CE-Symm assumes models come from BA

[sbliven]

Running CE-Symm on multi-model structures seems to concatenate all models. This is desirable for the biological assembly PDB files, but undesirable for ensembles.

For instance, running on 4tz5.B produces heap overflows as it tries to concatenate 25 models.

[sbliven]

This can cause inflation of the repeat number. Example: 2q4g.W has 8 models with 16 repeats each. Running with 8G of memory I can finish this structure, but get 128 repeats!

[lafita]

If I remember correctly the input to the CESymm method is actually the Atom array extracted from the Structure object.
I wonder if this could be a bigger problem related to how the representative Atoms of multi model structures are obtained.

[josemduarte]

@sbliven since 5.0.0, BioJava will by default produce bioassemblies by expanding into new chains (instead of new models). That is the default now if you do:

StructureIO.getBiologicalAssembly(String pdbId);

or otherwise you can explicitly set the flag (multiMode=true for expanding into models instead of chains):

StructureIO.getBiologicalAssembly(String pdbId, int bioAssemblyId, boolean multiModel);

I think the feature is also available in 4.2.x, but there it is not the default.

So it should be totally safe to remove the concatenation of models in CESymm.

[sbliven]

I need to look into this more, since I found a few cases where CE-Symm seems to be duplicating structures. We used to report the currect number of repeats for these, but now it's doubled. None of them have multiple models.

Name	Symm	Predicted Repeats	Predicted Symm
d1xmpa_	C2	2	4
d2hiyc_	C2	2	4
d1kkta_	C7	7	14