Dear all, Thank you for your helpful replies.
The keyword option worked fine for me. I think there is a bug in the GUI. Kind regards, Kyle ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Kyle Gregory <00003632e92fcc15-dmarc-requ...@jiscmail.ac.uk> Sent: 20 November 2024 15:17 To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Dual occupancy refinement in REFMAC5 You don't often get email from 00003632e92fcc15-dmarc-requ...@jiscmail.ac.uk. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Hi James, Thank you for this reply. Yes, I did want to try this but for some reason when I add to the group ID list I cannot change the group ID from 1 to 2 so I cannot define conformer A and B as separate group IDs. I wonder if this is a bug? Kind regards, Kyle ________________________________ From: James Holton <jmhol...@lbl.gov> Sent: 20 November 2024 15:00 To: Kyle Gregory <kg...@bath.ac.uk>; CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Dual occupancy refinement in REFMAC5 CAUTION: This email came from outside of the University. To keep your account safe, only click on links and open attachments if you know the person who sent the email, or you expected to receive this communication. I've never used this GUI, but I know that under the hood you want each A/B to have its own group ID and then specify that the two groups sum to one. The keywords look like this: occupancy refine occupancy group id 1 chain A residue 318 alt A occupancy group id 2 chain A residue 318 alt B occupancy group id 3 chain A residue 400 alt A occupancy group id 4 chain A residue 400 alt B occupancy group id 5 chain A residue 500 atom ZN occupancy group alts complete 1 2 occupancy group alts complete 3 4 occupancy group alts incomplete 5 Where here I am specifying that all of residue 318 is in either A or B and that the sum of every A and B should be 1.00, and all "A" atoms have the same occupancy as other "A" atoms, etc. Same for a residue 400 as well. I am also specifying that there is a Zn atom with unknown occupancy and to refine that too. No need to sum to anything. The GUI in your screenshot may be reflecting this syntax. My go-to documentation for refmac occupancy refinement is here: http://www.ysbl.york.ac.uk/refmac/data/refmac_keywords.html And my jiffy script for setting up keywords like the above given a PDB file is here: https://github.com/jmholton/refmac_tools_jmh/blob/main/refmac_occupancy_setup.com (note that I have uploaded it into github so that it looks like I know what I'm doing) Does that help? -James Holton MAD Scientist On 11/20/2024 6:09 AM, Kyle Gregory wrote: Dear all, I have a 1.5 angstrom resolution crystal structure with 6 residues that have dual conformation. In the past I haven't had this many, so I have refined the occupancies by iteratively adjusting them in coot. I'm trying to refine the occupancies in REFMAC5 using the 'conformer groups and occupancy refinement' option in parameterisation but I'm not getting the results I want. One attempt refined both conformers with an occupancy of 1, another refined both with an occupancy of 0.54. I was wondering if anyone would be able to help with correcting my inputs. I selected 'specify overlapping alternative conformation groups (constrain occupancies to sum to one)' and 'specify partial occupancy groups' where I have added chain 'A' and set residue 'from' and 'to' as both 318 (This was to just test this feature I will add the other 5 residues once it's working). I also have 'perform refinement of atomic occupancies' selected. I can't see what is wrong, I have also tried adding A/B to '(Alt)' column and also duplicating the row to specify the two conformers. Nothing has given me values I would expect (only ever 0.54 or 1.0 for both conformations). Any help would be greatly appreciated. Kind regards, Kyle ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## 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/
