Hi Mike, > I was trying to figure out what to eat today so naturally I started looking > for PDB libraries > with food components. I was looking for garlic related chemicals when I came > across this, > > http://molecules.gnu-darwin.org/ > > which seems to have many pdb files. My question I guess is, what does pymol > have > for an "API" to get molecule structures from various locations or do you just > have an > interface for pdb.org? Besides deciding on what to eat today, I was curious if > pymol has more generalized means of finding structure files.
We have an API for accessing structures remotely. For example, load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb, myMolecule You could easily create a PyMOL plugin (http://www.pymolwiki.org/index.php/Plugins_Tutorial) that takes advantage of this site very simply using the load command and formatted URLs. I hope your meal was tasty. Cheers, -- Jason >> ---------------------------------------- >> > From: jason.vertr...@schrodinger.com >> > Date: Fri, 2 Nov 2012 18:57:38 -0500 >> > To: pymol-users@lists.sourceforge.net >> > Subject: [PyMOL] Mobile PyMOL Problem and Solution >> > >> > Greetings, >> > >> > On Oct 28th, the folks at the PDB made some changes to their PDB Web >> > Services interface. This change broke Mobile PyMOL's ability to search >> > for and download PDBs. >> >> I haven't bothered to look at this specific situation but this a problem >> with many sites >> and automated interaction. NCBI has a nice eutils interface that has >> remained stable >> for a while, I'd been trying to get more groups to offer a web interface >> designed for >> automated interactions. FWIW, >> >> http://www.ncbi.nlm.nih.gov/books/NBK25500/ >> >> >> Do you have automated access to this library for example, >> >> http://www.ncbi.nlm.nih.gov/Structure/index.shtml >> >> they also have their own viwer, for example, >> >> http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml >> >> but pymol seems a bit more extensive. >> >> > >> > I have updated Mobile PyMOL and will soon resubmit it to the AppStore >> > for verification and release. This process takes typically takes no >> > less than 8 days. So, in the meantime for the 7,000 Mobile PyMOL users >> > please use the following technique to acquire structures: >> > (1) Using Safari on the iPad browse to the www.pdb.org and find the >> > structure you want. >> > (2) Click "Download Files" from the upper right hand side of the >> > structure's page and then select "PDB File (Text)". >> > (3) Click "Open in PyMOL". >> > >> > Happily, as a long-term solution, I've established contact with the >> > PDB Web Services Group and we'll now be made aware of future changes. >> > The PDB is an extremely valuable resource in the community and I'm >> > glad we could work this out. >> > >> > Cheers, >> > >> > -- Jason >> > >> > -- >> > Jason Vertrees, PhD >> > PyMOL Product Manager >> > Schrödinger, Inc. >> > >> > (e) jason.vertr...@schrodinger.com >> > (o) +1 (603) 374-7120 >> > >> > ------------------------------------------------------------------------------ >> > LogMeIn Central: Instant, anywhere, Remote PC access and management. >> > Stay in control, update software, and manage PCs from one command center >> > Diagnose problems and improve visibility into emerging IT issues >> > Automate, monitor and manage. Do more in less time with Central >> > http://p.sf.net/sfu/logmein12331_d2d >> > _______________________________________________ >> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
