Re: [PyMOL] [EXTERNAL] No cartoon view for custom PDB file

[Brown, Z. <zb...@cu...>]

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:
HETATM    1  N           0      -1.172   4.898   0.414                       N

Example:
ATOM      1  O5' U   2   1     197.678 159.150 189.116  1.00 35.29           O

It looks like it is missing chain ID and also residue number.
You could manually fix the PDB.  Have a look at some examples and work out what columns to keep/change.

hope that helps,
Zuben


________________________________
From: Neena Susan Eappen <nee...@gm...>
Sent: Saturday, July 3, 2021 9:26 AM
To: pymol-users <pym...@li...>
Subject: [EXTERNAL] [PyMOL] No cartoon view for custom PDB file

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