-dev@cgl.ucsf.edu Message-ID: <f2026a300905122115w3cd5df71mdc8090670593ad94@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1"
Dear Madam/Sir,
I am currently involved in a project which requires compiling the Chimerasource code from scratch. I have been using:
http://www.cgl.ucsf.edu/chimera/sourcecode.html
for reference, and I understand that surfacing library is not availabledue to licensing issues. Because I am not interested in using this feature, I wanted to know if it was still possible to compile the Chimerasource code. I know that it will be difficult but any knowledge or past experience that may help me would be greatly appreciated.
Thanks in advance,
Chris
Hi JD, I don't really understand your usage scenario. It seems to me that rotating around the chelation bond will either be like rotating around a hydrogen/heavy-atom bond (produces no relative motion) or around a ring bond (tears the structure apart). Nonetheless I think you can accomplish what you want one of two ways: 1) temporarily form a "real" bond with the metal and then destroy it afterward (bond/~bond commands) 2) use the roll command to rotate around the metal/chelating-atom axis (use an "axis" argument which is an atom spec selecting the metal and chelating atom; a "center" argument which is one of the two atoms; and a "models" argument which is the model(s) containing the metal and chelating residue). These arguments to the roll command are only available in the daily build. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On May 22, 2009, at 7:49 AM, Jean Didier Pie Marechal wrote:
Dear all, sorry to bother you again. I want to perform a conformational search rotating residues around their chelation bond with a metal. With the adjust torsion tool, I can't rotate around pseudo bond, and I actually need to transform the different pseudo bonds in bonds.
Could you authorize pseudo bonds to be rotated around? (in the contrary I'll continue with transforming pseudo bonds in bonds, but I thought that remaining with pseudo bonds is better especially when you do "add hydrogens" or other stuffs afterwards )
All the best, JD
Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona)
On May 26, 2009, at 2:15 PM, Eric Pettersen wrote:
2) use the roll command to rotate around the metal/chelating-atom axis (use an "axis" argument which is an atom spec selecting the metal and chelating atom; a "center" argument which is one of the two atoms; and a "models" argument which is the model(s) containing the metal and chelating residue). These arguments to the roll command are only available in the daily build.
Just to (possibly) clarify #2: the "models" will be the ones to move in the roll while any others remain fixed. If you want any part to move relative to another, they must be in different models. Even though the "axis" would contain the metal and one coordinating atom, "models" wouldn't necessarily have to include the metal. Also, I don't think it is necessary to give the "center" in this case, because by default it will lie on the axis. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/roll.html> Elaine
participants (3)
-
Elaine Meng -
Eric Pettersen -
Jean Didier Pie Marechal