> >Also note that by some conventions, "2OA2" in a PDB file really means > >atom "OA22". > > > I didn't know that. What conventions are those?
Well, PDB atom names are supposed to have the atomic symbol right justified in the first two columns followed by a remoteness indicator and then a branching number. However, that isn't a sufficient number of fields for all situations, such as when significant symmetry is present in a system, and so a third field is required. This numeric field occupies the first column when the atom symbol itself is only one character. With hydrogens, this first numeric field has the additional defined purpose of enumerating (NMR?) equivalent hydrogens, so you will see atoms like "2HD" and "3HD" in ARG for instance. However, in the Amber world, the atomic symbol always comes first. Thus a PDB hydrogen 2HH2 becomes HH22 in Amber. Going from PDB to Amber is easy, but the reverse is not trivial, since Amber "CD1" remains PDB "CD1", but Amber "HE2" becomes "2HE" and "HH22" becomes "2HH2". Ambiguity occurs when there is a four-letter atom name which is not a hydrogen. "OA22" in Amber would thus need to become "2OA2" in order to comply with the PDB convention of having the Atomic symbol right justified in the first two columns of the file. However, that convention is only explicitly enforced for amino acids, so in theory "OA22" would be legal for a non-amino acid, whereas "2OA2" is required if the residue is an amino acid. What a mess! Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > >Also note that by some conventions, "2OA2" in a PDB file really means > >atom "OA22". > > > I didn't know that. What conventions are those? > > >Furthermore, in your example, they [ATOM IDs] are not unique (a > mistake?). > > > yup, a mistake. > > >However, I am trying to bend PyMOL around to meet your needs a bit > >better. > > > >Towards this end, I've created a new setting "pdb_retain_ids" which > >preserves the original PDB serial numbers in the output file. > > > >In future PyMOL versions, so long as > > > >set retain_order, 1 > >set pdb_retain_ids, 1 > >set pdb_no_end_record, 1 > > > That's absolutely fantastic. Right now, I have to use PyMOL, MOE and > AMBER (sander and carnal are the real problems) on the same systems, and > anything that makes this less painful is great! I'll probably set > retain_order and pdb_retain_ids in my .pymolrc.py and upgrade to the CVS > version within the next couple of days. > > Thanks! > > -michael > -- > michael lerner > > > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
