Summary of conclusions from seeing the data file:
(1) In Miao's PDB file, the atoms had the correct names for a peptide, but the entire circular peptide was a single HET residue named UNK, instead of a series of standard amino acid residues with separate residue names and numbers. Thus ChimeraX could not recognize it as a peptide.
(2) However, even for cyclic peptides that are in the correct format and are recognized as peptides (for example, 6ugc chain A), ChimeraX has a bug where it does not draw a closed loop for the cartoon. I think we have a ticket for this bug, although I failed to find it when I searched just now.
Chimera does not have this bug, and will draw a closed loop ribbon for 6ugc chain A.
Sorry about the difficulties, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 28, 2023, at 11:19 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Miao, I can't figure out the issue unless you also provide the example PDB file... a picture is not enough information. If OK to share this data with others, you can send it to chimerax-users, or alternatively just to me.
Without the file, I can only guess that maybe the atom and residue names are not the usual atom and residue names for peptides/proteins.
Thanks, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 28, 2023, at 11:06 AM, Zhang, Miao via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Sir/Madam I have a small peptide that I want to show as cartoon. But chemira does not recognize it as a protein. I cannot show it as cartoon. I can only show it as surface, sphere, or sticks. How can I show cartoon? Many thanks Miao <image001.png>