Hello: I would like to make one figure consisting of two inhibitors from two different files. Is there a way that I can move inhibitor from one file w.r.t. the inhibitor from the second file? Thanks in advance, Madhavi
-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of [email protected] Sent: Wednesday, November 29, 2006 2:41 PM To: [email protected] Subject: PyMOL-users Digest, Vol 6, Issue 24 Send PyMOL-users mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/pymol-users or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of PyMOL-users digest..." Today's Topics: 1. Re: morphing between complexes (Nat Echols) 2. electrostatic potential structure (shivesh kumar) 3. Re: electrostatic potential structure (Martin H?fling) 4. Re: APBS and Pymol (Andreas Henschel) ---------------------------------------------------------------------- Message: 1 Date: Tue, 28 Nov 2006 14:04:59 -0800 (PST) From: Nat Echols <[email protected]> Subject: Re: [PyMOL] morphing between complexes To: pymol <[email protected]> Message-ID: <[email protected]> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > unfortunately I've already tried that server and I've seen that also in > that case, the ligand is stripped out.I obtain movies with only the > protein movements. I don't know if i have problems with my pdbs: > I have 245 residues + 1 ligand (246). it has the ATOM and not the HETATM > indication, could be this a problem? The server itself doesn't deal with heteroatoms, mostly because it makes dealing with the PDB even more of a nightmare than usual. The underlying CNS input file will handle any ligand you want as long as you have the correct topology and parameter files (e.g. from Gerard Kleywegt's HIC-UP server). I don't know of any program that will morph between *different* ligands, though. You can cheat by using a dummy ligand that has the conserved core, and adding in the rest manually once you have the interpolation. For instance, to show ATP hydrolysis, you use ADP in both PDB files, and later re-insert the original ATP in place of the ADP in the first frame(s). PyMOL makes this very easy. -Nat ------------------------------ Message: 2 Date: Wed, 29 Nov 2006 06:31:25 -0800 (PST) From: shivesh kumar <[email protected]> Subject: [PyMOL] electrostatic potential structure To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset="iso-8859-1" Dear all, How can I get the electrostatic potential structure of my protein molecule.Thanx in advance. S shivesh --------------------------------- Want to start your own business? Learn how on Yahoo! Small Business. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://sourceforge.net/mailarchive/forum.php?forum=pymol-users/attachmen ts/20061129/9e9aecab/attachment.html ------------------------------ Message: 3 Date: Wed, 29 Nov 2006 15:58:09 +0100 From: Martin H?fling <[email protected]> Subject: Re: [PyMOL] electrostatic potential structure To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset="iso-8859-1" Am Mittwoch, 29. November 2006 15:31 schrieb shivesh kumar: > Dear all, > How can I get the electrostatic potential structure of my protein > molecule.Thanx in advance. S what do you mean by "electrostatic potential structure"? The potential can be calculated with apbs (by hand or via plugin). This produces a map file which when loaded can be visualized as fieldlines or as equipotential surfaces. I think coloring of the ses of a protein is also possible. Cheers Martin ------------------------------ Message: 4 Date: Wed, 29 Nov 2006 20:40:31 +0100 From: Andreas Henschel <[email protected]> Subject: Re: [PyMOL] APBS and Pymol To: Anastassis Perrakis <[email protected]> Cc: [email protected], [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset="iso-8859-1" Hi Anastassis, I got the same error with a few pdb files. The problem is the following. The B-factor in the pymol-generated pdb file is somtimes set to values larger than 100 (119.63 in your case) thus occupying all its columns of the lovely PDB-format and not leaving any space to the preceding occupancy column (1.00 in your case). The script psize.py however parses these lines by splitting on white-spaces and crashes when converting the merged field ... The remedy is to modify psize.py like this: around line 108, replace words = string.split(subline) with words = line[30:38], line[38:46], line[46:54], line[54:60], line[60:66], line[72:76], line[76:78] ## PDB-format is fixed-space! Hope that works for you, in any case attached is my debugged psize.py file. Another error occurs when calculating the electrostatics of pdb 1F88, a transmembrane protein. The same thing happens on the pdb2pqr Server (http://nbcr.net/pdb2pqr): 'NoneType' object has no attribute 'getCoords' looks a bit like strange atom name problem, I get the script working by inserting: if not nextatom: return 0 in line 608, however I am not 100% sure whether its still sound... Cheers, Andreas Peter Adrian Meyer wrote: >Hi, > > > >>parseInput >> self.parseLines(file.readlines()) >> File "/usr/local/apbs-0.4.0/tools/manip/psize.py", line 116, in >>parseLines >> self.q = self.q + float(words[3]) >>ValueError: invalid literal for float(): 1.00119.63 >> >> >>Any clues ? >> >> > >It looks like it's reading from a pdb file when it's expecting a pqr file, >and that the split statement didn't produce the expected input due to the >B factor in the pdb file being too large. >Possibly you have to generate a pqr file before setting the grid (I'm not >farmilar enough with the apbs-pymol plugin to remember offhand). > >Good luck, > >Pete > > >Pete Meyer >Fu Lab >BMCB grad student >Cornell University > > > > > >----------------------------------------------------------------------- -- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys - and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVD EV >_______________________________________________ >PyMOL-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/pymol-users > > -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: [email protected] -------------- next part -------------- A non-text attachment was scrubbed... Name: psize.py Type: application/x-python Size: 19968 bytes Desc: not available Url : http://sourceforge.net/mailarchive/forum.php?forum=pymol-users/attachmen ts/20061129/79212d96/attachment.bin ------------------------------ ------------------------------------------------------------------------ - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDE V ------------------------------ _______________________________________________ PyMOL-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/pymol-users End of PyMOL-users Digest, Vol 6, Issue 24 ******************************************
