Hi, Fitmap has on option to fit each model sequentially (eachModel). Would it be possible in a future version to add an "eachChain" option to fit each polymer chain in a mult-chain model independently? This would be useful when quickly fitting oligomeric models to an EM map. Alternatively, is there another quick way to do this? I thought about using perframe, but that only take numerical ranges, not alphabetical Cheers Oli
Hi Oli, I guess you could "split" by chain, use fitting per model, then "combine" back into a single model (if that's what you wanted). <https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> Cheers, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 15, 2025, at 8:44 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
Fitmap has on option to fit each model sequentially (eachModel).
Would it be possible in a future version to add an "eachChain" option to fit each polymer chain in a mult-chain model independently? This would be useful when quickly fitting oligomeric models to an EM map. Alternatively, is there another quick way to do this? I thought about using perframe, but that only take numerical ranges, not alphabetical
Cheers Oli
Oh that does the trick and makes a very nice alias, thanks Elaine! alias fit_by_chain split $1; fitmap $1.* inmap $2 eachmodel true; combine $1.* close true where $1 is the model ID and $2 is the map ID thanks!! Cheers Oli
On Jul 15, 2025, at 11:50 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oli, I guess you could "split" by chain, use fitting per model, then "combine" back into a single model (if that's what you wanted).
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html>
Cheers, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 15, 2025, at 8:44 AM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
Fitmap has on option to fit each model sequentially (eachModel).
Would it be possible in a future version to add an "eachChain" option to fit each polymer chain in a mult-chain model independently? This would be useful when quickly fitting oligomeric models to an EM map. Alternatively, is there another quick way to do this? I thought about using perframe, but that only take numerical ranges, not alphabetical
Cheers Oli
participants (2)
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Elaine Meng -
Oliver Clarke