[Biojava-l] Alternative conformation skipped

[Enrico Morelli]

On Wed, 7 May 2025 11:29:03 -0700
Jose Duarte <jose.duarte at 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 <morelli at 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 at 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
------------------------------------------------------------