Re: [PyMOL] H-bond drawing?
Hi Claire, If it's only a few H-bonds, probably the quickest is the following: Select the first atom with ctrl-shift left-mouse button Select the second atom with crtl-shift right-mouse button then issue the command 'distance ' That should draw you a nice dashed bond. Hope it helps a bit, maybe Warren would have better ideas, but good luck! Cheers, Tsjerk Claire Sharpe wrote: Hi there, Sorry I'm going to ask probably a very basic question but could anyone tell me how to create H-bonds in pymol? I used SPDB viewer to model the interface between two dimers in a tetrameric molecule. I now need to create some good pictures of this for my thesis as SPDB isn't really good enough. I'd like to represent H-bonds (not bond distances just bonds) e.g between ThrOG1 of subunit A and Asp184OD1 of subunit D. I'm presuming that pymol can do this-if so would really appreciate it if anyone could tell me how to enter in the command line as I'm afraid I'm not used to it and thesis deadline looms on thurs! Many thanks, Claire *** Claire Sharpe Department of Biochemistry University of Cambridge 80, Tennis Court Road Cambridge. CB2 1GA U.K Tel: 01223 766045 Fax: 01223 766002 email: ce...@mole.bio.cam.ac.uk --- This SF.Net email sponsored by: ApacheCon 2003, 16-19 November in Las Vegas. Learn firsthand the latest developments in Apache, PHP, Perl, XML, Java, MySQL, WebDAV, and more! http://www.apachecon.com/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- ~ -- :) -- :) Tsjerk A. Wassenaar, M.Sc. -- :) Molecular Dynamics Group -- :) Dept. of Biophysical Chemistry -- :) University of Groningen -- :) Nijenborgh 4 -- :) 9747 AG Groningen -- :) The Netherlands -- :) ~ -- :) -- :) Hi! I'm a .signature virus! -- :) Copy me into your ~/.signature to help me spread! -- :) ~
RE: [PyMOL] H-bond drawing?
Hi Claire, All you need to do is: 1) Create selections for the two atoms you want to H-bond. There are several different ways to do this in PyMOL (see the manual for details), but for example, to bond chain A, Thr 15 OG1 chain D, Asp 184 OD1 you would do select donor, A/15/OG1 select acceptor, D/184/OD1 2) Create a h-bond object between these selections. The easiest way is to use PyMOL's "distance" command which draws a dashed line between them. It also shows the distance as a label, but you can turn this off distance hbond, donor, acceptor hide labels, x 3) Play with the settings to get it to look how you want. Dashed lines sometimes look a bit odd when you ray-trace them - I find that set dash_length, 0.15 set dash_radius, 0.09 set dash_width, 3.00 looks good. You can put these commands in your .pymolrc to save typing them all the time. Hope that helps, Gareth On Sun, 2003-11-09 at 09:58, Claire Sharpe wrote: > Hi there, > > Sorry I'm going to ask probably a very basic question but could anyone > tell me how to create H-bonds in pymol? > > I used SPDB viewer to model the interface between two dimers in a > tetrameric molecule. I now need to create some good pictures of this for > my thesis as SPDB isn't really good enough. I'd like to represent H-bonds > (not bond distances just bonds) e.g between ThrOG1 of subunit A and > Asp184OD1 of subunit D. I'm presuming that pymol can do this-if so would > really appreciate it if anyone could tell me how to enter in the command > line as I'm afraid I'm not used to it and thesis deadline looms on thurs! > > Many thanks, > > Claire > *** > > Claire Sharpe > > Department of Biochemistry > University of Cambridge > 80, Tennis Court Road > Cambridge. CB2 1GA > U.K > > Tel: 01223 766045 > Fax: 01223 766002 > email: ce...@mole.bio.cam.ac.uk > > > > > > --- > This SF.Net email sponsored by: ApacheCon 2003, > 16-19 November in Las Vegas. Learn firsthand the latest > developments in Apache, PHP, Perl, XML, Java, MySQL, > WebDAV, and more! http://www.apachecon.com/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users -- Gareth Stockwell European Bioinformatics Institute
RE: [PyMOL] H-bond drawing?
Hi there, Sorry I'm going to ask probably a very basic question but could anyone tell me how to create H-bonds in pymol? I used SPDB viewer to model the interface between two dimers in a tetrameric molecule. I now need to create some good pictures of this for my thesis as SPDB isn't really good enough. I'd like to represent H-bonds (not bond distances just bonds) e.g between ThrOG1 of subunit A and Asp184OD1 of subunit D. I'm presuming that pymol can do this-if so would really appreciate it if anyone could tell me how to enter in the command line as I'm afraid I'm not used to it and thesis deadline looms on thurs! Many thanks, Claire *** Claire Sharpe Department of Biochemistry University of Cambridge 80, Tennis Court Road Cambridge. CB2 1GA U.K Tel: 01223 766045 Fax: 01223 766002 email: ce...@mole.bio.cam.ac.uk
