Superimpose overall structure
Dear ChimeraX developers, Thank a bunch for developing this so gracious and powerful software for our community! May I ask how to superimpose the overall structures of two analogues? e.g., the E. coli sliding clamp beta is a ring-shaped homodimer (two chains), while the yeast sliding clamp PCNA is a ring-shaped homotrimer (three chains), and their overall structures are quite similar, but when I use the matchmaker to superimpose them, it seems always only use the chain A, but not the all chains, pls see figures below~ Stay safe and warm, Many thanks! [cid:d0647b0e-e6db-459b-9f0b-72ee21eb06c7] Best, Fengwei
Dear Fengwei, You're welcome!! If there were equal numbers of chains, you could specify multiple pairs of chains to fit with the "matchmaker" command option "pairing ss": <http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options> However, your situation where one structure has two chains and the other has three (but corresponding to a similar overall structure) is more complicated. In that case the easy "matchmaker" approach, where it figures out the residue pairing for you by aligning the chain sequences, cannot be used. Instead you would need to specify in the command line exactly which atoms to use for fitting, using the "align" command. This is more difficult, since you will need to know exactly which residues in which chains of one structure should be overlaid with which residues in which chains of the other. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> Command-line specification of chains, residues, atoms (scroll down for examples): <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#hierarchy> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 10, 2020, at 1:22 PM, Zheng, Fengwei <Fengwei.Zheng@vai.org> wrote:
Dear ChimeraX developers,
Thank a bunch for developing this so gracious and powerful software for our community!
May I ask how to superimpose the overall structures of two analogues? e.g., the E. coli sliding clamp beta is a ring-shaped homodimer (two chains), while the yeast sliding clamp PCNA is a ring-shaped homotrimer (three chains), and their overall structures are quite similar, but when I use the matchmaker to superimpose them, it seems always only use the chain A, but not the all chains, pls see figures below~ Stay safe and warm, Many thanks!
<Outlook-bkctx0ak.png> Best, Fengwei
Dear Elaine, Thank you so much for your prompt replying! Got it, Have a great weekend! Best, Fengwei ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, December 10, 2020 16:36 To: Zheng, Fengwei <Fengwei.Zheng@vai.org> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [External] Re: [chimerax-users] Superimpose overall structure Dear Fengwei, You're welcome!! If there were equal numbers of chains, you could specify multiple pairs of chains to fit with the "matchmaker" command option "pairing ss": <http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options> However, your situation where one structure has two chains and the other has three (but corresponding to a similar overall structure) is more complicated. In that case the easy "matchmaker" approach, where it figures out the residue pairing for you by aligning the chain sequences, cannot be used. Instead you would need to specify in the command line exactly which atoms to use for fitting, using the "align" command. This is more difficult, since you will need to know exactly which residues in which chains of one structure should be overlaid with which residues in which chains of the other. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> Command-line specification of chains, residues, atoms (scroll down for examples): <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#hierarchy> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 10, 2020, at 1:22 PM, Zheng, Fengwei <Fengwei.Zheng@vai.org> wrote:
Dear ChimeraX developers,
Thank a bunch for developing this so gracious and powerful software for our community!
May I ask how to superimpose the overall structures of two analogues? e.g., the E. coli sliding clamp beta is a ring-shaped homodimer (two chains), while the yeast sliding clamp PCNA is a ring-shaped homotrimer (three chains), and their overall structures are quite similar, but when I use the matchmaker to superimpose them, it seems always only use the chain A, but not the all chains, pls see figures below~ Stay safe and warm, Many thanks!
<Outlook-bkctx0ak.png> Best, Fengwei
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Elaine Meng -
Zheng, Fengwei