gt;
> From: Kamil Steczkiewicz [kamil.steczkiew...@gmail.com]
> Sent: Wednesday, July 07, 2021 2:29 AM
> To: Neena Susan Eappen
> Cc: Mooers, Blaine H.M. (HSC); zb2...@cumc.columbia.edu; pymol-users
> Subject: Re: [PyMOL] [EXTERNAL] No cartoo
Subject: Re: [PyMOL] [EXTERNAL] No cartoon view for custom PDB file
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
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
napisał(a):
> Hello
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
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
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
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
