From: Bob H. <ha...@st...> - 2006-10-30 14:36:01
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Does anyone know of a website that lets you indicate any PDB file and then 1) show the Ramachandran plot and, preferably, 2) allow clicking on the plot to see which residues are involved? Bob |
From: Karl O. <obe...@me...> - 2007-08-29 18:10:48
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Hi All, The Ramachandran command gives a nice plot with axes with the first button press, but with subsequent presses the axes are not displayed. If the structure is reset, they are displayed with the first click after the reset. Karl Karl M. Oberholser, Ph.D. Phone: Professor of Chemistry Voice: 717-766-0512 Chemistry & Biochemistry Dept. Fax: 717-691-6046 Messiah College e-mail: obe...@me... P.O. Box 3049 One College Avenue Grantham, Pa 17027 |
From: Bob H. <ha...@st...> - 2007-08-29 22:30:19
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Karl Oberholser wrote: > Hi All, > > The Ramachandran command gives a nice plot with axes with the first > button press, but with subsequent presses the axes are not displayed. > If the structure is reset, they are displayed with the first click > after the reset. I will check that out. It hasn't been tested much at all. Bob > > Karl > > > Karl M. Oberholser, Ph.D. Phone: > Professor of Chemistry Voice: 717-766-0512 > Chemistry & Biochemistry Dept. Fax: 717-691-6046 > Messiah College e-mail: obe...@me... > P.O. Box 3049 > One College Avenue > Grantham, Pa 17027 > > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Splunk Inc. >Still grepping through log files to find problems? Stop. >Now Search log events and configuration files using AJAX and a browser. >Download your FREE copy of Splunk now >> http://get.splunk.com/ > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Rolf H. <rh...@fl...> - 2006-10-30 14:51:57
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Bob Hanson wrote: >Does anyone know of a website that lets you indicate any PDB file and then > >1) show the Ramachandran plot > >and, preferably, > >2) allow clicking on the plot to see which residues are involved? > > The 'AstexViewer' from MSD at the EBI. It is a java applet. In the 'Graphs' menu there is a 'Rama' entry and you get an interactive window where you can click on a spot in the ramachandran plot and the corresponding residue is shown and in the structure viewer it is centered and zoomed in on it. It should work with any PDB code, for example: http://www.ebi.ac.uk/msd-srv/apps/Viewer/ViewerServlet?id=1deh Regards, Rolf |
From: Bob H. <ha...@st...> - 2006-10-30 20:24:05
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great. Yes, that was what I was after. I just added psi and phi to "getproperty polymerInfo" so in principle, if one wanted to do this sort of thing with Jmol, one could. We need to think about revising how Jmol calculates helix structure. I think it is over-assigning helix structure based on the simple algorithm: return (phi >= -160) && (phi <= 0) && (psi >= -100) && (psi <= 45); where psi is for the residue in question, and phi is for the next residue in line in the direction of the C terminus. Q: What is the origin of this calculation (Tim?) What this is doing is assigning as helix many residues that Rasmol and Astex and whatever is used in CIF generation call turns. It seems overly broad. What seems to be happening (for example, in 2hhd) is that helixes with large swings in psi are being counted as single helixes. You might not notice this when using Cartoons, but with Rockets, it is quite obvious that something is wrong, because rockets have to go from one end of a helix to the other directly. This is what Angel noticed. My preliminary fix is to temporarily assign two sorts of helix: ones for which (phi < 0 and psi < 25) and one for which that is not true. This forces a kink in a standard helix to close that helix and start another. This temporary assignment is for the algorithm only, not anything else -- in any other terms, a helix is a helix (so far). Rolf Huehne wrote: >Bob Hanson wrote: > > >>Does anyone know of a website that lets you indicate any PDB file and then >> >>1) show the Ramachandran plot >> >>and, preferably, >> >>2) allow clicking on the plot to see which residues are involved? >> >> >> >> >The 'AstexViewer' from MSD at the EBI. It is a java applet. >In the 'Graphs' menu there is a 'Rama' entry and you get an interactive >window where you can click on a spot in the ramachandran plot and the >corresponding residue is shown and in the structure viewer it is >centered and zoomed in on it. > >It should work with any PDB code, for example: > >http://www.ebi.ac.uk/msd-srv/apps/Viewer/ViewerServlet?id=1deh > >Regards, >Rolf > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
From: Rajarshi G. <rg...@in...> - 2006-10-30 14:57:06
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On Mon, 2006-10-30 at 08:32 -0600, Bob Hanson wrote: > Does anyone know of a website that lets you indicate any PDB file and then > > 1) show the Ramachandran plot > > and, preferably, > > 2) allow clicking on the plot to see which residues are involved? The webmol view on the PDB website ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- "whois awk?", sed Grep. |