Re: [ccp4bb] refmac fails on iodine ions

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Subject: Re: refmac fails on iodine ions
From: Judith Murray-Rust judith {- dot -} murray-rust {- at -} CANCER {- dot -} ORG {- dot -} UK
Date: 2007-06-06

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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

You need to put on the element column I-1 instead of I. For example

-----
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 -1

regards
Garib

On 6 Jun 2007, at 17:47, Judith Murray-Rust wrote:

> Dear refmac experts, following on from the iodide ion question,
> If I ask coot to get IOD, it lines up the I with C of CA in pdb file.
> Good. But to tell refmac that it is an iodide ion (not a metal) and
> get
> the correct scattering factor, presumably the atom type should be
> changed to I- ?? or have I misunderstood horribly ?
> J
> ----------------------
> Dr Judith Murray-Rust
> Structural Biology Lab
> Cancer Research UK
> London WC2A 3PX
>
>
>> -----Original Message-----
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
>> Behalf Of Garib Murshudov
>> Sent: 06 June 2007 17:14
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] refmac fails on iodine ions
>>
>> 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
>>
>>
>>
>>
>>
>
>

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CCP4bb <-- 2007 <-- June 2007 <-- 06 June 2007

Previous message:
Subject: Re: refmac fails on iodine ions
From: Judith Murray-Rust judith {- dot -} murray-rust {- at -} CANCER {- dot -} ORG {- dot -} UK
Date: 2007-06-06

Next message:
Subject: Post-doctoral Fellowship in Anesthetic Molecular Pharmacology
From: Patrick Loll pat {- dot -} loll {- at -} DREXEL {- dot -} EDU
Date: 2007-06-06