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

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

----------------------------------------
> 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...