Hi Neena, It's stored everything as a single object. Check the display -> sequence and you'll see what I mean. None of your residues have a number. I assume Pymol needs discrete residues to display a cartoon.
See an example line-- Yours: HETATM 1 N 0 -1.172 4.898 0.414 N Example: ATOM 1 O5' U 2 1 197.678 159.150 189.116 1.00 35.29 O It looks like it is missing chain ID and also residue number. You could manually fix the PDB. Have a look at some examples and work out what columns to keep/change. hope that helps, Zuben ________________________________ From: Neena Susan Eappen <neenasusan...@gmail.com> Sent: Saturday, July 3, 2021 9:26 AM To: pymol-users <pymol-users@lists.sourceforge.net> Subject: [EXTERNAL] [PyMOL] No cartoon view for custom PDB file Hello PyMOL users, I performed a geometry optimization of a peptide on gaussview and then saved the output log file as a PDB. However, when I open this PDB file (attached hereby) in Pymol, I cannot enable the cartoon view of the secondary structure; I can only enable the line and stick representation. Any insight on what might be going wrong? Many thanks, Neena
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