Wow! I am always amazed at the level of knowledge on this list. Thank you both.
> On Apr 16, 2020, at 8:32 AM, Ali Kusay <akus8...@uni.sydney.edu.au> wrote: > > Hi Adam, > > As Annemarie has mentioned you will need a way of generating the backbone for > the regions in the structure that have simply been resolved as Ca atoms. > Another way to do this is to simple model 3jav on itself using modeller, > modeller can make a reasonable guess as to where helices should be based on > where the Ca atoms current are. This is quite simple to do and you can > construct all chains at the same time, however, without validation I would > only recommend using it for visualisation purposes, I have attached an image > of what the protein looks like after modelling if you are interested in > taking this route. > > Cheers, > > Ali > > Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist > The University of Sydney School of Pharmacy | Faculty of Medicine and Health > 424, Brain and Mind Centre | The University of Sydney | NSW 2050 > > From: "honeg...@bioc.uzh.ch <mailto:honeg...@bioc.uzh.ch>" > <honeg...@bioc.uzh.ch <mailto:honeg...@bioc.uzh.ch>> > Date: Thursday, 16 April 2020 at 11:13 pm > To: "pymol-users@lists.sourceforge.net > <mailto:pymol-users@lists.sourceforge.net>" > <pymol-users@lists.sourceforge.net <mailto:pymol-users@lists.sourceforge.net>> > Subject: [PyMOL] incomplete secondary structure > > 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, > <https://protect-au.mimecast.com/s/1oetC0YKPvi46vD6uWIeGJ?domain=mobyle.rpbs.univ-paris-diderot.fr> > 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 > <mailto:h.adam.steinb...@gmail.com>> > To: pymol-users <pymol-users@lists.sourceforge.net > <mailto:pymol-users@lists.sourceforge.net>> > Subject: [PyMOL] incomplete secondary structure > Message-ID: <8b4fde28-444e-4f86-be2a-e2982eae4...@gmail.com > <mailto: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 <mailto:PyMOL-users@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/pymol-users > <https://protect-au.mimecast.com/s/0u1NC81V0PTQn3Znu1wlzv?domain=lists.sourceforge.net> > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > <https://protect-au.mimecast.com/s/5-CwC91WPRTxongoh3Aiqb?domain=sourceforge.net> > > ------------------------------ > > End of PyMOL-users Digest, Vol 167, Issue 5 > ******************************************* > <modelled_helicies.png>
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