Dear Alessio, There are two possible reasons: (1) your input file (PDB or mmCIF) has helix and sheet information, but that information does not list these residues in sheet - OR - (2) your input does not have helix and sheet information, so ChimeraX tries to guess it -- this should be mentioned in the Log when you open the file Either way, however, how to fix it is the same. You can manually assign the secondary structure type as helix, strand, or coil. (A) One way is to use the "setattr" command to assign values of the residue attribute named "ss_type" as 1 (helix) or 2 (strand) instead of 0 (coil): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html> <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue> For example, to assign residues 10-15 of chain A as strand, command: setattr /A:10-15 r ss_type 2 Here is a previous post with more details about setting secondary structure with commands: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> (B) Another way if you prefer using the graphical interface is to select the residue (e.g. Ctrl-click on residue) so that it has a green outline, then open the Selection Inspector (green magnifying glass icon in toolbar across top, or menu: Actions... Inspect). In the Selection Inspector tool, change from Inspect: "Atoms" to Inspect: "Residues", then set Secondary structure type to "strand" 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 Sep 9, 2024, at 1:16 AM, Alessio Nocentini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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Il giorno lun 9 set 2024 alle ore 10:16 Alessio Nocentini <alessio.nocentini@unifi.it> ha scritto: Dear Elaine,
I would like to ask for your support again. I have a visual problem with this type of protein (see attached image). The coils in the red square should be b-sheets. I do not know why Chimera or ChimeraX show them as coils. Are there settings to change to show them correctly?
Thank you Best regards
A