Currently AtomType is more ProteinAtomType (and nucleic acid).
Having element stored resolves the problem. However, it would be nice
to have less ambiguity in the AtomType as well.
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 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.
>>>
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