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[PyMOL] moving around the files
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From: Nalam, M. <Mad...@um...> - 2006-11-30 19:20:05
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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: pym...@li... [mailto:pym...@li...] On Behalf Of pym...@li... Sent: Wednesday, November 29, 2006 2:41 PM To: pym...@li... Subject: PyMOL-users Digest, Vol 6, Issue 24 Send PyMOL-users mailing list submissions to pym...@li... 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 pym...@li... You can reach the person managing the list at pym...@li... 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 <ec...@uc...> Subject: Re: [PyMOL] morphing between complexes To: pymol <pym...@li...> Message-ID: <Pin...@le...> Content-Type: TEXT/PLAIN; charset=3DUS-ASCII; format=3Dflowed > 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=20 CNS input file will handle any ligand you want as long as you have the=20 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=20 core, and adding in the rest manually once you have the interpolation.=20 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=20 frame(s). PyMOL makes this very easy. -Nat ------------------------------ Message: 2 Date: Wed, 29 Nov 2006 06:31:25 -0800 (PST) From: shivesh kumar <shi...@ya...> Subject: [PyMOL] electrostatic potential structure To: pym...@li... Message-ID: <200...@we...> Content-Type: text/plain; charset=3D"iso-8859-1" Dear all, How can I get the electrostatic potential structure of my protein molecule.Thanx in advance. S shivesh =20 --------------------------------- 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=3Dpymol-users/attachme= n ts/20061129/9e9aecab/attachment.html=20 ------------------------------ Message: 3 Date: Wed, 29 Nov 2006 15:58:09 +0100 From: Martin H?fling <mar...@gm...> Subject: Re: [PyMOL] electrostatic potential structure To: pym...@li... Message-ID: <200...@gm...> Content-Type: text/plain; charset=3D"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=20 calculated with apbs (by hand or via plugin). This produces a map file which=20 when loaded can be visualized as fieldlines or as equipotential surfaces. I=20 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 <ah...@bi...> Subject: Re: [PyMOL] APBS and Pymol To: Anastassis Perrakis <a.p...@nk...> Cc: ba...@bi..., pym...@li... Message-ID: <456...@bi...> Content-Type: text/plain; charset=3D"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=20 file is somtimes set to values larger than 100 (119.63 in your case)=20 thus occupying all its columns of the lovely PDB-format and not leaving=20 any space to the preceding occupancy column (1.00 in your case). The=20 script psize.py however parses these lines by splitting on white-spaces=20 and crashes when converting the merged field ... The remedy is to modify psize.py like this: around line 108, replace words =3D string.split(subline) with words =3D 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=20 transmembrane protein. The same thing happens on the pdb2pqr Server (http://nbcr.net/pdb2pqr): 'NoneType' object has=20 no attribute 'getCoords' looks a bit like strange atom name problem, I get the script working by=20 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, > > =20 > >>parseInput >> self.parseLines(file.readlines()) >> File "/usr/local/apbs-0.4.0/tools/manip/psize.py", line 116, in >>parseLines >> self.q =3D self.q + float(words[3]) >>ValueError: invalid literal for float(): 1.00119.63 >> >> >>Any clues ? >> =20 >> > >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=3Djoin.php&p=3Dsourceforge&CID=3D= DEVD EV >_______________________________________________ >PyMOL-users mailing list >PyM...@li... >https://lists.sourceforge.net/lists/listinfo/pymol-users > =20 > --=20 Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: ah...@bi... -------------- 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=3Dpymol-users/attachme= n ts/20061129/79212d96/attachment.bin=20 ------------------------------ ------------------------------------------------------------------------ - 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=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDE V ------------------------------ _______________________________________________ PyMOL-users mailing list PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users End of PyMOL-users Digest, Vol 6, Issue 24 ****************************************** |