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

[Kamil S. <kam...@gm...>]

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 <nee...@gm...>
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 <nee...@gm...>
> 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) <
>> Bla...@ou...> 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
>>>
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