Fwd: Aligning two residues same name
Changing residue name works. Deleted membrane, saved pdb without membrane. Loaded the two models. Command line: match :XXX :YYY How to put the difference in quantitative terms (rmsd)? Thanks francesco --- Francesco Pietra <chiendarret@yahoo.com> wrote:
Date: Mon, 4 Feb 2008 06:59:25 -0800 (PST) From: Francesco Pietra <chiendarret@yahoo.com> Subject: Aligning two residues same name To: chimera <chimera-users@cgl.ucsf.edu>
Task: compare/align a single-residue molecule before docking (naked molecule, mol2 or pdb file) with same residue as ligand in a protein after docking/MD (pdb file of a snapshot for complex embedded in a bilayer membrane). Should I change the residue name in one of the two models? Same name poses to me problems. Or there is a direct way? Thanks francesco pietra
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Hi Francesco, The RMSD from the command "match" is reported in the Reply Log (Favorites... Reply Log). http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html Best, Elaine On Feb 4, 2008, at 7:26 AM, Francesco Pietra wrote:
Changing residue name works. Deleted membrane, saved pdb without membrane. Loaded the two models. Command line: match :XXX :YYY
How to put the difference in quantitative terms (rmsd)? Thanks francesco
--- Francesco Pietra <chiendarret@yahoo.com> wrote:
Date: Mon, 4 Feb 2008 06:59:25 -0800 (PST) From: Francesco Pietra <chiendarret@yahoo.com> Subject: Aligning two residues same name To: chimera <chimera-users@cgl.ucsf.edu>
Task: compare/align a single-residue molecule before docking (naked molecule, mol2 or pdb file) with same residue as ligand in a protein after docking/MD (pdb file of a snapshot for complex embedded in a bilayer membrane). Should I change the residue name in one of the two models? Same name poses to me problems. Or there is a direct way? Thanks francesco pietra
____________________________________________________________________________________
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participants (2)
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Elaine Meng -
Francesco Pietra