Hi Neena, Thank you for attaching your PDB file. That was a good idea. It was very helpful for trouble-shooting.
Look inside yourPDB file with a text editor. Your pdbPDB file is incomplete in three ways: 1) The third column of atom types lacks CA (Calpha) atoms. PyMOL cannot recognize your coordinates as being from a protein. You can use PDBeditor.jar or any good text editor (not MS Word) to edit the atom records. If you need help selecting a text editor, check out https://mooerslab.github.io/pymolsnips/#editors. 2) Your PDB file lacks HELIX and SHEET records. PyMOL's cartoon function uses these in the default automatic mode. 3) Your PDB file lacks residue identifiers (resi) and residue names (resn). You might still be able to make a cartoon without them, but their absence will hinder making selections. Best regards, Blaine 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 _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
