Re: [ccp4bb] refmac fails on iodine ions

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

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

Previous 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

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: Judith Murray-Rust judith {- dot -} murray-rust {- at -} CANCER {- dot -} ORG {- dot -} UK
Date: 2007-06-06

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
>
>
>
>
>

CCP4bb navigation

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

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