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 Sent: 28 February 2019 00:14 To: Ashley Pike Cc: [email protected] 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 mailto:[email protected]> 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 [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected]

Hi Ashley, yes, the behavior is different now. Before we would restrain each residue to its nearest valid rotamer without considering density map, which works well in many cases but doesn't in some. In current version we optimize rotamers to minimize clashes (but we mind H-bonds) and maximize model-to-map fit. Clearly, it may happen that local model geometry is such that no optimal fit is possible, this is probably responsible for some outliers that remain after refinement. If you have a clear example where this does no work please send it to us and we will investigate. Pavel On 2/28/19 09:59, Oleg Sobolev wrote:

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 mailto:[email protected]> 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 mailto:[email protected]> *Sent:* 28 February 2019 00:14 *To:* Ashley Pike mailto:[email protected]> *Cc:* [email protected] mailto:[email protected] *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 mailto:[email protected]> 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

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