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:[EMAIL PROTECTED] 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,
[EMAIL PROTECTED] 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
[EMAIL PROTECTED]
