Hi Matthias, B-factor is an atom attribute so I guess you are interested in average B-factor for a residue? For floppy surface side chains that could be large while the backbone atom B-factor is small, so maybe you also want average B-factor for backbone or side chain separately. AlphaFold 2 and 3 save pLDDT as B-factor, ie per-atom, and AlphaFold 3 interestingly gives different pLDDT values on different atoms of a residue -- again maybe you would want an average. For AlphaMissense there are 19 pathogenicity scores for the 19 possible mutations. How do you envision plotting those per-residue? An average doesn't seem too useful. Maximum? Show 20 separate graphs? For B-factor and pLDDT I could imagine you might want graphs for every chain of a complex which could be painful to request 1 at a time for say a ribosome. The residue graphing should allow clicking or dragging on the graph to select corresponding residues. There a lot of unclear details about how this would work. In general ChimeraX tries to show residue attributes directly on the structure by colors (e.g. average bfactor, pLDDT, maximum mutation pathogenicity score). I don't have a clear picture of when it is more useful to show those kinds of scores with a graph where the horizontal axis is residue number. As Elaine points out, that makes more sense with a sequence alignment visualization. Tom
On Jan 29, 2025, at 9:27 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Matthias, Sorry, not in general. Although you can see a histogram of attribute values in the Render by Attribute tool, the X-axis is the attribute value, not atom or residue number. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/render.html>
The Sequence Viewer can show various attributes as headers, but currently just things like sequence conservation and RMSD over associated structures. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers>
Best, 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 Jan 29, 2025, at 2:44 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX team, I wondered if it is possible to generate a line or scatter plot of an attribute value (B factor, Alphafold pLDDT scores, or AlphafoldMissense score…) over the residue number? For example something like this (taken fromhttps://journals.plos.org/plosone/article?id=10.1371/journal.pone.0089116) :
<image001.png>Specifically, for the AlphafoldMissense data, such a plot would be more informative then the default histogram that is displayed when fetching the scores when looking for functional hotspots in your POI. Many thanks, MAtthias
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/