[phenixbb] Rotamer restraints in phenix.real_space_refine

[Oleg Sobolev]

Hi Ashley,

Indeed, apart from strategy defaults, the rotamer fitting algorithm itself
was changed between 1.13 and 1.14. It is possible it behaves slightly
different (we were hoping for the better behavior in most cases). I'm not
sure that it is possible to get exact 1.13 behavior in 1.14. I would expect
you get small amount of rotamer outliers (<1%). Otherwise we probably
should investigate. Sometimes inclusion of hydrogen atoms could help get a
better refined model.

Best regards,
Oleg Sobolev.

On Thu, Feb 28, 2019 at 4:24 AM Ashley Pike <ashley.pike at sgc.ox.ac.uk>
wrote:

> Oleg,
>
> Thanks - so behaviour has changed. Running with local_grid + rotamer
> restraints=true seems to optimise rotamers (although does not necessarily
> eliminate outliers). Is there an equivalent combination that enforces
> rotamers (ie. doesn’t allow outliers)? This is behaviour of 1.13 with just
> rotamer_restraints=true (and no local_grid _search). In my case, I can't
> really justify having rotamer outliers when refining against 4A cryo-em
> maps.
>
> Many thanks,
>
> Ashley
>
>
>
> *From:* Oleg Sobolev <osobolev at lbl.gov>
> *Sent:* 28 February 2019 00:14
> *To:* Ashley Pike <ashley.pike at sgc.ox.ac.uk>
> *Cc:* phenixbb at phenix-online.org
> *Subject:* Re: [phenixbb] Rotamer restraints in phenix.real_space_refine
>
>
>
> Hi Ashley,
>
>
>
> Do you have "local_grid_search" box checked in refinement
> settings->strategy when running 1.14? This should be on by default since
> 1.14, but it was not the case in 1.13. Sometimes people using .eff files
> from 1.13 in later versions end up without old defaults for refinement
> strategy, disabling rotamer fitting.
>
>
>
> I can have a closer look if you send me the .log file (off-list).
>
>
>
> Best regards,
>
> Oleg Sobolev.
>
>
>
> On Wed, Feb 27, 2019 at 10:56 AM Ashley Pike <ashley.pike at sgc.ox.ac.uk>
> wrote:
>
> Hi - Am I right in thinking that rotamer restraints behaves differently in
> latest official release (1.14-3260) compared to last but one official
> release (1.13-2998)? Issuing rotamer_restraints=True from command line or
> GUI used to give 0% rotamer outliers in the molprobity analysis at end of
> log in 1.13-2998 but now in 1.14 gives non-zero for same input model. It is
> as if they are not being applied.
>
>
>
> In the old log file it used to clearly print - **Update rotamer
> restraints*** after every macrocycle, in the 1.14 logs this is omitted.
>
>
>
> Many thanks,
>
> Ashley
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20190228/68085e8e/attachment-0001.htm>