Hi David Occupancis of input file are very suspicious and not all atoms of resides are present, some occupancies are zero. In refmac zero occupancy means it does not exist. It may explain the problem In refinement we could add an option to make occuancies one if there are no alts but it would be dangerous thing to do.
Since occupancies are suspect I would check input pdb file carefully. regards Garib On 24 Mar 2012, at 18:39, David Schuller wrote: > CCP4 6.2.0 > Refmac_5.6.0117 > Scientific Linux 6.1 > > In my current model, I notice that several sidechains are falling apart, > despite having gone through a few rounds of refinement with REFMAC5 and model > building with COOT. The worst examples were all Glu and Arg residues. > > I tried switch to the REFMAC5 executable on the updates page, which was > Refmac_5.6.0114, with no obvious difference. > > Eventually I noticed that these are all residues containing atoms with > occupancy less than 1.00, which must be a carry over from the MR search > model. I set all the occupancies to 1.00 and this seems to have fixed the > problem. > > This seems counter-intuitive to me. If the occupancies are set low, shouldn't > the geometry restraints be stronger relative to the density refinement? > > Cheers, > > ATOM 1479 N GLU A 7 -51.844 -33.605 37.318 1.00 60.26 N > ATOM 1480 CA GLU A 7 -53.137 -33.849 37.966 1.00 59.28 C > ATOM 1481 CB GLU A 7 -52.997 -33.664 39.476 1.00 61.37 C > ATOM 1482 CG GLU A 7 -52.799 -32.212 39.905 0.48 60.42 C > ATOM 1483 CD GLU A 7 -53.349 -32.573 41.635 0.00 54.47 C > ATOM 1484 OE1 GLU A 7 -52.557 -31.998 42.106 0.83 52.26 O > ATOM 1485 OE2 GLU A 7 -55.014 -32.911 42.408 0.68 50.75 O > ATOM 1486 C GLU A 7 -54.293 -32.985 37.412 1.00 62.61 C > ATOM 1487 O GLU A 7 -55.444 -33.240 37.737 1.00 63.42 O > ATOM 3165 N ARG A 77 -46.032 -33.003 26.272 1.00 55.82 N > ATOM 3166 CA ARG A 77 -44.959 -32.368 27.071 1.00 60.92 C > ATOM 3167 CB ARG A 77 -44.050 -31.428 26.231 1.00 54.56 C > ATOM 3168 CG ARG A 77 -42.702 -31.102 26.892 1.00 69.21 C > ATOM 3169 CD ARG A 77 -42.278 -29.628 26.867 0.46 63.93 C > ATOM 3170 NE ARG A 77 -41.587 -29.303 25.625 0.79 61.76 N > ATOM 3171 CZ ARG A 77 -41.607 -28.610 24.146 0.00 37.32 C > ATOM 3172 NH1 ARG A 77 -43.177 -26.956 23.467 0.85 60.52 N > ATOM 3173 NH2 ARG A 77 -41.267 -28.245 23.427 0.95 58.82 N > ATOM 3174 C ARG A 77 -45.585 -31.698 28.281 1.00 64.89 C > ATOM 3175 O ARG A 77 -45.949 -32.377 29.262 1.00 77.93 O > > > -- > ======================================================================= > All Things Serve the Beam > ======================================================================= > David J. Schuller > modern man in a post-modern world > MacCHESS, Cornell University > schul...@cornell.edu Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
