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Re: [ccp4bb] refmac fails on iodine ions
 

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CCP4bb <-- 2007 <-- June 2007 <-- 06 June 2007
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Subject: Re: refmac fails on iodine ions
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-06-06 		Next message:
Subject: Drug Discovery Workshop, Oxford, September 10-14
From: barry {- dot -} hardy {- at -} TELE2 {- dot -} CH barry {- dot -} hardy {- at -} TELE2 {- dot -} CH
Date: 2007-06-06


Subject: Re: refmac fails on iodine ions
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-06-06
Residue name of iodine should IOD. Otherwsie there is a clash of
names with some other residue names (ionisine)

Garib

On 6 Jun 2007, at 16:56, alexander.pautsch@boehringer-ingelheim.com
wrote:

> Dear All,
>
> I am having trouble with refmac dictionaries when refining a
> structure that contains an iodine ion.
> the PDB entry should be correct and according to the convention
> (water added for comparison):
> -----
> ATOM 2838 O HOH W 102 6.018 39.720 31.127 1.00
> 21.43 O
> ATOM 2839 I I B 1 19.956 22.770 18.597 1.00
> 30.00 I
> -----
>
>
> refmac hovever comes up with the following error:
> -----
> ......
> Number of chains : 3
> I am reading library. Please wait.
> mon_lib.cif
> Open failed: Unit: 7, File: /xray/CCP4-6.0.1/ccp4-6.0.1/lib/data/
> monomers/i/IR.cif (logical: /xray/CCP4-6.0.1/ccp4-6.0.1/lib/data/
> monomers/i/IR.cif)
>
> Refmac_5.2.0019: Open failed: File: /xray/CCP4-6.0.1/ccp4-6.0.1/
> lib/data/monomers/i/IR.cif
>
> Times: User: 1.4s System: 0.0s Elapsed: 0:01
> -----
>
> I figured that it tries to read the wrong dictionary (although the
> correct one ( I.cif) is present in the same directory). Explicitly
> supplying I.cif with a LIB_IN card does not help
>
> thanks for your help
>
> alex
>
>
> PS:probably this has been on the bb in the past, but I could not
> dig it out
>
> Dr. Alexander Pautsch
> Protein Crystallography /Structural Research
> Boehringer Ingelheim Pharma GmbH & Co. KG Deutschland
> Birkendorferstrasse 65
> 88400 BIBERACH, Germany
> tel. +49 - (0)7351 - 54 4683
> fax. +49 - (0)7351 - 83 4683
> email alexander.pautsch@bc.boehringer-ingelheim.com
>
>
>


CCP4bb navigation

CCP4bb <-- 2007 <-- June 2007 <-- 06 June 2007
Previous message:
Subject: Re: refmac fails on iodine ions
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-06-06 		Next message:
Subject: Drug Discovery Workshop, Oxford, September 10-14
From: barry {- dot -} hardy {- at -} TELE2 {- dot -} CH barry {- dot -} hardy {- at -} TELE2 {- dot -} CH
Date: 2007-06-06


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