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I am refining a structure and am encountering a problem when I put my model through Refmac. I doing manual intervention with O version 10.0.3, and refinement with Refmac version 5.2.0019 in CCP4 6.0.1 using the ccp4i GUI. My structure contains multiple chains that have gaps in the sequence number. This is in order to maintain continuity with other related proteins. Every time I refine my models in Refmac it removes the bonds between these residues that I have just created in O. It is not only annoying, but the resulting maps then have positive Fo-Fc density where the bond should be! I am worried that my R and Rfree are being hurt by the missing bonds during refinement. I have tried telling the program that the residues are linked by pasting links (below) at the top of the pdb after model building in O, but it still removes them. Please help. There must be a way to tell Refmac to leave my bonds alone, but I can't find anything in the Refmac GUI. Is there something I can do if I run Refmac from a .com file? Thanks in advance. LINK C GLN E 59 N GLY E 61 LINK C PHE E 93 N LEU E 96 LINK C LYS E 129 N ASP E 132 LINK C ASP F 62 N GLY F 64 LINK C TYR F 100 N GLU F 105 LINK C SER F 182 N ASN F 186 LINK C TYR F 187 N SER F 189 LINK C GLY M 63 N TYR M 65 LINK C TYR M 100 N GLU M 105 LINK C SER M 182 N ASN M 186 LINK C TYR M 187 N SER M 189 LINK C GLN L 59 N GLY L 61 LINK C PHE L 93 N LEU L 96 LINK C LYS L 129 N ASP L 132 Peter J. Miller Collins Laboratory Department of Biochemistry and Biophysics University of North Carolina at Chapel Hill 919-966-9410
