[phenixbb] low res structures and Phenix

Green, Todd green at cbse.uab.edu
Tue Aug 21 07:11:15 PDT 2007


should be volume 62 rather than 26

B. DeLaBarre and *A.T. Brunger*, Considerations for the refinement of 
low resolution crystal structures, /Acta Crystallographica D/ *62*, 
923-932 (2006).

cheers-
todd


-----Original Message-----
From: phenixbb-bounces at phenix-online.org on behalf of Pavel Afonine
Sent: Mon 8/20/2007 8:40 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] low res structures and Phenix
 
Here is a nice discussion about low resolution refinement:

B. DeLaBarre and *A.T. Brunger*, Considerations for the refinement of 
low resolution crystal structures, /Acta Crystallographica D/ *26*, 
923-932 (2006).

Pavel.

Tom Terwilliger wrote:
> Hi John,
>
> I'll answer the first of your questions...
> -Tom T
>
>
>   
>> I have a couple of questions regarding low res structures in Phenix 
>> (about 3.5 angstroms res).
>>
>> 1.  Can Phenix do B-factor sharpening for improved maps?  If not 
>> what program do people usually use for this?
>>     
>
> If you are using the AutoSol wizard, you can use the keywords:
>
> correct_aniso=True   b_overall=20.0
>
> to force correction of any anisotropy in your data and to set the 
> overall B to 20.0.  Note that this will affect all the maps produced 
> by the AutoSol wizard.  I have not yet found this to improve the 
> quality of the resulting model; if it works for you please let me know!
>
>
> You can also use phenix.xtriage to do this:
>
> phenix.xtriage perfect.mtz hklout=output.mtz aniso.action=True 
> aniso.final_b=user_b_iso aniso.b_iso=77
>
> will set the b_iso of perfect.mtz to 77
>
>
>
>   
>> 2.  How can one optimize Ksol and Rprobe (bulk solvent model) in Phenix?
>>
>> 3.  Are there any other suggestions for dealing with low resolution 
>> structures in Phenix?
>>
>> Thanks,
>> John Bruning
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>     
>
>
>
>
> Thomas C. Terwilliger
> Mail Stop M888
> Los Alamos National Laboratory
> Los Alamos, NM 87545
>
> Tel:  505-667-0072                 email: terwilliger at LANL.gov
> Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
> PHENIX web site: http:www.phenix-online.org
> ISFI Integrated Center for Structure and Function Innovation web 
> site: http://techcenter.mbi.ucla.edu
> TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>   
_______________________________________________
phenixbb mailing list
phenixbb at phenix-online.org
http://www.phenix-online.org/mailman/listinfo/phenixbb


This email was scanned with Mcafee's Anti-Virus appliance, but this 
is no guarantee that no virus exists. You are asked to make sure you
have virus protection and that it is up to date.

-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: application/ms-tnef
Size: 4117 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20070821/1002b7ab/attachment-0003.bin>


More information about the phenixbb mailing list