[phenixbb] phenix.refine and torsion-angle ncs

[Antony Oliver]

Dear phenix.bb / Jeff / Nat

I think I've found out (possibly) what the issue was.  If you click on "NCS options" in the phenix.refine window, there is a check-box "Fix rotamer outliers first" and "Check for consistency between NCS-related sidechains"  - both which are selected by default.  A quick uncheck of these options seems to have cured my ills for today.

With thanks,

Tony.

---
Dr Antony W Oliver

Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
Science Park Road
University of Sussex
Falmer, Brighton, BN1 9RQ

email: antony.oliver at sussex.ac.uk<mailto:antony.oliver at sussex.ac.uk>
tel (office): +44 (0)1273 678349
tel (lab): +44 (0)1273 677512


From: Jeff Headd <jjheadd at lbl.gov<mailto:jjheadd at lbl.gov>>
Reply-To: PHENIX user mailing list <phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>>
Date: Thu, 21 Jun 2012 07:57:36 -0700
To: PHENIX user mailing list <phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>>
Subject: Re: [phenixbb] phenix.refine and torsion-angle ncs

Yes, that's possible, assuming that one of the sidechains is rotameric and the other isn't. The rotamer will only be changed, though, if it's an improved fit to the map.

Jeff

On Thu, Jun 21, 2012 at 7:54 AM, Nathaniel Echols <nechols at lbl.gov<mailto:nechols at lbl.gov>> wrote:
On Thu, Jun 21, 2012 at 7:49 AM, Jeff Headd <jjheadd at lbl.gov<mailto:jjheadd at lbl.gov>> wrote:
> It is not necessary to exclude residues when using the torsion angle NCS
> restraints, even if they are in different rotamers. The potential used to
> restrain related torsions automatically shuts off in cases where the related
> torsions are sufficiently different, such as for different rotameric states.

One possibility here is that the sidechains forming crystal contacts
are in non-rotameric conformations - in this case, wouldn't the
rotamer correction try to adjust them to agree with other chains?

-Nat
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