[x] Will your PR merge into the dev branch?
Exceptions will be made for urgent bugfixes.
[x] Have you forked from dev?
If not, please rebase your PR onto the most recent dev tip.
[x] Does your PR title succinctly describe the changes? Explain to a new user by completing the sentence: 'This PR will: ...'
[x] Fill out the template below.
Description of the Change
This fix is changing the rotamer neighborhood and step size of sampling in the chi sampling steps. For the rotamer neighborhood, we were exploring 60 degrees on either side of the idea rotamer, effectively leading to sampling around the entire chi angle. We have now reduced this to 24. We did this by exploring different rotamer neighborhoods from 10-30 (note that this is on both side of the idea rotamer). Based on reduction in rotamer outliers, Rfree values, and manual examination, 24 was chosen.
We also reduced the step size to 6 from 10. Within the 48 degrees around the ideal rotamer, we sample every 6 degrees rather than 10. We did this by exploring different step sizes from 3-10. Based on reduction in Rfree values and manual examination, 6 was chosen.
This does result in lower sampling (for each ideal rotamer we used to have 12 conformers, now we have 8).
Pull Request Checklist
devbranch?Exceptions will be made for urgent bugfixes.
dev?If not, please rebase your PR onto the most recent
devtip.Explain to a new user by completing the sentence: 'This PR will: ...'
Description of the Change
This fix is changing the rotamer neighborhood and step size of sampling in the chi sampling steps. For the rotamer neighborhood, we were exploring 60 degrees on either side of the idea rotamer, effectively leading to sampling around the entire chi angle. We have now reduced this to 24. We did this by exploring different rotamer neighborhoods from 10-30 (note that this is on both side of the idea rotamer). Based on reduction in rotamer outliers, Rfree values, and manual examination, 24 was chosen.
We also reduced the step size to 6 from 10. Within the 48 degrees around the ideal rotamer, we sample every 6 degrees rather than 10. We did this by exploring different step sizes from 3-10. Based on reduction in Rfree values and manual examination, 6 was chosen.
This does result in lower sampling (for each ideal rotamer we used to have 12 conformers, now we have 8).