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Re: [ccp4bb] refmac fails on iodine ions
 

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CCP4bb <-- 2007 <-- June 2007 <-- 06 June 2007
Previous message:
Subject: refmac fails on iodine ions
From: alexander {- dot -} pautsch {- at -} BOEHRINGER-INGELHEIM {- dot -} COM alexander {- dot -} pautsch {- at -} BOEHRINGER-INGELHEIM {- dot -} COM
Date: 2007-06-06 		Next message:
Subject: Re: refmac fails on iodine ions
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-06-06


Subject: Re: refmac fails on iodine ions
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-06-06
Two things I think
1) I is a metal so you need to move the atom name 1 space to the left -
more like this:
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

And the monomer library calls this IOD so I guess you need

ATOM 2838 O HOH W 102 6.018 39.720 31.127 1.00
21.43 O
ATOM 2839 I IOD B 1 19.956 22.770 18.597 1.00
30.00 I

Eleanor

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
>
>
>

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CCP4bb <-- 2007 <-- June 2007 <-- 06 June 2007
Previous message:
Subject: refmac fails on iodine ions
From: alexander {- dot -} pautsch {- at -} BOEHRINGER-INGELHEIM {- dot -} COM alexander {- dot -} pautsch {- at -} BOEHRINGER-INGELHEIM {- dot -} COM
Date: 2007-06-06 		Next message:
Subject: Re: refmac fails on iodine ions
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-06-06


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