El 6 May 2007 a las 20:34, Bob Hanson escribió: > If the PDB file has the element symbol field filled, then there is no > problem. 11.1.32 fixes this issue with Hg as mercury when the file does > not contain this information by assigning H to any atom name starting > with H (He, Hf, Hg) in ATOM records. -- Mercury could only appear in > HETATM records, I think. But, yes, earlier versions of Jmol did not > properly assign H in just this situation.
Well, on the case I've seen, Jmol was assigning properly, the problem was in the file, that "H" was one column to the left to where it should. The PDB convention is four columns, and usually the C / O / H etc. goes in the second (i.e., the element name is right-justiified, followed by 2 alphanumeric identifiers). On that file, since they needed 3 numeric IDs, they shifted the H to the left, and so Jmol read HG22 as mercury (in other files, more PDB-compiant, it would have been 2HG2). There were also "helium" reads; I don't know how HH and HD were being read. I was just guessing that in David's files the same could be happening. Anyway, as Bob says, adding the element symbol at the proper columns (77 and 78) prevents any of these troubles, but I see many people don't do that. ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
