Dear all,
I have a modelling problem, which probably has something to do with the solvent mask. There is a positive density blob at the surface of my protein, which I can more or less satisfy with a Hepe (EPE). Hepes is in the buffer, the sulfonic acid H-bonds to a lysine side chain and a main chain N, one of the ring nitrogens to a glutamate side chain. At occupancy 1.0 I get B-factors twice as high as the protein and negative difference density. Thus, I set the occupancy to 0.5 and get the whole EPE covered in positive difference density at 3 sig, peaking at 6 sig. This positive density is much larger than without EPE. On first glance, this looked contradictory to me: more positive density after putting more atoms there. I can only guess that the solvent at the place of the EPE is set to 0 (instead of 0.5), so I get positive density because of only 0.5 occupied EPE. Can I refine with half a ligand and half solvent? Greetings Gottfried I should add that I am refining with refmac version 5.8.0419. parameters: SCALE TYPE SIMPLE SOLVENT YES Sorry for the confusion because of hijacking another thread of the bulletin board. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
