On Aug 7, 2009, at 10:30 AM, Dina Schneidman wrote:
> Currently AtomType is more ProteinAtomType (and nucleic acid). Of course, because that was handled in the original pdb reading code :-)
> Having element stored resolves the problem. However, it would be nice > to have less ambiguity in the AtomType as well. 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.
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 Russeldrussel@gmail.com > 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 Russeldrussel@gmail.com >>> 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. >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev