Dear Jan, Thanks for your thoughts! If by "model" you mean an atomic model, if you open structures from the Protein Database it will already show in the Log for each protein chain entity the associated UniProt identifier, and clicking that link in the Log fetches the sequence from UniProt, opens it in a sequence window, associates it with the structure chain(s), etc. The UniProt sequence also has features marked on it and there is an interface for selecting the features on the structure. See screenshots below and User Guide help pages, e.g. <https://rbvi.ucsf.edu/chimerax/docs/user/modelinfo.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#uniprot> There isn't currently an user interface to getting molecular weight, but a relatively simple python script could add up atomic weights. However, points to consider: do you mean only protein and/or nucleic acid chain entities, and not all the waters, ligands, etc. that also might be in a structure? Would it need to include hydrogens, in which case you'd have to add hydrogens first? What about residues that are in the sequence information but missing from the coordinates, such as flexible termini, truncated sidechains, etc.? I hope this helps, 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 Oct 4, 2024, at 2:59 PM, Jan-Hannes Schaefer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX community,
Thanks for your work and effort in making ChimeraX available to all of us. I would love to see a function in future versions of ChimeraX to measure the molecular weight of the model and link it to the uniprot entry? Let me know if this is something you would like to add.
Yours, Jan
