Hi all, I'm wondering if the RMSD function in Chimera will correctly calculate RMSD when two molecules are compared. For example, if a benzene ring is flipped, will the RMSD stay the same? Furthermore, how does Chimera do this comparison? Thanks! Kevin
Hi Kevin, The "rmsd" and "match" commands do not figure out which atoms are chemically equivalent or symmetrically arranged and try all of the possibilities. If the atoms are not specified by name in the command, they will be sorted by name and the sorted lists used for pairing. You can explicitly give the atom names in the command in whatever order you like, however. For a ring that could be flipped, for example, you could issue two "rmsd" commands and then take the lower of the resulting RMSD values. The commands including all the atom names could be rather ugly and long, but you could possibly minimize the pain with aliases if the names are stereotyped (say within standard PDB residues PHE and TYR). More details on how these commands work: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 11, 2009, at 4:04 PM, Kevin Wu wrote:
Hi all, I'm wondering if the RMSD function in Chimera will correctly calculate RMSD when two molecules are compared. For example, if a benzene ring is flipped, will the RMSD stay the same? Furthermore, how does Chimera do this comparison? Thanks! Kevin
I forgot to mention that I recommend using the Chimera snapshot from Aug 20, or even a newer daily build, because now commas in command- line atom specifications imply ordering -- in version 1.3, comma- separated models, residues, or atoms are not necessarily used in the order typed. To specify atoms in a particular order in those older versions it is necessary to enter something like @ca@cb@cd1@ce1 whereas in the newer versions, @ca,cb,cd1,ce1 also specifies order. Elaine On Sep 11, 2009, at 4:59 PM, Elaine Meng wrote:
Hi Kevin, The "rmsd" and "match" commands do not figure out which atoms are chemically equivalent or symmetrically arranged and try all of the possibilities. If the atoms are not specified by name in the command, they will be sorted by name and the sorted lists used for pairing. You can explicitly give the atom names in the command in whatever order you like, however. For a ring that could be flipped, for example, you could issue two "rmsd" commands and then take the lower of the resulting RMSD values. The commands including all the atom names could be rather ugly and long, but you could possibly minimize the pain with aliases if the names are stereotyped (say within standard PDB residues PHE and TYR).
More details on how these commands work: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 11, 2009, at 4:04 PM, Kevin Wu wrote:
Hi all, I'm wondering if the RMSD function in Chimera will correctly calculate RMSD when two molecules are compared. For example, if a benzene ring is flipped, will the RMSD stay the same? Furthermore, how does Chimera do this comparison? Thanks! Kevin
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