[phenixbb] [Fwd: Re: number of cycles]

[Maia Cherney]

-------- Original Message --------
Subject: 	Re: [phenixbb] number of cycles
Date: 	Tue, 01 Mar 2011 19:50:57 -0700
From: 	Maia Cherney <chern at ualberta.ca>
To: 	Jeff Headd <jjheadd at lbl.gov>
References: 	<40FBFA09-3C52-460A-A6A1-7D08F6496AD2 at umich.edu> 
<AANLkTin=8_ddvihNSDyLp9k1iSpV9fVj6A2ndvoUTJ6O at mail.gmail.com> 
<0171D39299ABC14AAAA75ABABDD0BBB63868BF23AA at NIHMLBX12.nih.gov> 
<A8FA87FE-7DF1-48BE-AA44-E19BB7D0E6E0 at crystal.harvard.edu> 
<4CAC89B8.9090909 at lbl.gov> <4D12B58C.1030604 at ualberta.ca> 
<4D12E866.9070602 at lbl.gov> <4D138B20.5050001 at ualberta.ca> 
<4D14E51F.2040305 at lbl.gov> <4D164065.3050709 at ualberta.ca> 
<4D165AE5.8090905 at lbl.gov> <4D6C0DB1.5040003 at ualberta.ca> 
<4D6C9271.6000301 at lbl.gov> <4D6DA14C.6060806 at ualberta.ca> 
<AANLkTi=GXvoGWsB+3+NNBNFvVtzc0Q0ag1Ln_U6FqHqO at mail.gmail.com>



Thanks, Jeff.

Though I don't see any clashes for any orientations. But this feature is 
really great.

Jeff Headd wrote:
> 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
>>
>>     
>
>
>