If this problem continues, please let me know. I consider it a bug in previous Jmol versions, and I believe I have fixed it. We should not ever see ATOM....HG22 read as mercury again.
Angel Herraez wrote: >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 > > ------------------------------------------------------------------------- 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
