Re: [ccp4bb] REFMAC5 residues with bad geometry

2012-03-24 Thread Garib N Murshudov
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 b

Re: [ccp4bb] REFMAC5 residues with bad geometry

2012-03-24 Thread David Schuller
On 03/24/12 15:15, Kendall Nettles wrote: David, how can you justify reducing occupancy of some parts of amino acids? I don't have to, since I didn't do it. Read again the bit about this being a carryover from the MR model. Cheers, I don't understand this. I can understand deleting stuff

[ccp4bb] REFMAC5 residues with bad geometry

2012-03-24 Thread David Schuller
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 RE