Save all non-clashing rotamers with the protein

[amin-sagar]

Hello.
I am trying to find a way to save the whole protein structures with all rotamers of the mutated residue which don't have clashes.
The xl.mutate function uses only the highest probability rotamer.
I tried using the repacking function with radius set to zero to sample only the mutated residue but this leads to the repack function getting stuck.
I know I can save the rotamer ensemble and then superimpose it with the protein as a separate step but I am wondering if there is a way to do this in chiLife that I missed.

Thanks,
Amin.

[mtessmer]

Hi Amin, Sorry for the delayed reply I have been a little more busy than usual as we are interviewing for summer interns right now. Currently, there is no way to do this, however, it should definitely be an option. I will open a github issue and since this should be an easy fix I hope to get it done by the end of this weekend. Thank, Maxx

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On Fri, Nov 8, 2024 at 12:16 AM amin-sagar ***@***.***> wrote: Hello. I am trying to find a way to save the whole protein structures with all rotamers of the mutated residue which don't have clashes. The xl.mutate function uses only the highest probability rotamer. I tried using the repacking function with radius set to zero to sample only the mutated residue but this leads to the repack function getting stuck. I know I can save the rotamer ensemble and then superimpose it with the protein as a separate step but I am wondering if there is a way to do this in chiLife that I missed. Thanks, Amin. — Reply to this email directly, view it on GitHub <#167>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEOQ3HSUJMQFFIC5K4UWGHTZ7RXOFAVCNFSM6AAAAABRM6D56SVHI2DSMVQWIX3LMV43ASLTON2WKOZSGY2DGMRVGE2DKNA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[mtessmer]

pr #179 makes xl.mutate and xl.save more versatile, allowing mutating with specific rotamers, or all rotamers and saving of specific frames.