Hi Peer, Normally, if one defines some residues with an occupancy below 1.0, the nonbonding contact restraints with other residues are switched off. It is already some time ago, but if I recall correctly, I had similar problems that nonbonding contact restraints were not switched off for residues related by crystallographic symmetry if they were not exactly on a crystallographic axis. I don't know if this is the problem that you are facing, but here is what I did in the past:
For Xplor (and I guess the same is true for Phenix), one can explicitly switch on or off any interaction one likes, and did is what I did using Xplor. So you might want to have a look at Phenix. For Buster, I, or better, the global phasing people, created a gelly file to specifically exclude troublesome restraints. Again, I don't know if this is your problem, but if so, I would look at Phenix or Buster to see if you can refine your structure with one of those programs. Best, Herman Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Peer Mittl Gesendet: Donnerstag, 26. August 2021 11:54 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] chain on 2-fold axis? Der CCP4 community, Is there a refinement program that can handle protein monomers sitting on crystallographic 2-folds? This is probably a strange question but we have the following situation. We have a 2.6 Ang datasets in SG P3221 (Rpim=4%, Isa=19.6) and a clear molrep solution with 2 chains, albeit with tNCS (0/0/0.5) that can be refined to around 27/33% Rfactor. According to Vm a third chain could be present. So far so good, but there is clear difference ED for a third chain sitting exactly on the 2-fold. Since the protein has a peculiar shape, one can tell even its orientation. I can relax the symmetry to P32 (or even P1) and place the missing chain with 50% occupancy on the 2-fold. This model can be refined, but I do not like this work around, because the data is clearly P3221. Any hints on similar crystal pathologies and how they have been handled would be helpful. All the best, Peer ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/<https://www.jiscmail.ac.uk/policyandsecurity> ######################################################################## 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/
