On Mon, Mar 29, 2010 at 9:19 PM, Eric Martz <[email protected]>wrote:
> Dear Bob,
>
> Wow, what a great day it was today! (Bob was visiting us at UMass
> Amherst.) Thanks so much for coming. Next time you come anywhere in
> the Northeast do let me know and I'll try to join the fun again.
>
[Boston ACS meeting, August]
>
> We were discussing adding hydrogens vs. bond order and the need to
> know that info for all HETERO compounds in the PDB. Turns out
> apparently it is conveniently available in a CIF file!
>
> At http://www.wwpdb.org (the WorldWide site), click on Chemical
> Component Dictionary. You can download components.cif. It appears to
> me that for every compound, the hydrogens and the bond orders are
> specified. This file is updated weekly.
>
>
yes, and all for only 94 Mb.... If these are available for individual
3-letter name ATOM and HET components, then perhaps we could download them
on the fly for a given structure, but realistically I don't know....
> In fact, this dictionary includes all the standard residues (amino
> acids and nucleotides) as well as nonstandard ones and all ligands.
> See e.g. data_gly, data_his, data_da (deoxy adenosine), etc.
> For background, see
> http://proteopedia.org/wiki/index.php/Standard_Residues
> http://proteopedia.org/wiki/index.php/Non-Standard_Residues
> http://proteopedia.org/wiki/index.php/Ligands
> http://proteopedia.org/wiki/index.php/Protein_Data_Bank
>
> Thus, in fact, the info appears to be readily available from which
> Jmol could add hydrogens and set bond orders for every component of
> every PDB file!
>
The real issue is where to place them. Carbons are easy, but OH, NH, and NH2
are not trivial at all. And pH. There are other programs that do this; I
would recommend using them.
Bob
>
> -Eric
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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