Thank you. I had not noticed the pattern that columns 13-14 at least sometimes contain the element symbol, whether one- or two-character.
Questions: * Is this pattern documented in the PDB specification? * If this pattern can be relied on, why are columns 77-78 also dedicated to the element symbol? * Should reliance on the pattern be hidden behind a BioJava method? ________________________________ From: [email protected] [mailto:[email protected]] On Behalf Of Andreas Prlic Sent: Friday, April 23, 2010 6:52 PM To: Andy Thomas-Cramer Cc: [email protected] Subject: Re: [Biojava-l] PDBFileParser and Atom element symbol Hi Andy, you could check with Atom.getFullname(), which contains the space characters from the PDB file: e.g Calpha: " CA ", Calcium "CA " in addition the parent group of a Calpha atom is usually an AminoAcid and for Calciums it is a Hetatom group... Andreas On Fri, Apr 23, 2010 at 3:58 PM, Andy Thomas-Cramer <[email protected]> wrote: Is there an easy way to identify the type of atom referenced by an Atom object? For example, if Atom.getName() is "CA", is the element calcium or the atom carbon alpha? If not, would it be feasible to add a method providing this in Atom, AtomImpl, and parsing it in PDBFileParser, using the columns defined at http://www.wwpdb.org/documentation/format32/sect9.html#ATOM? _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l -- ----------------------------------------------------------------------- Dr. Andreas Prlic Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego (+1) 858.246.0526 ----------------------------------------------------------------------- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
