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From: Mike M. <mar...@ho...> - 2012-11-26 00:00:18
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---------------------------------------- > Date: Sun, 25 Nov 2012 23:49:26 +0100 > From: sp...@us... > To: pym...@li... > Subject: Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries > > Hi Mike, > > you can fetch molecular files from any web address with the "load" > command. Examples: > > File type recognized from file extension: > > PyMOL> load > http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb Thanks, it sounded like the original poster was refering to a larger facility to find pdb files in a variety of libraries. If I know where the file is I can usually get it with wget but if tere is some search API or facility that may be helpful. I am finding some pdb collections online but thought they may be listed somewhere. In any case, I eventually realized that the pdb does not have the hydrogens and I can't find one that may. Would it be reasonable to try to use pymol to add them? I only need "artists conception" as presumably the DFT optimization will make it more accurate. > > File type given with "format" argument: > > PyMOL> load > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5280443&disopt=3DSaveSDF, > format=sdf > > Also, Mobile PyMOL (for the iPad) has it's own server capabilities, > including support for PubChem, PDB, Dropbox, etc. > > Cheers, > Thomas > > Mike Marchywka wrote, On 11/25/12 17:26: >> 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. > > -- > Thomas Holder > PyMOL Developer > Schrödinger Contractor > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |