Re: [ccp4bb] SA composite omit maps in Phenix

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: SA composite omit maps in Phenix
From: Jason C Porta jporta {- at -} UNMC {- dot -} EDU
Date: 2009-10-06

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Subject: Postdoctoral researcher position at SSRL
From: Ana Gonzalez ana {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2009-10-06

Subject: Re: SA composite omit maps in Phenix
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2009-10-06

Hi Jason,

I just replied to very similar question to someone in person.

Your options are:

- all about SA omit maps and more:
http://www.phenix-online.org/documentation/autobuild.htm
ask Tom Terwilliger should you have any questions.

- also, a good thing to check (the best actually; this option is
available):
Acta Cryst. (2008). D64, 515-524
Iterative-build OMIT maps: map improvement by iterative model building
and refinement without model bias

- You can use Average Kick Maps (see above slides) with the region in
question omitted. This is available in phenix.refine. Some details about
kick maps are in the slide #20:
http://cci.lbl.gov/~afonine/rsr/afonine_05OCT2009_.pdf

Please let me know if you have any questions or/and need any help.

Cheers,
Pavel.

On 10/6/09 1:21 PM, Jason C Porta wrote:
> After searching the documentation and archives, I could not find an
> answer to a question regarding Phenix maps.
>
> I am trying to make an Fo-Fc composite omit map of a structure that
> has the solvent deleted. I want to create a map using Fo-Fc as the
> coefficient and with composite omit phases.
>
> How would I do this in Phenix?
>
> Also, what kind of map is being generated by default? What is the FP
> coefficient?
>
> Thanks in advance for any assistance
>
> Sincerly,
>
> Jason Porta
> Doctoral Candidate
> Dept. Biochemistry & Molecular Biology
> University of Nebraska Medical Center
> Omaha, NE 68198
> (402) 559-5533
>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: SA composite omit maps in Phenix
From: Jason C Porta jporta {- at -} UNMC {- dot -} EDU
Date: 2009-10-06

Next message:
Subject: Postdoctoral researcher position at SSRL
From: Ana Gonzalez ana {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2009-10-06