Re: [PyMOL] embeding pymol in a web page
On Mon, Mar 29, 2004 at 11:37:22AM +0100, Jonathan Barber wrote: > On Thu, Mar 25, 2004 at 10:13:42AM +, Einat Sitbon wrote: > > > > Hello PyMolers, > > > > I'm wondering if there is a possibility to embed a pymol script in a web > > site. > > What I have in mind is something equivalent to the chime plug-in, using > > pymol. > > Any suggestions? > > One way I've tried to achieve this is to have a CGI on the webserver > that sends a Pymol script to the client. > > If the client's browser has Pymol set up to recognise Pymol scripts, > then it'll execute the script. This requires the CGI to set the MIME > type type and to set the filename of the script to have the correct > suffix (to make Explorer on Windows work properly). > > The downloaded script is then executed by Pymol, which can uses Python's > socket abilities to download PDB files and run Pymol commands on them. > > Et volia! A little convoluted, and by no means as elegent as having a > browser plugin, but it does allow you to use Pymol for visulation over > the web. > > I've got the code for this kicking around somewhere, if anyone is > interested then contact me and I'll look for it and stick it on the web. A few people have expressed interest in the code, so I've put it up at the following URL: http://www.compbio.dundee.ac.uk/~jon/pymol.cgi -- Jon
Re: [PyMOL] embeding pymol in a web page
On Mon, 29 Mar 2004, Nat Echols wrote:
> > The downloaded script is then executed by Pymol, which can uses Python's
> > socket abilities to download PDB files and run Pymol commands on them.
>
> H, I like this idea. Can PyMOL open files directly over the web? It
> would be nice to simply type
>
> PyMOL> load http://server/1cll.pdb, calmodulin
>
Kristian Rother's rTools (http://www.rubor.de/bioinf/pymol_rubor.html)
comes with a "pdb" command that's similar:
pdb (pdb-id) - get PDB structure (pdb-id) from the local disk,
or from the PDB server.
which does everything that I want, but it might be nice to have PyMOL
parse urls like that. Shouldn't be hard, especially with read_pdbstr.
Hmmn .. in fact, if you feel like playing around a bit, you can go into
cmd.py and change the definition of _load. At the top, right after it
says 'r = 1', add this:
#print "oname",oname,"finfo",finfo,"ftype",ftype
if ftype == loadable.pdb and finfo.startswith('http://'):
import urllib
from importing import read_pdbstr
print "requesting file",finfo
pdbstr = urllib.urlopen(finfo).read()
r = read_pdbstr(pdbstr,oname,state,finish,discrete)
And change the 'if' on the next line to an 'elif'. That will make this
work with simple urls. For example, you can type something like
load http://www.umich.edu/~mlerner/1rx1.pdb
or
load http://www.umich.edu/~mlerner/1rx1.pdb, nifty
and it'll work. More complicated urls seem to break PyMOL's parser. If
you uncomment the print statement in my little code snippet above, you can
see what goes wrong with, e.g. a url from the PDB like this
http://www.rcsb.org/pdb/cgi/explore.cgi?job=download;pdbId=1RX1;page=&opt=show&format=PDB&pre=1
but I haven't played around with the parser at all.
-michael
--
This isn't a democracy;|_ |Michael Lerner
it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
-Torrence, Bring It On| - against HTML email X | Biophysics
| / \ | mler...@umich
Re: [PyMOL] embeding pymol in a web page
> The downloaded script is then executed by Pymol, which can uses Python's > socket abilities to download PDB files and run Pymol commands on them. H, I like this idea. Can PyMOL open files directly over the web? It would be nice to simply type PyMOL> load http://server/1cll.pdb, calmodulin
Re: [PyMOL] embeding pymol in a web page
On Thu, Mar 25, 2004 at 10:13:42AM +, Einat Sitbon wrote: > > Hello PyMolers, > > I'm wondering if there is a possibility to embed a pymol script in a web > site. > What I have in mind is something equivalent to the chime plug-in, using > pymol. > Any suggestions? One way I've tried to achieve this is to have a CGI on the webserver that sends a Pymol script to the client. If the client's browser has Pymol set up to recognise Pymol scripts, then it'll execute the script. This requires the CGI to set the MIME type type and to set the filename of the script to have the correct suffix (to make Explorer on Windows work properly). The downloaded script is then executed by Pymol, which can uses Python's socket abilities to download PDB files and run Pymol commands on them. Et volia! A little convoluted, and by no means as elegent as having a browser plugin, but it does allow you to use Pymol for visulation over the web. I've got the code for this kicking around somewhere, if anyone is interested then contact me and I'll look for it and stick it on the web. Taking the idea further, and musing idly, a server-client could be set up between the web server and the client to allow further communication. Of course all of this is completly insecure, although the Python code could be sandboxed. > Thanks, Einat. > > > Einat Sitbon > Department of Molecular Genetics > Weizmann Institute of Science > Tel: 972-8-9344911 > > To reply, please change the mmm in the reply-to address to hotmail > > _ > Protect your PC - get McAfee.com VirusScan Online > http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963 > > > > --- > This SF.Net email is sponsored by: IBM Linux Tutorials > Free Linux tutorial presented by Daniel Robbins, President and CEO of > GenToo technologies. Learn everything from fundamentals to system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users -- Jon
RE: [PyMOL] embeding pymol in a web page
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 | An ActiveX verson of PyMOL is partially developed, but it won't be release | before PyMOL 1.0 -- so we're talking months to years. However, once we have | one plugin built, it shouldn't be too hard to create others (Netscape, Java, | etc.). Although I understand, that the most widespread browser on the most widespread OS should be supported first (especially if you want to attack Chime), I really think, that an Active X plugin (Windows-only, MS IE-only) is a bad sollution. Those people allready have Chime, whereas Linux and Mac users and the happy few using Mozilla can't use this tool. Therefore an alternative to Chime, which would support Mozilla and the other OS-platforms should be preferred. Keep up the good work! - -- Bye, Marc Saric http://www.marcsaric.de -BEGIN PGP SIGNATURE- Version: GnuPG v1.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFAZ9UqvKxJUF29wRIRAp3BAJ9EPSNgGuDWFFoiJ+n4VqczmksrngCfQag3 fT5WtQwDexwbQBJlFJWmZXw= =ISTM -END PGP SIGNATURE-
RE: [PyMOL] embeding pymol in a web page
Einat, On Thu, 2004-03-25 at 18:50, Warren DeLano wrote: > For web-page embeddable molecular graphics today, look to Jmol: > http://jmol.sourceforge.net Another alternative is the AstexViewer Java applet - free, but unfortunately closed source. http://www.astex-technology.com/AstexViewer/visualisation/index.html The MSD at EBI have developed an extended version, in use here: http://www.ebi.ac.uk/msd-srv/apps/Viewer/ViewerServlet?id=1atp It has some nice features, like showing the sequence of the protein and allowing you to zoom in on a residue when clicked in the sequence. I'm not sure about the licence position on the EBI version though; if you're interested, I'm sure someone from the MSD group could help out. Gareth -- --- Gareth Stockwell EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD gar...@ebi.ac.uk Tel 01223 492548 http://www.ebi.ac.uk/~gareth
RE: [PyMOL] embeding pymol in a web page
Einat, That is a longstanding goal of the PyMOL project, but there are various hurdles to be surmounted, including creating an API for embedding PyMOL and a secure API/language-subset for controlling it via the network. Another problem is that each platform has a different optimal technology for building plugins. An ActiveX verson of PyMOL is partially developed, but it won't be release before PyMOL 1.0 -- so we're talking months to years. However, once we have one plugin built, it shouldn't be too hard to create others (Netscape, Java, etc.). For web-page embeddable molecular graphics today, look to Jmol: http://jmol.sourceforge.net I think it is the best open-source option if migrating away from Chime. Cheers, Warren > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Einat Sitbon > Sent: Thursday, March 25, 2004 2:14 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] embeding pymol in a web page > > > Hello PyMolers, > > I'm wondering if there is a possibility to embed a pymol > script in a web site. > What I have in mind is something equivalent to the chime > plug-in, using pymol. > Any suggestions? > > Thanks, Einat. > > > Einat Sitbon > Department of Molecular Genetics > Weizmann Institute of Science > Tel: 972-8-9344911 > > To reply, please change the mmm in the reply-to address to hotmail > > _ > Protect your PC - get McAfee.com VirusScan Online > http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963 > > > > --- > This SF.Net email is sponsored by: IBM Linux Tutorials > Free Linux tutorial presented by Daniel Robbins, President and CEO of > GenToo technologies. Learn everything from fundamentals to system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
