Low tech but simple.
Exclude both conformers from the refinement. (set occs to 0.00 so you still
see the coordinates in COOT)
Look at the difference map density and make a rough estimate of occupancy
from peak heights for a "fixed" bit of the conformers..
The relative ratios for different states s
I would be tempted to try phenix.ensemble_refinement instead.
Look at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3949522/
or
https://phenix-online.org/phenixwebsite_static/mainsite/files/presentations/ensemble_refinement_burnley_at_al_10DEC2012.pdf
or https://elifesciences.org/articles/00311
T
Hi,
I should be a bit more specific.
We have many crystal structures to indicate that a loop adopts conformation
A and conformation B, or - the loop can be disordered where the electron
density is washed out. These states are dependent on how we perturb the
system.
We have a series of data, as
Dear Matt,I believe this study we made may well assist your evaluations:-(IUCr) Experience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystalsjournals.iucr.orgBest wishes,John Emeritus Professor John R Hell
Hi Matt,
this can be done with SHELXL, even at 2-3A resolution. Anomalous data
do help reduce the correlation between B-factor and occupancy
(see e.g. https://doi.org/10.1126/science.1254840 to stick with Pavel's
example)
SHELXL prints the correlation coefficient between occupancy and
b-factor,
Well - occupancy refinement is particularly imprecise, and highly
correlated with temperature factors.
Also the population for a surface ARG or LYS may well have more than two
conformations, whereas some internal residue is better defined.
There is also the Q of solvent - dual occupancies will gene
Hi Matt,
I believe figure 3 here:
https://www.nature.com/articles/s41467-018-06957-w
is relevant to your question.
Pavel
On Tue, Sep 5, 2023 at 11:32 AM Matt McLeod wrote:
> Hi all,
>
> I am trying to get some insight in the accuracy/precision of occupancy
> refinements. I have done some 2-sta
Hi all,
I am trying to get some insight in the accuracy/precision of occupancy
refinements. I have done some 2-state occupancy refinements and have observed
the refinement achieving ~0.25-0.3 occupancy for the minor population. This
population, when observing the electron density maps, had es
, Jose A.
; Schreuder, Herman /DE
Cc: CCP4BB@jiscmail.ac.uk
Betreff: [EXTERNAL] Re: [ccp4bb] Occupancy refinement of overlapping electron
density of a residue and ligand
EXTERNAL : Real sender is prvs=1214477c0d=t...@em.uni-frankfurt.de
Dear Dale, Jose, Herman,
For Dale,
The contour level
019 07:58
> An: Schreuder, Herman /DE
> Cc: CCP4BB@jiscmail.ac.uk
> Betreff: [EXTERNAL] Re: [ccp4bb] Occupancy refinement of overlapping
> electron density of a residue and ligand
>
> EXTERNAL : Real sender is prvs=1214477c0d=t...@em.uni-frankfurt.de
>
>
>
> Hi Herman,
>
>
. November 2019 07:58
An: Schreuder, Herman /DE
Cc: CCP4BB@jiscmail.ac.uk
Betreff: [EXTERNAL] Re: [ccp4bb] Occupancy refinement of overlapping electron
density of a residue and ligand
EXTERNAL : Real sender is prvs=1214477c0d=t...@em.uni-frankfurt.de
Hi Herman,
Thanks for the suggestion
. November 2019 07:30
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] Occupancy refinement of overlapping electron
density of a residue and ligand
EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk
Hi Nestor,
I think the reason for Arg side chain to curl up is because I refined
ther than
refine occupancies. Seems that the Arg side chain is curled up
Nestor
-Original Message-
From: CCP4 bulletin board On Behalf Of Heng-Keat Tam
Sent: Tuesday, November 5, 2019 10:55 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Occupancy refinement of overlapping elect
Dear HK,
If you believe that R120 only adopts one conformation then you should not
refine the occupancies of the side chain atoms. It makes no physical sense to
have occupancies less than one for these atoms, but occupancy equal to one for
the rest of the protein (unless you believe the side ch
Dear HK,
No that's not quite correct - 'occupancy group alts complete' means that both
R120 and the ligand are constrained so that their occupancies sum to unity. In
contrast, 'occupancy group alts incomplete' means that the occupancies of R120
and the ligand will not be constrained to sum to u
Dear all,
I have problem with occupancy refinement by Refmac5 for an overlapping electron
density of part of residue (an arginine) and part of ligand (tetracyclic
compound) (attached figures in Dropbox with a link as shown below).
https://www.dropbox.com/sh/ppmfp5dnpy1b9e9/AAAV79bOzPHQUrVYp9loM
Hi Mike,
Is it reasonable to refine occupancy in phenix at 2.2 A resolution?
>
yes, but only for those atoms that need it.
FYI: there is a Phenix mailing list for Phenix-specific questions.
Pavel
Dear all,
Is it reasonable to refine occupancy in phenix at 2.2 A resolution?
Thank you.
Mike Colaneri
You are right that refining occupancy and B value at the same time cant
be done with REFMAC, and probably wouldnt work anyway at 2.9A
However, if you set the ligand occupancy to 0.7 say, and refine the
residue B factors, the occupancy should not be set back to 1.0. It
certainly isnt in the local
Dear CCP4ers,
While trying to refine a protein-ligand structure (reso=2.9A) I notice that
the density (2Fo-Fc)for the ligand is discontinuous. I also notice that the
density for the residues in the ligand binding pocket (LBP) is also very
feeble. And when I refine the ligand occupancy the density
Dear All,
I have a question about the occupancy refinement of a ligand. I have a
dataset of 2.3 angstrom and the ligand binds in multiple conformations in
the active site.
My question is if it is possible to tell which orientation(s) has/have the
highest occupancy based on occupancy refinement.
W
Zheng Zhou wrote:
Hi, Ed
I am dealing the similar problem. I checked CNS qindividual.inp. But how
do I refine one compound with two or more possible conformations (mainly
due to one bond rotation), each of wihich has a different occupancy?
Thanks in advance.
Hi Zheng,
Others can answer bet
Hi, Ed
I am dealing the similar problem. I checked CNS qindividual.inp. But how do
I refine one compound with two or more possible conformations (mainly due to
one bond rotation), each of wihich has a different occupancy? Thanks in
advance.
Joe
On Dec 17, 2007 2:24 PM, Edward Berry <[EMAIL PROTE
I thought that I would never have to disagree with both Eleanor and
Tassos in the same email, let alone risk being burnt at a stake as a
heretic for doubting the Gospel according to Kleywegt, but in my
but ... but ... i haven't even said anything! i'm innocent! my name is being
used in vain!
I think the correlation between occupancy and B-factor depends
also on the size of the ligand (relative to resolution).
Bob Stroud, I think, has estimated occupancy by comparing
the integrated electron density of the ligand with that of
a well-defined, isolated water (assumed to be at unit occuanc
In the danger of getting corrected by George twice in the same time
(burning stakes excluded...)
I am not doubting at all if its doable, but if the final result will
be more accurate / useful.
Thinking about it, with 1.5 A data it is very likely to be more
accurate than manual handling,
but
I would also ask what is the actual goal in refining the occupancy of the
ligand?
While I agree wholeheartedly with George, the B-factors will adequately
model a lower ligand occupancy. Usually the question you want to resolve
is "Is the ligand really bound in the active site, or is this an artif
I thought that I would never have to disagree with both Eleanor and
Tassos in the same email, let alone risk being burnt at a stake as a
heretic for doubting the Gospel according to Kleywegt, but in my
experience, given the very fortunate position that you have data to
1.5A, the refinement of o
I have already changed occupancies as Eleanor mentioned, and got
approximate values. But my hope is to try to get much precise ones if
possible.
I never expected to preach the 'Kleywegt Gospel' in the ccp4bb,
but in this case what you need is more accurate answers, not more
precise ones
(or be
ou mentioned.
Isaac
--
Dr Isaac Westwood
Department of Pharmacology
University of Oxford
Mansfield Road
Oxford
OX1 3QT
tel: 01865 271595
email: [EMAIL PROTECTED]
From: Eleanor Dodson <[EMAIL PROTECTED]>
Date: 2007年 12月 17日 19:02:28:JST
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4b
I dont think REFMAC can refine occupancy, but the way I would tackle it
is to first refine B factors, then if those for the ligand are much
higher than for the protein maybe test changing those occupancies to 0.7
, 0,5 and so on..
But in fact B factors and occupancies are highly correlated, an
Dear all,
This is my first mail to CCP4BB.
I'm now refining crystal structures of an enzyme at a resolution of
1.5A using refmac5 through CCP4i. Before X-ray data collections,
the substrate and co-factor ions were soaked into the crystals. Their
occupancies seem to be less than the unity because
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