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Re: [ccp4bb] w average & riding hydrogens
 

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CCP4bb <-- 2008 <-- January 2008 <-- 02 January 2008
Previous message:
Subject: w average & riding hydrogens
From: Roni Gordon rgordon {- at -} UHNRESEARCH {- dot -} CA
Date: 2008-01-02 		Next message:
Subject: phase combination
From: aka akaka druida236 {- at -} HOTMAIL {- dot -} COM
Date: 2008-01-02


Subject: Re: w average & riding hydrogens
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-01-02
Try the version 5.4
www.ysbl.york.ac.uk/YSBLPrograms/index.jsp

We have fixed this and some other irregular behaviours

Garib

On 2 Jan 2008, at 21:42, Roni Gordon wrote:

> Hi all,
>
> I observed a very strange phenomenon with a high-resolution dataset
> phased via rigid-body refinement (using the apo target); the "generate
> all hydrogens" option seems to throw w_average out of whack:
>
> ========================
> Without riding hydrogens:
> ========================
>
> CGMAT cycle number = 1
>
> w_average 0.320431173
> GRID VALUES:
> 0.109375 Angstrom for D
> 5.18181801 Angstrom^2 for B
>
> R/Rfree: 0.3210/0.3262
> Overall FOM: 0.6653
> ML based su of positional parameters = 0.3351
> ML based su of thermal parameters = 14.0097
>
> After 10 rounds:
> R/Rfree = 0.225/0.283, FOM = 0.755
> RMSD B/A/C = 0.016/1.579/0.107
>
> ========================
> With riding hydrogens:
> ========================
>
> CGMAT cycle number = 1
>
> w_average 7.62235823E-6
> GRID VALUES:
> 0.109375 Angstrom for D
> 5.133333321 Angstrom^2 for B
>
> R/Rfree: 0.3184/0.3261
> Overall FOM: 0.0023
> ML based su of positional parameters = 30945.4297
> ML based su of thermal parameters = *************
>
> After 10 rounds:
> R/Rfree = 0.529/0.551, FOM = 0.012
> RMSD B/A/C = 1.558/49.687/10.240
>
>
> I've never seen such drastic behaviour before, especially with
> something
> so benign as riding hydrogens. Toggling this parameter alone seems to
> cause the aforementioned effects (i.e. success vs utter failure).
>
> I'm using Refmac v5.2.0019 from CCP4 6.0.2.
>
> Any thoughts/suggestions?
>
> Thanks,
>
> Roni Gordon
>

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CCP4bb <-- 2008 <-- January 2008 <-- 02 January 2008
Previous message:
Subject: w average & riding hydrogens
From: Roni Gordon rgordon {- at -} UHNRESEARCH {- dot -} CA
Date: 2008-01-02 		Next message:
Subject: phase combination
From: aka akaka druida236 {- at -} HOTMAIL {- dot -} COM
Date: 2008-01-02


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