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Dear Andreas, did you try the option '-t' to make SHELXE try harder, or other building related options (take a look at the SHELX web page for talks and presentations). Can you make use of the phases without model building? (sfall) Since you seem to get a PDB-file, could you use the coordinates to calculate the phases off it? You can also provide the PDB-file as input file and restart phasing. Best, Tim On Monday, July 10, 2017 5:51:57 PM CEST Andreas Förster wrote: > Dear all, > > since SHELX is now part of CCP4, this question is not entirely off-topic. > > I'm trying to solve structures by S-SAD. Substructure looks weak but ok if > the right resolution cutoff is picked in SHELXD. > > SHELXE is happy to do its thing for a while but then gives up with a > "Peptide occupancy has refined to negative value" error in one hand. The > other hand is quite obviously (CC for partial structure, number of residues > built) wrong, but the PDB obtained with the antimatter peptides looks like > protein, is 80% complete and quite obviously the right solution. > > Because of the error, SHELXE doesn't write phases. How do I get these? (I > could do MR, but there must be a more elegant way...) Better yet, what > might cause the "negative occupancy" error and how do I avoid it? > > Thanks and all best. > > > Andreas -- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - Principal Investigator Biology and Chemistry OFLC/104 CH-5232 Villigen PSI Phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A