On Wed, 7 May 2025 11:29:03 -0700
Jose Duarte <jose.dua...@rcsb.org> wrote:
> There's a call to get alt locs, e.g. something like this:
>
> if (g.hasAltLoc()) {
> System.out.println("## alt locs");
> System.out.println(g.getAltLocs().size());
> for (Group altLoc: g.getAltLocs()) {
> for (Atom a : altLoc.getAtoms()) {
> System.out.println(a);
> }
> }
> }
>
> Also do note the javadoc for getAltLocs to see what the exact
> behaviour is:
>
> https://github.com/biojava/biojava/blob/5a699eb6465509b853463ae34ec04c4d90bc2a54/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java#L344-L364
>
Thanks, it's working but we have some concerns because the alt locs property
refers to an atom property and we cannot understand why you decided to
associate this property to a group of atoms.
For instance, in the pdb 4KL8 the alternative conformation is reported for the
FCO group, how can I identify just the alternative conformation of the iron ion?
Regards
>
>
> On Wed, 7 May 2025 at 03:40, Enrico Morelli <more...@cerm.unifi.it>
> wrote:
>
> > Dear all,
> >
> > we are trying to read the HETATM of the following cif
> > https://files.rcsb.org/view/4KL8.cif with this code:
> >
> > for (Chain c : structure.getChains()) {
> > for (Group g : c.getAtomGroups(GroupType.HETATM)) {
> > for (Atom a : g.getAtoms()) {
> > System.out.println(a);
> >
> > }
> > }
> > }
> >
> > But we realized that your methods doesn't read all the alternative
> > conformation of some of the hetatm in the structure.
> > For instance it reads FE 12360 but not FE 12361_
> >
> > HETATM 12360 FE FE A FCO W 7 . ? 27.605 -32.546 26.346 0.33
> > 9.74 ? 501 FCO M FE 1
> > HETATM 12361 FE FE B FCO W 7 . ? 27.573 -32.629 26.079 0.67
> > 10.53 ? 501 FCO M FE 1
> >
> >
> > Is it possible to read both or at least the one with the higher
> > occupancy?
> >
> > Thank you very much in advance
> >
> > Regards
> > --
> > -----------------------------------------------------------
> > Enrico Morelli
> > System Administrator | Programmer | Web Developer
> >
> > CERM - Polo Scientifico
> > via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY
> > ------------------------------------------------------------
> > _______________________________________________
> > Biojava-l mailing list - Biojava-l@biojava.org
> > https://mailman.open-bio.org/mailman/listinfo/biojava-l
> >
--
-----------------------------------------------------------
Enrico Morelli
System Administrator | Programmer | Web Developer
CERM - Polo Scientifico
via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY
------------------------------------------------------------
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