Nat, Thanks for your comments. I guess I was thinking of cases where there was at least some weak density, such that by setting "build_alternates_ringer=True", Phenix would automatically add alternative rotamers and refine the relative occupancies. Regarding my disordered domains, I'm looking forward to hearing from Pavel about this new feature! Best, Damian On Apr 4, 2011, at 11:48 AM, Nathaniel Echols wrote:

On Mon, Apr 4, 2011 at 11:11 AM, Damian Ekiert wrote:

...

On a final note, regarding those pesky missing side chains: any thoughts on trying to employ a "Ringer"-like approach to model some of these (Fraser, et al., Nature 2009, 462(7273):669-673)? Is this practical (maybe this would add to many additional parameters)?

This is potentially useful for finding and building alternate conformers (something that most programs don't do - the only one I'm aware of is qFit: http://smb.slac.stanford.edu/qFitServer/qFit.jsp). But Ringer still relies on having some interpretable (albeit weak) density for the sidechains, and was designed to look at static rather than dynamic disorder. (A somewhat artificial distinction, but appropriate enough when talking about refinement.) It is also limited to relatively high resolution, usually better than 2.0A, not because of data-to-parameter ratio, but because the maps at lower resolutions just don't have enough detail to detect alternate conformations with any degree of confidence.

Regarding missing or patchy domains, Pavel recently added a feature that should at least improve the phases and refinement behavior, but I'll let him describe it since I don't really understand what it does. I do not know of cases where people have found a reasonable way to model these explicitly, other than placing a rigid domain and letting the B-factors go crazy.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Hi Henry, while on the subject.. I remember I promised to let you know but keep forgetting (although most likely you figured this out yourself): phenix.refine can handle any number of alternative conformations (there used to be an artificial limit of 4, but we improved this a while ago). Pavel. On 4/5/11 11:40 AM, van den Bedem, Henry wrote:

Damien,

That's pretty much what qFit does--it automatically adds alternate conformations (main-chain and side-chain) at occupancies it computes from a constrained fit to the data. It then uses phenix to further refine coords/adp's/occupancies. Like Nat said--you need better than 2A data.

Henry

-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Damian Ekiert Sent: Tuesday, April 05, 2011 11:00 AM To: PHENIX user mailing list Subject: Re: [phenixbb] Modeling Disordered Domains

Nat,

Thanks for your comments. I guess I was thinking of cases where there was at least some weak density, such that by setting "build_alternates_ringer=True", Phenix would automatically add alternative rotamers and refine the relative occupancies.

Regarding my disordered domains, I'm looking forward to hearing from Pavel about this new feature!

Best,

Damian

On Apr 4, 2011, at 11:48 AM, Nathaniel Echols wrote:

...

...

On a final note, regarding those pesky missing side chains: any thoughts on trying to employ a "Ringer"-like approach to model some of these (Fraser, et al., Nature 2009, 462(7273):669-673)? Is this practical (maybe this would add to many additional parameters)? This is potentially useful for finding and building alternate conformers (something that most programs don't do - the only one I'm aware of is qFit: http://smb.slac.stanford.edu/qFitServer/qFit.jsp). But Ringer still relies on having some interpretable (albeit weak) density for the sidechains, and was designed to look at static rather

On Mon, Apr 4, 2011 at 11:11 AM, Damian Ekiert wrote: than dynamic disorder. (A somewhat artificial distinction, but appropriate enough when talking about refinement.) It is also limited to relatively high resolution, usually better than 2.0A, not because of data-to-parameter ratio, but because the maps at lower resolutions just don't have enough detail to detect alternate conformations with any degree of confidence.

Regarding missing or patchy domains, Pavel recently added a feature that should at least improve the phases and refinement behavior, but I'll let him describe it since I don't really understand what it does. I do not know of cases where people have found a reasonable way to model these explicitly, other than placing a rigid domain and letting the B-factors go crazy.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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