You got error in column positioning in PDB file - I added two whitespaces after ATOM mark. It probably couldn't parse the PDB file properly as the PDB file is column-specific format. It works now. Chk attached file in PyMOL. Kamil
wt., 6 lip 2021 o 23:13 Neena Susan Eappen <neenasusan...@gmail.com> napisał(a): > 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 >>> >> _______________________________________________ > 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
opt21_kamil.pdb
Description: Binary data
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