fwiw, I did find mol2 format at this location which is just fine for my scripts,
http://zinc.docking.org/substance/1633229
Thanks.
----------------------------------------
> From: marchy...@hotmail.com
> To: spel...@users.sourceforge.net; pymol-users@lists.sourceforge.net
> Date: Sun, 25 Nov 2012 19:00:08 -0500
> Subject: Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or
> related libraries
>
>
>
>
>
>
> ----------------------------------------
> > Date: Sun, 25 Nov 2012 23:49:26 +0100
> > From: spel...@users.sourceforge.net
> > To: pymol-users@lists.sourceforge.net
> > 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
> >
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