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. Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. ---------------------------------------- > From: marchy...@hotmail.com > To: jason.vertr...@schrodinger.com; pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] Mobile PyMOL Problem and Solution > Date: Fri, 2 Nov 2012 20:43:41 -0400 > > > > > > > ---------------------------------------- > > 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 > ------------------------------------------------------------------------------ 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
