Dear Derek,
When using servalcat refine_spa_norefmac, you can:
* fix ADPs with the option --adp fix
* or set very high weight for the ADP restraints:
--adpr_weight ADPR_WEIGHT ADP restraint weight (default: 1.000000)
You can also play with jelly body options:
--jellybody Use jelly body restraints
--jellybody_params sigma dmax Jelly body sigma and dmax
(default: [0.01, 4.2])
Map blurring is also available:
--blur BLUR Sharpening or blurring B
All available options are listed when running this command:
servalcat refine_spa_norefmac -h
Cheers,
Martin
On 16/12/2024 14:59, Guillaume Gaullier wrote:
Hello Derek,
You might receive more answers if you post cryoEM questions to the
CCPEM list: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=ccpem
<https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=ccpem>
Not sure why you need to refine a B-factor, at this resolution it
won't tell you much, even with only one per chain or per tetramer.
For the rigid-body fit, I suggest following one of the approaches I
mentioned in this other discussion:
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;f355f637.2411
<https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;f355f637.2411>
You can subsequently run phenix.real_space_refine with coordinate
refinement turned off and B-factor refinement turned on: you will get
one B-factor per atom, but then you could take the chain- or
tetramer-average as your final value?
Regarding which map to refine against: phenix and servalcat both
accept or even require half-maps as input, so you mostly don't get to
choose. Half-maps are always assumed to be un-filtered/un-sharpened
(which is how they are when taken fresh out of your cryoEM 3D
refinement job, at least in RELION and CryoSPARC).
Whether using a sharpened map is justified for coordinate refinement
(if your model refinement program of choice accepts a single map) is
worth asking and discussing. But for B-factor refinement you need the
"raw" map, because with enough sharpening you could drive atomic
B-factors to any arbitrarily low value, and in this case they would no
longer describe the experimental uncertainty (and I don't know what
else one would need atomic B-factors for).
I hope this helps,
Guillaume
------------------------------------------------------------------------
*From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Derek
Logan <0000ac2332bb2871-dmarc-requ...@jiscmail.ac.uk>
*Sent:* Monday, December 16, 2024 3:39:34 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] Cryo-EM rigid body with 1 ADP per chain
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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