From: Michael B. <mb...@uv...> - 2003-11-07 23:30:46
|
Hi there, I'm switching to pymol from swiss pdb viewer because I simply needed better quality final images, but one of the coolest features of spdbv was the 'magic fit' where a single mouse click would superpose overall alignment of, say, the same protein from two different bacterial organisms (obviously high homology situation) opened in two different 'layers'. In pymol, it looks like the 'align' command is what I want (don't know if pymol uses the layers analogy), but I'm having difficulty understanding if I am to use parentheses and brackets as shown in the refman.pdf, and the use of this punctuation style doesnt seem to be defined in the pdf. USAGE align (source), (target) [,cutoff [,cycles [,gap [,extend \ [,skip [,object [,matrix [, quiet ]]]]]]]] (This style of outlining command formats is probably old hat to programmers, but that's not me.) So, is this the right command for superposition alignments in pymol, after loading pdb files x and y, for instance? Sorry for such a basic question; its getting late and I'm floundering :0) Thank you, --Michael |
From: Warren L. D. <wa...@de...> - 2003-11-08 00:58:31
|
Michael, Welcome to PyMOL! I don't think PyMOL is a replacement for SPDV -- the feature sets are distinct, and you should be able to use both together. Yes, I think "align" is what you want. After... load x.pdb load y.pdb This would do an all-matched-atoms alignment: align x, y And this would do a CA-only alignment: align x////ca, y////ca To see which atoms are aligned, add and object name: align x////ca, y////ca, object=alignment Cheers, Warren -- mailto:wa...@de... Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -----Original Message----- From: pym...@li... [mailto:pym...@li...] On Behalf Of Michael Bovee Sent: Friday, November 07, 2003 3:31 PM To: pym...@li... Subject: [PyMOL] homologous alignments? Hi there, I'm switching to pymol from swiss pdb viewer because I simply needed better quality final images, but one of the coolest features of spdbv was the 'magic fit' where a single mouse click would superpose overall alignment of, say, the same protein from two different bacterial organisms (obviously high homology situation) opened in two different 'layers'. In pymol, it looks like the 'align' command is what I want (don't know if pymol uses the layers analogy), but I'm having difficulty understanding if I am to use parentheses and brackets as shown in the refman.pdf, and the use of this punctuation style doesnt seem to be defined in the pdf. USAGE align (source), (target) [,cutoff [,cycles [,gap [,extend \ [,skip [,object [,matrix [, quiet ]]]]]]]] (This style of outlining command formats is probably old hat to programmers, but that's not me.) So, is this the right command for superposition alignments in pymol, after loading pdb files x and y, for instance? Sorry for such a basic question; its getting late and I'm floundering :0) Thank you, --Michael |
From: Claire S. <ce...@mo...> - 2003-11-09 09:58:28
|
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...@mo... |
From: Gareth S. <ga...@eb...> - 2003-11-10 08:53:40
|
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...@mo... > > > > > > ------------------------------------------------------- > 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 > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users -- Gareth Stockwell <ga...@eb...> European Bioinformatics Institute |
From: Tsjerk W. <t.a...@ch...> - 2003-11-10 09:02:13
|
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 <Return>' 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...@mo... > > > > > >------------------------------------------------------- >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 >PyM...@li... >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! -- :) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
From: <ca...@mr...> - 2004-01-19 15:47:52
|
Hello, I am unable to read the archive at the moment.... so can anyone tell me the command that allows colouring of the edge of helices and strands (usually grey). I think this was posted recently but I don't have it in any of my saved scripts. Many thanks, Camille Dr Camille Shammas Medical Research Council Laboratory of Molecular Biology Hills Road, Cambridge CB2 2QH, UK. Tel: +44 (0)1223 402407 Mobile: 07812035842 E-mail: ca...@mr... |
From: Warren L. D. <wa...@de...> - 2004-01-19 17:47:10
|
Camille, If I understand your question, you're looking for the setting which creates a discrete color transition at the edges of helices and strands, instead of blending. It is: set cartoon_discrete_colors, on For example color grey, name ca color yellow, ss s and name ca color red, ss h and name ca set cartoon_discrete_colors, on Cheers, Warren -- mailto:wa...@de... Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: pym...@li... [mailto:pymol-users- > ad...@li...] On Behalf Of ca...@mr... > Sent: Monday, January 19, 2004 7:37 AM > To: Warren L. DeLano > Cc: 'Michael Bovee'; pym...@li... > Subject: Re: [PyMOL] homologous alignments? > > Hello, > I am unable to read the archive at the moment.... so can anyone tell > me the command that allows colouring of the edge of helices and strands > (usually grey). I think this was posted recently but I don't have it in > any of my saved scripts. > > Many thanks, > Camille > > Dr Camille Shammas > Medical Research Council Laboratory of Molecular Biology Hills Road, > Cambridge CB2 2QH, UK. > Tel: +44 (0)1223 402407 > Mobile: 07812035842 > E-mail: ca...@mr... > > > > ------------------------------------------------------- > The SF.Net email is sponsored by EclipseCon 2004 > Premiere Conference on Open Tools Development and Integration See the > breadth of Eclipse activity. February 3-5 in Anaheim, CA. > http://www.eclipsecon.org/osdn > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |