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 representat
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 coor
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:
HETATM1 N 0 -1.172 4.898 0.414
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
