Yes. First create in coot alternative conformations for the residues in the loop. Use the "split all of a single residue" option. This is the default. Then use the "rotate/translate zone option" to move one of the conformations to the alternative position. For this you have to select the first and the last alternative residue of the same conformation (either A or B). Within an alternative zone all options like real space refinement and regularize zone work. In the past, including non-alternate residues and alternate residues in one command did not work. I do not know the current status. However, commands like real space refine zone will automatically refine the connecting peptide bond with the flanking (non-alternate) residues. Once building is done, you can just refine the structure with Refmac.
Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Shyamosree Bhattacharya Gesendet: Mittwoch, 27. November 2013 03:54 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] trying to trace main chain of loop region in two alternative ways Hello everyone, The electron density of my structure displays two alternative traces for the main chain in a loop region. Is there a way I can refine the structure with both the alternative main chains in place with 50% occupancy each? Thanks, Shy -- Shyamosree Bhattacharya 4th year Graduate Student Department of Chemistry Forest Lab 1550 Linden Drive Room No. 6541 Madison WI 53706
