Dear list, In my structure there are some residues in alternative conformations that I would like to refine. I have mostly run Phenix for refinement but recently, I have switched to Refmac and since I have no much of experience I dig into the ccp4 archive and found some tips from Eleanor Dodson and James Holton.
I am currently running refmac from ccp4i2 (ccp4-8.0.015). In this interface, when you specify partial occupancies group, a table appears where you can set Group ID, chain, from residue, to residue, (atom) and, (alt). In my case, Group ID is always 1 and I cannot change it into a different value, which is contrary to what James shared in his examples (shown below) # typical lysozyme % refmac_occupancy_setup.com <http://refmac_occupancy_setup.com/> 193l.pdb occupancy refine occupancy group id 1 chain A residue 1 alt A occupancy group id 2 chain A residue 1 alt B occupancy group id 3 chain A residue 59 alt A occupancy group id 4 chain A residue 59 alt B occupancy group id 5 chain A residue 86 alt A occupancy group id 6 chain A residue 86 alt B occupancy group id 7 chain A residue 109 alt A occupancy group id 8 chain A residue 109 alt B occupancy group alts complete 1 2 occupancy group alts complete 3 4 occupancy group alts complete 5 6 occupancy group alts complete 7 8 My first questions are - If you do not introduce any value in the table, can refmac recognize alternative conformations from the input pdb and refine them? - Could it be that there issome issue in my setup for running Refmac? No idea about where the mistake is. Any help will be really appreciate. Best, Marian Marian Oliva CSIC-Centro de Investigaciones Biológicas Margarita Salas 9, Ramiro de Maeztu 28040-Madrid (Spain) phone: 0034 91 1097301 e-mail: mar...@cib.csic.es **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. ######################################################################## 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/
