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=> _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
