On Aug 7, 2009, at 10:30 AM, Dina Schneidman wrote:
Of course, because that was handled in the original pdb reading code :-)Currently AtomType is more ProteinAtomType (and nucleic acid).
AtomType really needs to be the type of the atom. Otherwise, any code which uses them will have to have all sorts of logic to look at the element, whether it is in a protein etc.Having element stored resolves the problem. However, it would be nice to have less ambiguity in the AtomType as well.
It would be much simpler to put the logic on the edges (ie in code that creates Atoms). From what I understand, the mol2 atom types that Hao is using are compatible with the PDB protein atom types, so we perhaps should standardize on those.
A simpler hack is to just prefix hetatoms with "H" since I'm pretty sure the atom types for ATOM records are all well defined. My guess is that hetatom types in the PDB are a bit of a mess, but perhaps things are better than that :-)
On Thu, Aug 6, 2009 at 11:19 PM, Daniel Russel<> wrote: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 somehavehave no element (eg water), but for those it doesn't really matter whatgets 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._______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev_______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev_______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev_______________________________________________ IMP-dev mailing list https://salilab.org/mailman/listinfo/imp-dev