modeling two chains while preserving their structural orientation wrt each other
Dear All,
I am working on modeling a protein with two chains (heterodimer). I have used two separate pdb files for each chain and oriented the two template structures appropriately before the modeling. Modeller is able to model both the chains, however not preserving the orientation of both the chains. I am seeking suggestions for how to specify restraints to preserve the orientation of both the chains with respect to each other. Please provide your suggestions.
Thanks and Regards
shivu
On 12/4/20 9:08 AM, shivu shiv wrote: > I am working on modeling a protein with two chains (heterodimer). > I have used two separate pdb files for each chain and oriented the two > template structures appropriately before the modeling. > Modeller is able to model both the chains, however not preserving the > orientation of both the chains.
If you are confident of this orientation, put the two chains in a single PDB file, as is done in the example in the manual: https://salilab.org/modeller/9.25/manual/node29.html
Modeller extracts internal distance restraints from each template separately, so if your two chains are two separate templates, there will be no inter-chain restraints.
Ben Webb, Modeller Caretaker
Thanks Ben, It worked.
On Fri, Dec 4, 2020 at 11:55 AM Modeller Caretaker < modeller-care@salilab.org> wrote:
> On 12/4/20 9:08 AM, shivu shiv wrote: > > I am working on modeling a protein with two chains (heterodimer). > > I have used two separate pdb files for each chain and oriented the two > > template structures appropriately before the modeling. > > Modeller is able to model both the chains, however not preserving the > > orientation of both the chains. > > If you are confident of this orientation, put the two chains in a single > PDB file, as is done in the example in the manual: > https://salilab.org/modeller/9.25/manual/node29.html > > Modeller extracts internal distance restraints from each template > separately, so if your two chains are two separate templates, there will > be no inter-chain restraints. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >
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shivu shiv