Hello PyMOL users, Please take a look at the two attached PDB files (opt 20 and opt 21); I formatted opt21.pdb file to match with that of opt20.pdb for PyMOL to recognize the former as a peptide. However, now I can neither see a line nor cartoon representation of the opt21 peptide anymore. *Any insights on what could be wrong in the opt21 PDB file?*
Many thanks, Neena On Sat, 3 Jul 2021 at 23:38, Neena Susan Eappen <neenasusan...@gmail.com> wrote: > 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 >> >
opt20.pdb
Description: Binary data
opt21.pdb
Description: Binary data
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