Re: [ccp4bb] DM - NCS averaging after phaser molecular replacement run-confused about coefficients

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CCP4bb <-- 2008 <-- April 2008 <-- 04 April 2008

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Subject: Re: Error in configuration of hydroxyproline in HYP.cif
From: "Brick, Peter" p {- dot -} brick {- at -} IMPERIAL {- dot -} AC {- dot -} UK
Date: 2008-04-04

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Date: 2008-04-04

Subject: Re: DM - NCS averaging after phaser molecular replacement run-confused about coefficients
From: "Randy J {- dot -} Read" rjr27 {- at -} CAM {- dot -} AC {- dot -} UK
Date: 2008-04-04

On Apr 4 2008, hari jayaram wrote:

> Hi everyone, I have a phaser molecular replacement solution for my
> membrane protein which crystallized in spacegroup P3. The diffraction
> data is good to about 3.3 A. The model I used had 39% homology to the
> given protein. A solvent content analysis suggests that there probably
> are three dimers in the ASU ( to give about 67% solvent) Phaser
> sucessfuly found two dimers in the ASU with good density and a third
> dimer with very weak almost "non-existent" density. I am now trying to do
> some NCS-averaging using DM to see If I can improve the desnity for dimer
> 3 and have a question about the different co-efficients I should be using
> for the averaging DM run.
>
>Question1:
>The phaser output mtz file has a PHWT and a PHIC . For carrying out DM with
>flattening, averaging and histogram matching which phases do I use PHIC or
>PHWT along with observed Fo. Also for the weight do I use the FOM.
>
>Question2:
>The output mtz from DM run either way above , now has a PHIDM and a PHWT
>along with a FWT and FC. Which coefficients should I be using to get a map
>after DM for building.
>
>FWT and PHWT
>or
>Fo and PHIDM
>or
>FWT and PHIDM.
>
>
>Thank you for your help
>Hari
>

In the MTZ file produced by Phaser, the FWT/PHWT pair provide the 2mFo-DFc
map coefficients that should reduce model bias. I'd suggest starting DM
from these coefficients, which you can do by adding "FDM=FWT PHIDM=PHWT" to
the LABIN command for DM. (If you want to do this from the current ccp4i
GUI for DM, the only way is to use the Run&View Com File command.)

After running DM, the map coefficients to view in coot are FDM/PHIDM.

Good luck!

Randy Read

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CCP4bb <-- 2008 <-- April 2008 <-- 04 April 2008

Previous message:
Subject: Re: Error in configuration of hydroxyproline in HYP.cif
From: "Brick, Peter" p {- dot -} brick {- at -} IMPERIAL {- dot -} AC {- dot -} UK
Date: 2008-04-04

Next message:
Subject: Off-topic: fungus contamination of SF9 cells
From: Filipp Frank filipp {- dot -} frank {- at -} MAIL {- dot -} MCGILL {- dot -} CA
Date: 2008-04-04