Thank you so much Kamil and Blaine for the insights, that worked very well!
On Wed, 7 Jul 2021 at 05:04, Mooers, Blaine H.M. (HSC) < blaine-moo...@ouhsc.edu> wrote: > Hi Neena, > > Adding to Kamil's explanation, the role of each column for a ATOM record > in the PDB file is explained here: > https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM. > > > The PDBeditor.jar program can help you retain the fixed file format of the > PDB file: http://www.bioinformatics.org/pdbeditor/wiki/. > > Best regards, > > Blaine > > ________________________________________ > 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 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 > > > wt., 6 lip 2021 o 23:13 Neena Susan Eappen <neenasusan...@gmail.com > <mailto: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 > <mailto: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<mailto: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< > https://urldefense.proofpoint.com/v2/url?u=https-3A__mooerslab.github.io_pymolsnips_-23editors&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=_0_SlrKbnune5f30F7yXXfCZeqLy4On9xiqmMCnp8i8&s=kNiqLqCiIujYjPxmB4ojZgo5FPlLYD2sh_pNAf8a9QI&e= > >. > > 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< > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=_0_SlrKbnune5f30F7yXXfCZeqLy4On9xiqmMCnp8i8&s=zOVDhVRXeYBhd3YRxmRvI82_GPmugMqg-4nXdTiwvLM&e= > > > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe< > https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=_0_SlrKbnune5f30F7yXXfCZeqLy4On9xiqmMCnp8i8&s=ASKJ73KuITt7Dqx6TGi5LziWphhpFKsW1cP7pRo1KYw&e= > > >
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