[phenixbb] Modeling Disordered Domains

Pavel Afonine pafonine at lbl.gov
Tue Apr 5 11:45:48 PDT 2011


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: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] 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 Mon, Apr 4, 2011 at 11:11 AM, Damian Ekiert
>> <dcekiert at scripps.edu>  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
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