Re: [ccp4bb] SAD: Refine against anomalous data

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

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Subject: Re: a question about procheck
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2007-08-10

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From: Kim Henrick henrick {- at -} EBI {- dot -} AC {- dot -} UK
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Subject: Re: SAD: Refine against anomalous data
From: "Sanishvili, Ruslan" rsanishvili {- at -} ANL {- dot -} GOV
Date: 2007-08-10

Folks,
Don't take this as an argument with software people - I have a side note about structures.
Back in the day when I used to solve Structural Genomics structures, we almost always knew substitution rate from masspec and Se always refined to lesser occupancy. Could it be the decay instead?
Cheers,
N.

-----Original Message-----
From: CCP4 bulletin board on behalf of Ethan Merritt
Sent: Fri 8/10/2007 11:20 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] SAD: Refine against anomalous data

On Friday 10 August 2007 04:53, Clemens Vonrhein wrote:
> It should be trivial to put this into REFMAC too
> (Garib!): just add cards like
>
> FPRIme

>
> so that a user can do
>
> FPRIme Se -4.5
>
> REFMAC then corrects C by the difference f'(CuKa)-(-4.5) (after
> reading the f'(CuKa) from atomsf.lib).
>
> And suddenly all those partially substituted Se-MET are becoming 100%
> substituted again ... a kind of 'in-silico expression system'.

I heartily endorse this suggestion.
I have been wanting a way to instruct refmac to accept a user-defined
f' term since about forever.

Failing that, it would be nice if the ccp4i interface to refmac had
a slot for specifying an alternative ATOMSF file. As it is one has
to edit the command script by hand in order to change ATOMSF.

A follow-on request is that the entire scattering factor table,
including such user-specified values, be dumped in the output
cif and pdb files.

--
Ethan A Merritt Courier Deliveries: 1959 NE Pacific
Dept of Biochemistry
Health Sciences Building
University of Washington - Seattle WA 98195-7742

CCP4bb navigation

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

Previous message:
Subject: Re: a question about procheck
From: Jiamu Du jiamudu {- at -} GMAIL {- dot -} COM
Date: 2007-08-10

Next message:
Subject: Re: a question about procheck
From: Kim Henrick henrick {- at -} EBI {- dot -} AC {- dot -} UK
Date: 2007-08-11