Dear all,
I am wondering - isn't such a line missing?
occupancy refine ncycle 5
(another number of cycles than 5 can be specified)
We will implement specification of the number of occupancy refinement
cycles in the i2 task.
By the way, me (as a user) prefer to set occupancy manually to get
B-values comparable to neighbour atoms. (It usually needs few iterations
as B-values need to be checked after refinement.)
Cheers,
Martin
On 20/11/2024 15:00, James Holton wrote:
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
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