I've done that at 6 Å with a large X-ray structure a long while ago and
I think the trick was to define your own groups, by way of example
snipped from the .eff file:
adp {
individual {
isotropic = None
anisotropic = None
}
group_adp_refinement_mode = one_adp_group_per_residue \
two_adp_groups_per_residue \
*group_selection
group = chain A
group = chain B
group = chain C
group = chain D
tls = None
}
}
I wonder if you could define equivalent TLS groups ?
Phil Jeffrey
Princeton
On 12/16/24 9:39 AM, Derek Logan wrote:
Hi everyone,
I would like to do a quick rigid-body refinement of a model against a
low resolution (6 Å) cryo-EM map. The model consists of four tetramers
and I want to refine each tetramer as a rigid body, either with one
(anisotropic?) ADP per tetramer or at the most one per chain. I haven't
yet found a good way to do this. With phenix.refine the default is one
ADP per residue and I can't see how to change that behaviour (at least
through the Phenix GUI). I tried Servalcat but I can't see a way to
restrict it to rigid body only. Given more time, I hope to reach a
fuller understanding of each program, but I need to solve the immediate
problem in the next couple of days (what with Christmas coming up...)
Any suggestions?
I have also understood that the best practice is to refine against the
unsharpened map, correct?
Thanks
Derek
_____________________________________________________
*Derek Logan*
Professor | Biochemistry and Structural Biology
Centre for Molecular Protein Science
Lund University, Box 124, 221 00 Lund, Sweden
www.cmps.lu.se
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