Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries

[Mike M. <mar...@ho...>]

fwiw, I did find mol2 format at this location which is just fine for my scripts,

http://zinc.docking.org/substance/1633229

Thanks.

----------------------------------------
> From: mar...@ho...
> To: sp...@us...; pym...@li...
> 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: 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...
>
> ------------------------------------------------------------------------------
> 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...