<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Dear Buster users,<div>I am dealing with a pentameric structure composed of two different short (80 aa) polypeptide chains, A and B, that are 40% identical. In the crystal packing it looks to be no preferred orientation for the ring with respect to the two different proteins. I would like to combine the two chains in the same structure and refine with Buster to get the relative occupancy. We know from gel electrophoresis of the two proteins coexpressed that the relation is 3:2 (A to B) between them, both in crystals and in solution. The crystals diffract to about 2.0 Å resolution but the spots are streaky. The R-values when refining with only one of the polypeptide chains are much lower for A compared to B. </div><div><br></div><div>My attempt to do the refinement in Buster using first pdb2occ and then run with the command -Gelly failed with the comment:</div><div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><br></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">Interpreting CONSTANT and FREE cards: </div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> =====NOTE BUSTER_CONSTANT OCC FixOcc</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> *** ERROR found in interpreting atom specifier from CONSTANT card</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> *** ERROR specifier=FixOcc</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> *** ERROR does not match any atoms</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> *** ERROR *** found processing constant cards</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> *** ERROR *** (on call to GELLY_PROCESS_CONSTANT_CARDS_OWN</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"> *** ERROR *** by s/r GELLY_PROCESS_CONST_COMBINE_CARDS_OWN)</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><br></div><div style="margin: 0px;">How should I do to be able to proceed? Is it possible to refine double occupancy on all the five polypeptide chains or is it required that I keep some of them with fixed occupancy?</div><div style="margin: 0px;">Best regards,</div><div style="margin: 0px;">Anna</div><div style="margin: 0px;"><br></div><div style="margin: 0px; font-size: 11px; font-family: Menlo; min-height: 13px;"><br></div><div apple-content-edited="true">
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