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choderalab / ensembler

Automated omics-scale protein modeling and simulation setup.
http://ensembler.readthedocs.io/
GNU General Public License v2.0
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Ensembler does not retain disulfide bond records from original PDB files. #93

Open MehtapIsik opened 7 years ago

MehtapIsik commented 7 years ago

While trying to use Ensembler pipeline to model Human Serum Albumin, I realized disulfide bond information from original PDB files are not retained after model generation step.

Here is what I have run:

$ ensembler init
$ ensembler gather_templates --gather_from uniprot --query 'ALBU_HUMAN'
$ ensembler align
$ ensembler build_models
$ ensembler cluster

I included the original PDB file of PDB ID: 1AO6 and output of ensembler modelling step as examples: 20170530_reporting_ensembler_ssissue.zip

Ensembler output structure after modelling step (1AO6_A_ensembler_model.pdb) doesn't have the SSBOND section that specifies which cysteines are disulfide bonded. This section exists the original PDB file downloaded from RCSB (1ao6.pdb).

How can we adjust ensembler to keep disulfide bridge information?