When you look at the coordinate file for 3jav in a text editor, you'll see that for the parts of the structure which give you a "AssignSS-Warning: Ignoring incomplete residue" feedback, the coordinate file contains C-Alpha coordinates only, while in the parts which render the secondary structure properly, you have coordinates for all heavy atoms. The header contains secondary structure information only for those residues where full coordinates are available, and the dss command is unable to assign secondary structure from C-Alpha only.
If you really want to obtain a cartoon representation for the whole molecule, you either have to use a method to determine the secondary structure from C-alpha atoms only, and assign the secondary structure to the molecule using the "alter" command (laborious), or submit your coordinates to a server capable of modelling a full atom structure from the Alpha trace (e.g. SABBAC 1.3, https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::SABBAC, caution: you need to submit each chain separately, since the server cannot deal with multi-chain models. Annemarie Today's Topics: 1. incomplete secondary structure (h. adam steinberg) ---------------------------------------------------------------------- Message: 1 Date: Wed, 15 Apr 2020 10:51:07 -0500 From: "h. adam steinberg" <h.adam.steinb...@gmail.com> To: pymol-users <pymol-users@lists.sourceforge.net> Subject: [PyMOL] incomplete secondary structure Message-ID: <8b4fde28-444e-4f86-be2a-e2982eae4...@gmail.com> Content-Type: text/plain; charset="utf-8" Hi all, When I open 3jav the backbone shows many helices, but Pymol doesn?t draw them as helices when showing the cartoon. Clearly there is something that is not perfect with the deposited cyro structure. If I run the dss command, the cartoon structure isn?t fixed, and I get repeats of the following error for each residue from 1-2750 for each chain: AssignSS-Warning: Ignoring incomplete residue /3jav//D/2750 ? Does anyone know how I can fix the secondary structure without having to manually assign it to each helix? Thanks! Adam -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ ------------------------------ Subject: Digest Footer _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ------------------------------ End of PyMOL-users Digest, Vol 167, Issue 5 *******************************************
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