Re: [PyMOL] CONECT table
Thanks, works beautifully! Just FYI, it's not my structure, I was tasked with making a few pretty pictures, that's all :) Markus From: Engin Özkan [mailto:eoz...@uchicago.edu] Sent: Tuesday, October 07, 2014 7:35 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] CONECT table fetch hide everything show cartoon, all select NlinkedGlyco, resn NAG+BMA+MAN+FUC or byres (polymer within 2.0 of resn NAG+BMA+MAN+FUC) show sticks, NlinkedGlyco hide sticks, name C+CO+N This should do. Also, are you sure about NDG? If you are talking about N-linked glycosylation, as far as I know, there are no NDG (alpha monomer of N-actyl-D-glucosamine) in glycoproteins. NDG in N-linked sugars is usually an incorrectly modeled NAG (beta-N-acetyl-D-glucosamine), and the PDB is replete with this mistake (about a third of N-linked sugars are incorrectly named/modeled according to a paper by Thomas Lütteke). If this is your structure, I suggest you correct it. If you have to have NDG (because of an incorrect existing file from PDB), then add NDG to the two places I have common monomer names for sugars. Also, add galactose and sialic acid to that list; I don't remember their three-letter codes of the top of my head. Engin On 10/7/14 2:43 PM, Markus Heller wrote: D'uh. Thanks for pointing this out. Follow-up question: I want to show my glycosylated protein as cartoon, with the glycosides *and* the side chains they're attached to shown in sticks. How do I do that? I show the protein as cartoon: Load foo.pdb Hide lines As cartoon Then I select the glycosides Select gluco, resn NDG Show sticks, gluco This only shows me the glycoside, but NOT the side chain it's attached to. I tried Select gluco, bound_to resn NDG Show sticks, gluco But that doesn't work, shows no side chains. Any help much appreciated! Thanks and Cheers Markus -Original Message- From: David Hall [mailto:li...@cowsandmilk.net] Sent: Monday, October 06, 2014 4:40 PM To: Markus Heller Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] CONECT table http://www.pymolwiki.org/index.php/Connect_mode -David On Oct 6, 2014, at 6:35 PM, Markus Heller <mailto:mhel...@cdrd.ca> wrote: Hello, How can I get PYMOL to use the CONECT table from a PDB file? My protein is glycosylated, and I'd like to properly and automatically display the glycosides including their linkage to the protein. Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca<mailto:mhel...@cdrd.ca> | www.cdrd.ca<http://www.cdrd.ca> Follow us: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- Slashdot TV. Videos for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg. clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Engin Özkan, Ph.D. Assistant Professor Dept of Biochemistry and Molecular Biology University of Chicago Phone: (773) 834-5498 http://ozkan.uchicago.edu -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/os
Re: [PyMOL] CONECT table
Thanks for the info about the Pymol wiki page on Selection algebra. I looked at it before, but I must have never gotten the proper syntax ☹ From: Andreas Warnecke [mailto:4ndreas.warne...@gmail.com] Sent: Tuesday, October 07, 2014 4:26 PM To: Markus Heller Cc: David Hall; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] CONECT table Hi, It appears that the following: Select gluco, bound_to resn NDG Show sticks, gluco does not work. I'm not sure if the glycosylation is handled as a separate residue, but you could try: select glucoasp, byres (neighbor (resn NDG)) show sticks, glucoasp FYI: There are pages on selection algebra on the Pymol wiki that may give more inspiration. Hope this gets you started, /Andreas On Oct 7, 2014 10:02 PM, "Markus Heller" mailto:mhel...@cdrd.ca>> wrote: D'uh. Thanks for pointing this out. Follow-up question: I want to show my glycosylated protein as cartoon, with the glycosides *and* the side chains they're attached to shown in sticks. How do I do that? I show the protein as cartoon: Load foo.pdb Hide lines As cartoon Then I select the glycosides Select gluco, resn NDG Show sticks, gluco This only shows me the glycoside, but NOT the side chain it's attached to. I tried Select gluco, bound_to resn NDG Show sticks, gluco But that doesn't work, shows no side chains. Any help much appreciated! Thanks and Cheers Markus -Original Message- From: David Hall [mailto:li...@cowsandmilk.net<mailto:li...@cowsandmilk.net>] Sent: Monday, October 06, 2014 4:40 PM To: Markus Heller Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net> Subject: Re: [PyMOL] CONECT table http://www.pymolwiki.org/index.php/Connect_mode -David > On Oct 6, 2014, at 6:35 PM, Markus Heller > mailto:mhel...@cdrd.ca>> wrote: > > Hello, > > How can I get PYMOL to use the CONECT table from a PDB file? My protein is > glycosylated, and I'd like to properly and automatically display the > glycosides including their linkage to the protein. > > Thanks and Cheers > Markus > > -- > Markus Heller, Ph.D. > NMR Scientist > CDRD - The Centre for Drug Research and Development > 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: > (604) 827-1147 > Direct: (604) 827-1122 | F: (604) > 827-1299 | E: > mhel...@cdrd.ca<mailto:mhel...@cdrd.ca> | > www.cdrd.ca<http://www.cdrd.ca> > > > > > > > Follow us: > > This email and any files transmitted with it are confidential and intended > solely for the addressee. If you are not the named addressee you should not > disseminate, distribute, copy, or alter this email. > > > > > -- > Slashdot TV. Videos for Nerds. Stuff that Matters. > http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg. > clktrk ___ > PyMOL-users mailing list > (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: > http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] CONECT table
fetch / hide everything show cartoon, all select NlinkedGlyco, resn NAG+BMA+MAN+FUC or byres (polymer within 2.0 of resn NAG+BMA+MAN+FUC) show sticks, NlinkedGlyco hide sticks, name C+CO+N This should do. Also, are you sure about NDG? If you are talking about N-linked glycosylation, as far as I know, there are no NDG (alpha monomer of N-actyl-D-glucosamine) in glycoproteins. NDG in N-linked sugars is usually an incorrectly modeled NAG (beta-N-acetyl-D-glucosamine), and the PDB is replete with this mistake (about a third of N-linked sugars are incorrectly named/modeled according to a paper by Thomas Lütteke). If this is your structure, I suggest you correct it. If you have to have NDG (because of an incorrect existing file from PDB), then add NDG to the two places I have common monomer names for sugars. Also, add galactose and sialic acid to that list; I don't remember their three-letter codes of the top of my head. Engin On 10/7/14 2:43 PM, Markus Heller wrote: D'uh. Thanks for pointing this out. Follow-up question: I want to show my glycosylated protein as cartoon, with the glycosides *and* the side chains they're attached to shown in sticks. How do I do that? I show the protein as cartoon: Load foo.pdb Hide lines As cartoon Then I select the glycosides Select gluco, resn NDG Show sticks, gluco This only shows me the glycoside, but NOT the side chain it's attached to. I tried Select gluco, bound_to resn NDG Show sticks, gluco But that doesn't work, shows no side chains. Any help much appreciated! Thanks and Cheers Markus -Original Message- From: David Hall [mailto:li...@cowsandmilk.net] Sent: Monday, October 06, 2014 4:40 PM To: Markus Heller Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] CONECT table http://www.pymolwiki.org/index.php/Connect_mode -David On Oct 6, 2014, at 6:35 PM, Markus Heller wrote: Hello, How can I get PYMOL to use the CONECT table from a PDB file? My protein is glycosylated, and I'd like to properly and automatically display the glycosides including their linkage to the protein. Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | www.cdrd.ca Follow us: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- Slashdot TV. Videos for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg. clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Engin Özkan, Ph.D. Assistant Professor Dept of Biochemistry and Molecular Biology University of Chicago Phone: (773) 834-5498 http://ozkan.uchicago.edu -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] CONECT table
Oh, and it should be glucoasn, of course. :-P On Oct 8, 2014 1:26 AM, "Andreas Warnecke" <4ndreas.warne...@gmail.com> wrote: > Hi, > > It appears that the following: > Select gluco, bound_to resn NDG > Show sticks, gluco > > does not work. I'm not sure if the glycosylation is handled as a separate > residue, but you could try: > select glucoasp, byres (neighbor (resn NDG)) > show sticks, glucoasp > > FYI: There are pages on selection algebra on the Pymol wiki that may give > more inspiration. > > Hope this gets you started, > > /Andreas > On Oct 7, 2014 10:02 PM, "Markus Heller" wrote: > >> D'uh. Thanks for pointing this out. >> >> Follow-up question: I want to show my glycosylated protein as cartoon, >> with the glycosides *and* the side chains they're attached to shown in >> sticks. How do I do that? >> >> I show the protein as cartoon: >> >> Load foo.pdb >> Hide lines >> As cartoon >> >> Then I select the glycosides >> >> Select gluco, resn NDG >> Show sticks, gluco >> >> This only shows me the glycoside, but NOT the side chain it's attached to. >> >> I tried >> >> Select gluco, bound_to resn NDG >> Show sticks, gluco >> >> But that doesn't work, shows no side chains. >> >> Any help much appreciated! >> >> Thanks and Cheers >> Markus >> >> -Original Message- >> From: David Hall [mailto:li...@cowsandmilk.net] >> Sent: Monday, October 06, 2014 4:40 PM >> To: Markus Heller >> Cc: pymol-users@lists.sourceforge.net >> Subject: Re: [PyMOL] CONECT table >> >> http://www.pymolwiki.org/index.php/Connect_mode >> >> -David >> >> > On Oct 6, 2014, at 6:35 PM, Markus Heller wrote: >> > >> > Hello, >> > >> > How can I get PYMOL to use the CONECT table from a PDB file? My >> protein is glycosylated, and I'd like to properly and automatically display >> the glycosides including their linkage to the protein. >> > >> > Thanks and Cheers >> > Markus >> > >> > -- >> > Markus Heller, Ph.D. >> > NMR Scientist >> > CDRD - The Centre for Drug Research and Development >> > 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: >> > (604) 827-1147 >> > Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | >> > www.cdrd.ca >> > >> > >> > >> > >> > >> > >> > Follow us: >> > >> > This email and any files transmitted with it are confidential and >> intended solely for the addressee. If you are not the named addressee you >> should not disseminate, distribute, copy, or alter this email. >> > >> > >> > >> > >> > -- >> > Slashdot TV. Videos for Nerds. Stuff that Matters. >> > http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg. >> > clktrk ___ >> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> > Archives: >> > http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> >> >> -- >> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer >> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports >> Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper >> Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer >> >> http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] CONECT table
Hi, It appears that the following: Select gluco, bound_to resn NDG Show sticks, gluco does not work. I'm not sure if the glycosylation is handled as a separate residue, but you could try: select glucoasp, byres (neighbor (resn NDG)) show sticks, glucoasp FYI: There are pages on selection algebra on the Pymol wiki that may give more inspiration. Hope this gets you started, /Andreas On Oct 7, 2014 10:02 PM, "Markus Heller" wrote: > D'uh. Thanks for pointing this out. > > Follow-up question: I want to show my glycosylated protein as cartoon, > with the glycosides *and* the side chains they're attached to shown in > sticks. How do I do that? > > I show the protein as cartoon: > > Load foo.pdb > Hide lines > As cartoon > > Then I select the glycosides > > Select gluco, resn NDG > Show sticks, gluco > > This only shows me the glycoside, but NOT the side chain it's attached to. > > I tried > > Select gluco, bound_to resn NDG > Show sticks, gluco > > But that doesn't work, shows no side chains. > > Any help much appreciated! > > Thanks and Cheers > Markus > > -Original Message- > From: David Hall [mailto:li...@cowsandmilk.net] > Sent: Monday, October 06, 2014 4:40 PM > To: Markus Heller > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] CONECT table > > http://www.pymolwiki.org/index.php/Connect_mode > > -David > > > On Oct 6, 2014, at 6:35 PM, Markus Heller wrote: > > > > Hello, > > > > How can I get PYMOL to use the CONECT table from a PDB file? My protein > is glycosylated, and I'd like to properly and automatically display the > glycosides including their linkage to the protein. > > > > Thanks and Cheers > > Markus > > > > -- > > Markus Heller, Ph.D. > > NMR Scientist > > CDRD - The Centre for Drug Research and Development > > 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: > > (604) 827-1147 > > Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | > > www.cdrd.ca > > > > > > > > > > > > > > Follow us: > > > > This email and any files transmitted with it are confidential and > intended solely for the addressee. If you are not the named addressee you > should not disseminate, distribute, copy, or alter this email. > > > > > > > > > > -- > > Slashdot TV. Videos for Nerds. Stuff that Matters. > > http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg. > > clktrk ___ > > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: > > http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > -- > Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer > Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports > Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper > Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer > > http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] CONECT table
D'uh. Thanks for pointing this out. Follow-up question: I want to show my glycosylated protein as cartoon, with the glycosides *and* the side chains they're attached to shown in sticks. How do I do that? I show the protein as cartoon: Load foo.pdb Hide lines As cartoon Then I select the glycosides Select gluco, resn NDG Show sticks, gluco This only shows me the glycoside, but NOT the side chain it's attached to. I tried Select gluco, bound_to resn NDG Show sticks, gluco But that doesn't work, shows no side chains. Any help much appreciated! Thanks and Cheers Markus -Original Message- From: David Hall [mailto:li...@cowsandmilk.net] Sent: Monday, October 06, 2014 4:40 PM To: Markus Heller Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] CONECT table http://www.pymolwiki.org/index.php/Connect_mode -David > On Oct 6, 2014, at 6:35 PM, Markus Heller wrote: > > Hello, > > How can I get PYMOL to use the CONECT table from a PDB file? My protein is > glycosylated, and I'd like to properly and automatically display the > glycosides including their linkage to the protein. > > Thanks and Cheers > Markus > > -- > Markus Heller, Ph.D. > NMR Scientist > CDRD - The Centre for Drug Research and Development > 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: > (604) 827-1147 > Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | > www.cdrd.ca > > > > > > > Follow us: > > This email and any files transmitted with it are confidential and intended > solely for the addressee. If you are not the named addressee you should not > disseminate, distribute, copy, or alter this email. > > > > > -- > Slashdot TV. Videos for Nerds. Stuff that Matters. > http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg. > clktrk ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: > http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] CONECT table
http://www.pymolwiki.org/index.php/Connect_mode -David > On Oct 6, 2014, at 6:35 PM, Markus Heller wrote: > > Hello, > > How can I get PYMOL to use the CONECT table from a PDB file? My protein is > glycosylated, and I'd like to properly and automatically display the > glycosides including their linkage to the protein. > > Thanks and Cheers > Markus > > -- > Markus Heller, Ph.D. > NMR Scientist > CDRD - The Centre for Drug Research and Development > 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) > 827-1147 > Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | www.cdrd.ca > > > > > > > Follow us: > > This email and any files transmitted with it are confidential and intended > solely for the addressee. If you are not the named addressee you should not > disseminate, distribute, copy, or alter this email. > > > > > -- > Slashdot TV. Videos for Nerds. Stuff that Matters. > http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg.clktrk > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Slashdot TV. Videos for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] CONECT table
Hello, How can I get PYMOL to use the CONECT table from a PDB file? My protein is glycosylated, and I'd like to properly and automatically display the glycosides including their linkage to the protein. Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | www.cdrd.ca Follow us: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- Slashdot TV. Videos for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
