---
>
> Da: Eleanor Dodson
> Inviato: lunedì 4 gennaio 2021 15:43:03
> A: Napolitano Silvia
> Cc: CCP4BB@JISCMAIL.AC.UK
> Oggetto: Re: [ccp4bb] B-factors very high
>
> Well - you dont give the resolution of your data or the "
On 04/01/2021 14:38, Silvia Napolitano wrote:
Dear CCP4 Community,
I am currently working on the structure of a monomeric protein of 23KDa. The protein is
generally quite "loopy" and I think I am mid-way refinement.
At the moment I am struggling, among other things, with an extremely high
B-fac
Dear Silvia,
While high Bs can be a sign that parts of your model are incorrect (and
therefore some careful manual rebuilding may be required), for things like
poorly-ordered surface loops, they can simply be truth.
A point worth remembering for newbies: your goal is to produce the model that
.AC.UK
Subject: Re: [ccp4bb] B-factors very high
Hmm - this is extracted from your log file: it looks more sensible..
2899: b_iso_mean = 66.62
2907: b_iso_min= 63.50 (limit = 1.00)
2908: b_iso_max= 68.13 (limit = 80.00)
2909: b_iso_mean = 66.62
The average B
---
> *From:* CCP4 bulletin board on behalf of Eleanor
> Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
> *Sent:* Monday, January 4, 2021 3:44:33 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] B-factors very high
>
> That polygon is no
Dear Eleanor,
You are absolutely right.
However, in Polygon, you could compare the models selected by resolution, by
size, etc.
I use this occasion to wish you and others a happy New Year !
Sacha Urzhumtsev
- Le 4 Jan 21, à 15:44, Eleanor Dodson
<176a9d5ebad7-dmarc-requ...@jiscma
*Da:* Eleanor Dodson
*Inviato:* lunedì 4 gennaio 2021 15:43:03
*A:* Napolitano Silvia
*Cc:* CCP4BB@JISCMAIL.AC.UK
*Oggetto:* Re: [ccp4bb] B-factors very high
Well - you dont give the resolution of your data or the "wilson B"
which will be recorded in the data processing log.
If the res
iscmail.ac.uk>
Sent: Monday, January 4, 2021 3:44:33 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] B-factors very high
That polygon is not very useful I dont think. The statistics need to be given
separately for structures solved at given resolutions.
Eleanor
On Mon, 4 Jan 2021 at 14:43
That polygon is not very useful I dont think. The statistics need to be
given separately for structures solved at given resolutions.
Eleanor
On Mon, 4 Jan 2021 at 14:43, Eleanor Dodson
wrote:
> Well - you dont give the resolution of your data or the "wilson B" which
> will be recorded in the dat
Well - you dont give the resolution of your data or the "wilson B" which
will be recorded in the data processing log.
If the resolution is 3A or less a) it is hard to refine a B value, and b)
it certainly should be high..
So more information is needed.
Eleanor
On Mon, 4 Jan 2021 at 14:39, Silvia
metric. Perhaps I will do a
little reading and talk to some experts around here.
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ian Tickle
Sent: Tuesday, March 07, 2017 10:27 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] B-factors/Occupancies
>
> Yong
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Ian
> Tickle
> *Sent:* Tuesday, March 07, 2017 9:02 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [EXTERNAL] Re: [ccp4bb] B-factors/Occupancies Versus "Local
> Resolut
Of Ian Tickle
Sent: Tuesday, March 07, 2017 9:02 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] B-factors/Occupancies Versus "Local Resolution"
Hi Jacob
I'm a bit puzzled that you say that what you call 'local resolution' is used
'to model disordered
Hi Jacob
I'm a bit puzzled that you say that what you call 'local resolution' is
used 'to model disordered regions' in cryo-EM. AFAIK it does no such
thing: resolution is certainly used as a _metric_ of the EM map quality but
it's not used for modelling. High resolution EM maps (which I assume i
On Monday, 06 March, 2017 19:54:23 Keller, Jacob wrote:
> Dear Crystallographers (and cryo-EM practitioners,)
>
> I do not understand why there is a discrepancy between what crystallographers
> use to models disordered regions (b-factors/occupancies) and what the cryo-EM
> world uses ("local res
Dear Crystallographers (and cryo-EM practitioners,)
I do not understand why there is a discrepancy between what crystallographers
use to models disordered regions (b-factors/occupancies) and what the cryo-EM
world uses ("local resolution.") I am tempted to say that "local resolution" is
a misno
ce of
B-factor model. It will improve your data/parameter ratio.
HTH,
Robbie
Netherlands Cancer Institute
www.cmbi.ru.nl/pdb_redo
Sent from my Windows Phone
From: Ethan Merritt
Sent: 2013-01-25 01:36
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] B-factor
On Thursday, January 24, 2013 03:52:12 pm Urmi Dhagat wrote:
> Hi all,
>
> I have been refining twinned data (at 3.1 A resolution) using refmac. My R
> and Rfree values are 19.6 and 26.2 respectively with NCS restraints and
> isotropic B-factor refinement.. I am not sure weather it is a good id
On Thu, Jan 24, 2013 at 3:52 PM, Urmi Dhagat wrote:
> If Rfree reflections are refined my refmac upon switching from phenix to
> refmac then does this contaminate the Rfree set ? Should swiching between
> refinement programs Phenix and Refmac be avoided?
Repeating what was said earlier today: i
Hi all,
I have been refining twinned data (at 3.1 A resolution) using refmac. My R and
Rfree values are 19.6 and 26.2 respectively with NCS restraints and isotropic
B-factor refinement.. I am not sure weather it is a good idea to refine
individual B-factors at this resolution.
I have also tr
Dear Brad,
the flexibility, that is how far a protein is stabilized with cold and heat
denaturation of a protein,
this inturn depends on
1.solvation enthalpy of nonpolar moieties(need more energy,so there needs to
be some randomness)
2.shift in temparature due to the enthalpy associated with tra
On Tuesday 13 November 2007 06:41, Brad Bennett wrote:
>
> I would be interested then to know how the community feels about the
> correlation of B-factors to protein flexibility. It is generally accepted
> that these are linked but are there any new papers that address this?
This is the basis of
Hello all:
There are studies, some much older and some relatively new, by Kossiakoff,
Karplus and others showing that B-factors of amide nitrogen atoms are not
correlated to their hydrogen/deuterium exchange behavior. Along similar
lines, I would be interested then to know how the community feels
These are B factors RELATIVE to your TLS parameters.
You need to run tlsanl to get back to something comparable to the
individual B factors..
Eleanor
CRAIG MCELROY wrote:
Hi all,
I'm working on the structure of a heterodimer phased by molecular replacement
using data to 2.9 angstroms. After
Hi all,
I'm working on the structure of a heterodimer phased by molecular replacement
using data to 2.9 angstroms. After MR I performed a rigid body refinement in
CNS, if I then refine using mlf in CNS I get B-factors ranging from ~37-119
and r= 0.26 free_r= 0.35 whereas if I perform a TLS rest
Hey Elizabeth,
To answer your second question first, I think if the atom name for water
is "W", it is read as a density peak by shelxl. If you change "W" to "O",
it will read it as water and refine it.
I have some idea about your question about the B-factor. Arg and Met can
often be seen in alterna
Dear all,
I am refining a perfectly twinned structure at 1.8 A using
Shelxl.Currently the Rfactors/Rfree are 20/28%.
I have a problem with the B-values that I get after refinement. Within the
same residue I may get very low numbers or very high numbers as I show
below:
ATOM415 N ARG 1091
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