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

----------------------------------------
> From: jas...@sc...
> Date: Mon, 26 Nov 2012 10:37:52 -0600
> Subject: Re: was: [PyMOL] Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
> To: mar...@ho...
> CC: pym...@li...
>
> 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.

Thanks, I didn't know it would be that simple and that looks like a good way to learn
python. Although I am curious now if I had a pdb that lacks hydrogens, like I did in this case,
what pymol facilities are there for adding them? Apparently you have some editing
capabilites and analyses, I thought there may be some way to guess approximately where
the hydrogens should go and then export the new file. This is probably obvious 
from a quick google search on basic capabilites but it also sounds as if there
may be less well known specialized tools for doing less common things like this.


>
> I hope your meal was tasty.
>
how can you enjoy it without the pdb file on the screen and optimizing in DFT? LOL.





> Cheers,

Thanks.

>
> -- Jason
>
>
> >> ----------------------------------------
> >> > From: jas...@sc...
> >> > Date: Fri, 2 Nov 2012 18:57:38 -0500
> >> > To: pym...@li...
> >> > 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) Jas...@sc...
> >> > (o) +1 (603) 374-7120
> >> >
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> >> > _______________________________________________
> >> > PyMOL-users mailing list (PyM...@li...)
> >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> > Archives: http://www.mail-archive.com/pym...@li...
> >>
> >
>
>
>
> --
> Jason Vertrees, PhD
> Director of Core Modeling Product Management
> Schrödinger, Inc.
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120