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
[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]
