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.
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. 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! -Eric ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
