CE-Symm assumes models come from BA #808

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1. sbliven commented on Oct 25, 2018

   

   sbliven

   on Oct 25, 2018

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   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!

   😕React with 😕2Reacted by Aleix Lafita and Sudarsan Mansingh
2. lafita

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   bugBugs and bugfixesBugs and bugfixes

   on Oct 25, 2018
3. lafita commented on Oct 25, 2018

   

   lafita

   on Oct 25, 2018

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   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.
4. josemduarte commented on Oct 25, 2018

   

   josemduarte

   on Oct 25, 2018

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   @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.
5. sbliven commented on Oct 26, 2018

   

   sbliven

   on Oct 26, 2018

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   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