A common lament on Kabat fabs. You need to modify the LINK statement for this purpose for the residues in question.
Read the REFMAC log and PDB and you will see that it recognized the link but still did not use it. The correct format for the link statement needs the 'gap' in the pdb file refmac writes replaced with 'TRANS' I squawked this a while ago. BR -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of John Pak Sent: Thursday, April 05, 2007 7:40 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] antibody refinement in REFMAC with Kabat numbering Hi all. I'm currently refining an Fab structure. All was going reasonably well until I renumbered the PDB according to the Kabat numbering convention. After which, REFMAC does not refine the inserted residues properly (ie. residues 82A, 82B, 100A, 100B, 100C, etc.). It refines these residues into a steric jumble. I think REFMAC can't recognize that the residues are connected or something. So my question is, how do you refine this type of PDB in REFMAC? Or do you just wait until the refinement is done, then change all the residue numbers and connect entries in the header afterwards?
