here is an extract from the documentation. is it a help?
i will try to find examples. eleanor This keyword defines number of cycles of refinement. Occupancy refinement (version 5.6.0037) from Tidied up occupancy group id <number> chain <chain1> ... <chainn> residue <number> atom <name> alt <code> or occupancy group id <number> chain <chain1> ... <chainn> residue from <number> to <number> atom <name> alt <code> occuppancy group alts complete/incomplete <id1> ... <id2> occupancy refine ncycle <number? Where id defines occupancy group id. This may be referenced by the command occupancy group alts <id>. Example: occupancy group id 1 chain A # chain A belongs to occupancy group 1 occupancy group id 1 chain B residues from 200 to 500 # all residues between residues 200 and 500 of chain A belong to the group with id 1 occupancy group id 2 chain C residue 250 alt A # all atoms of residue 250 of chain C with alt code A belonge to group 2 occupancy group id 2 chain D residue 250 atom OW # atom OW of the residue 250 of chain d belong to the group 3 occupancy group alts complete 1 2 # occupancy group 1 and two are mutually exclusive. Moreover sum of their occupancise should be equal to 1 (subkeyword complete) occupancy group alts incomplete 1 3 # sum of occupancies of occupancy group 1 and 3 must be less than 1 (and more than 0 obviously) occupancy refine ncycle <number> occupancy refine # refine occupancies. Refinement of occupancy parameters will be carried out at every ncycle-th cycle. Defalt is 1, i.e. occupancy and restrained refinements are carried out one after another at every cycle. If occupancy refine has not been defined then group definitions will only be used in making decision about non-bonded contacts. Atoms belonging to the alternative groups (e.g. group 1 and 2) do not see each other and therefore there is no non-bonding (vdw or other) interaction between them. Of course user can use external restrain <https://docs.google.com/document/d/1jLq687SCyfsndmjrE37aoUBsuEBY6kQHzXSDDIwNT-s/edit#bookmark=id.37wcjv5> t <https://docs.google.com/document/d/1jLq687SCyfsndmjrE37aoUBsuEBY6kQHzXSDDIwNT-s/edit#bookmark=id.37wcjv5> keyword to enforce bonds between mutually exclusive atoms. On Sat, 5 Jun 2021 at 16:40, Marina Gárdonyi < marina....@pharmazie.uni-marburg.de> wrote: > Hello everyone, > > I am trying to refine structures with Refmac. > > The problem is that nobody from my working group is familiar with this > programm. They are using Phenix exclusively. > > That's why I need your help. I would like to refine the occupancy. I > know that I need a keyword file for this, but I have no idea how to > create such a keyword file. > > Can someone maybe send me a sample file? I think that would help me. I > have found essential keywords, but I don't know how to build up such a > file. > > Thank you very much in advance! > > Best regards, > Marina > > -- > Marina Gárdonyi > > PhD Student, Research Group Professor Dr. Klebe > > Department of Pharmaceutical Chemistry > > Philipps-University Marburg > > Marbacher Weg 6, 35032 Marburg, Germany > > Phone: +49 6421 28 21392 > > E-Mail: marina....@pharmazie.uni-marburg.de > > http://www.agklebe.de/ > > ######################################################################## > > 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/ > ######################################################################## 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/
