Well, we certainly wouldn't want C alpha and calcium to get them the
same AtomType, right? That would mess all sorts of things up since you
couldn't, eg, do as Hao is doing and index his force field based on
the AtomTypes.
On Aug 6, 2009, at 10:56 PM, Dina Schneidman wrote:
I care :)
for example Calcium and Calpha atom will have the same atom name "CA"
there is a reason for having this column in PDB format.
On Thu, Aug 6, 2009 at 10:46 PM, Daniel Russel<>
wrote:
On Aug 6, 2009, at 10:36 PM, Dina Schneidman wrote:
the right way to determine the element is from element field in pdb,
since from atom type it can be ambiguous.
When is it ambiguous? Is if often enough that we care? Certainly
some have
have no element (eg water), but for those it doesn't really matter
what gets
written out.
if the element is not
determined and stored when the pdb is read than the information is
lost. I suggest just to fix the writer.