Thank you Blaine and Zuben for your insights and troubleshooting the problem! I understood the formatting issue with the current PDB file, will do the necessary changes.
Regards, Neena On Sat, 3 Jul 2021 at 09:59, Mooers, Blaine H.M. (HSC) < blaine-moo...@ouhsc.edu> wrote: > 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 >
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