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: [email protected] > 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] > > > > >
