[phenixbb] number of cycles

[Keitaro Yamashita]

Dear Jeff,

Are B-factors taken into account if both orientations don't clash?
This is the function of Coot to detect flip.
I think it's nice if it is automatically done... already implemented?

Thanks,

Keitaro

2011/3/2 Jeff Headd <jjheadd at lbl.gov>:
> Hi Maia,
>
> Phenix.refine analyzes Asn, Gln, and His residues at each macrocycle
> and determines which orientation is likely correct given the local
> environment of the sidechain. The best orientation will have no steric
> clashes and satisfy local H-bond donors/acceptors. In cases where
> there are other model errors in the region of the sidechain and both
> orientations clash significantly, you'll see the **PLEASE CHECK
> MANUALLY** warning which indicates that there are likely multiple
> misfit sidechains that need to be corrected, and refinement alone is
> not powerful enough to escape the false minimum.
>
> If you want to turn this feature off, you can add main.nqh_flips=False
> to your refinement call or
>
> main {
>  nqh_flips=False
> }
>
> to your param file. However, we highly recommend leaving this option
> on as it is an excellent diagnostic of model errors.
>
> If you have any further questions please let me know.
>
> Thanks,
> Jeff
>
> On Tue, Mar 1, 2011 at 5:45 PM, Maia Cherney <chern at ualberta.ca> wrote:
>> Hi,
>>
>> I am using now the latest phenix version and I am curious how to understand
>> these lines:
>>
>>
>> Flipped N/Q/H residues before refinement:
>> A  28 HIS
>> A  72 HIS
>> A 141 GLN
>> A 202 GLN
>> A 296 ASN
>> ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
>> ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
>> A 353 ASN
>> A 388 HIS
>>
>> Maia
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>