Re: [PyMOL] incomplete secondary structure
If you need a convenient method for C-alpha only secondary structure assignment, I can recommend SST: https://pymolwiki.org/index.php/Sst Cheers, Thomas > On Apr 16, 2020, at 2:50 PM, honeg...@bioc.uzh.ch wrote: > > 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" > To: pymol-users > 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 > *** > ___ > 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 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ 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
Re: [PyMOL] incomplete secondary structure
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 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>" > 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>" > 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" <mailto:h.adam.steinb...@gmail.com>> > To: pymol-users <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 > *** > ___ 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
[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, 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" To: pymol-users 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 *** ___ 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
[PyMOL] incomplete secondary structure
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___ 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
