the right way to determine the element is from element field in pdb, since from atom type it can be ambiguous. 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.
On Thu, Aug 6, 2009 at 7:12 PM, Keren Laskerkerenl@salilab.org wrote: > yes - probably should not be stored, but still doing something like: > atom = IMP::atom::Atom::create(p,IMP::atom::AT_CA) > connecting this atom to a molecule ( with residue and chain of course) > and then writing the molecule as pdb, results in a error unknown element in > get_element. > On Aug 6, 2009, at 7:05 PM, Daniel Russel wrote: > >> It should get it from the aromtype for all properly initialized atom >> types. If it isn't currently doing that blame Dina :-) we should be able to >> fix it easily. >> >> I'm not sure there is a reason to store the element in the particle rather >> than just look it up from the atomtype when get_element is called. Is there? >> >> >> >> On Aug 6, 2009, at 6:31 PM, Keren Lasker kerenl@salilab.org wrote: >> >>> seems that now element is needed for writing atoms in pdb format. >>> Would not it make sense to set the value of element in Atom::create()? >>> _______________________________________________ >>> 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 >