Model missing residues in Chimera X
Dear Chimera X community, I’m a new user of Chimera X and I have a question about the built-in Modeller function in Chimera X Previously in Chimera 2, we use the “Model/Refine Loop” function to model missing residues in the experimental structure, before any further calculation or simulations. The “Model/Refine Loop” function uses Modeller and the function provides modeled, complete structures in which the non-missing residues do not move. In Chimera X, a similar function is “Modeller Comparative” but it works differently. The “Modeller Comparative” performs a modeling for the full structure with the given sequence. Is possible in Chimera X to model the missing residues, without moving the existent residues? Thank you for your kind advice in advance! Thanks, Amy -- Amy He Chemistry Graduate Teaching Assistant Hadad Research Group Ohio State University he.1768@osu.edu<mailto:he.1768@osu.edu>
Hi Amy, Chimera had two main options for running Modeller, (1) comparative (whole chain) and (2) loop remodeling or filling in missing segments. ChimeraX does not have the loop modeling option yet, sorry, although we are planning to add it in the future. This capability is listed in the "missing features" section of the ChimeraX download page. For now, you could use Chimera for loop modeling. For comparative modeling, ChimeraX has the advantage over Chimera in that it can model multi-chain multimers and complexes (Chimera's comparative modeling is single chain only). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 23, 2021, at 5:52 AM, He, Amy via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera X community, I’m a new user of Chimera X and I have a question about the built-in Modeller function in Chimera X
Previously in Chimera 2, we use the “Model/Refine Loop” function to model missing residues in the experimental structure, before any further calculation or simulations. The “Model/Refine Loop” function uses Modeller and the function provides modeled, complete structures in which the non-missing residues do not move.
In Chimera X, a similar function is “Modeller Comparative” but it works differently. The “Modeller Comparative” performs a modeling for the full structure with the given sequence.
Is possible in Chimera X to model the missing residues, without moving the existent residues?
Thank you for your kind advice in advance! Thanks, Amy -- Amy He Chemistry Graduate Teaching Assistant Hadad Research Group Ohio State University he.1768@osu.edu
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Hello Elaine, That is very helpful. Thank you very much for your kind advice! Best, Amy -- Amy He Chemistry Graduate Teaching Assistant Hadad Research Group Ohio State University he.1768@osu.edu From: Elaine Meng <meng@cgl.ucsf.edu> Date: Friday, July 23, 2021 at 11:39 AM To: He, Amy <he.1768@buckeyemail.osu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Model missing residues in Chimera X Hi Amy, Chimera had two main options for running Modeller, (1) comparative (whole chain) and (2) loop remodeling or filling in missing segments. ChimeraX does not have the loop modeling option yet, sorry, although we are planning to add it in the future. This capability is listed in the "missing features" section of the ChimeraX download page. For now, you could use Chimera for loop modeling. For comparative modeling, ChimeraX has the advantage over Chimera in that it can model multi-chain multimers and complexes (Chimera's comparative modeling is single chain only). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 23, 2021, at 5:52 AM, He, Amy via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera X community, I’m a new user of Chimera X and I have a question about the built-in Modeller function in Chimera X
Previously in Chimera 2, we use the “Model/Refine Loop” function to model missing residues in the experimental structure, before any further calculation or simulations. The “Model/Refine Loop” function uses Modeller and the function provides modeled, complete structures in which the non-missing residues do not move.
In Chimera X, a similar function is “Modeller Comparative” but it works differently. The “Modeller Comparative” performs a modeling for the full structure with the given sequence.
Is possible in Chimera X to model the missing residues, without moving the existent residues?
Thank you for your kind advice in advance! Thanks, Amy -- Amy He Chemistry Graduate Teaching Assistant Hadad Research Group Ohio State University he.1768@osu.edu
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participants (2)
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Elaine Meng -
He, Amy