Posted on behalf of Gert Vriend:
This article didn't make it to Nature Methods (...), but might be of interest
to theoreticians interested in B-factor distributions:
https://journals.calstate.edu/pump/article/view/2409/2168
Gert Vriend
#
> If I am not wrong, I remember that someone proposed to standardize
> B-factors of protein atoms as “BS = B - Bave”, where Bave is the average
> B-factor of the protein.
This will make some of BS negative (if B
Dear Oliviero,
On one aspect of your query, this analysis dissected the different sources
of disorder contributions to B factors:-
Diamond, R Acta Cryst (1990). *A46*, 425-435
All best wishes,
John
On Thu, Apr 5, 2018 at 2:49 PM, Oliviero Carugo <
oliviero.car...@univie.ac.at> wrote:
> Dears,
>
On Thursday, 05 April 2018 15:49:44 Oliviero Carugo wrote:
> Dears,
>
> everybody knows that B-factors may change amongst different crystal
> structures and that they need to be standardized when different protein
> crystal structures are compared.
>
> If I am not wrong, I remember that someone
Oliviero,
We published a paper in 2003 in which we normalized B-factors
to do a comparison of relative mobility or flexibility. The reference
is: Gourinath et al. Structure 11:1621-1627 (2003). The jargon
we used for Bave of the protein is . In our case, to be
conservative in our interpretatio
Dears,
everybody knows that B-factors may change amongst different crystal
structures and that they need to be standardized when different protein
crystal structures are compared.
If I am not wrong, I remember that someone proposed to standardize
B-factors of protein atoms as “BS = B - Bave”
g to my request below.
>
> To be explicit, my question relates to B-factor blurring (+B correction), not
> to B-factor sharpening (-B correction).
>
> thanks
>
> Mike
>
>
> Begin forwarded message:
>
>> From: Mike Lawrence
>> Subject: [ccp4bb
My sincere thanks to all who are responding to my request below.
To be explicit, my question relates to B-factor blurring (+B correction), not
to B-factor sharpening (-B correction).
thanks
Mike
Begin forwarded message:
> From: Mike Lawrence
> Subject: [ccp4bb] B-factor blurring
Another useful reference:
Liu C & Xiong Y (2014). Electron Density Sharpening as a General
Crystallographic Technique. *J. Mol. Biol.* 426, 980-993.
http://www.ncbi.nlm.nih.gov/pubmed/24269527
Ho Leung Ng
University of Hawaii at Manoa
Assistant Professor, Department of Chemistry
h...@hawaii.edu
Mike,
you can have a look here (from page 52 and on):
http://phenix-online.org/presentations/fem_06MAY2014.pdf
There it is shown that map kurtosis can be used as an optimization
criterion for choosing the best sharpening B.
Pavel
On Mon, Nov 17, 2014 at 5:01 PM, Mike Lawrence wrote:
> Dear
Hi Mike,
my favourite summary on B factor sharpening/blurring is here:
Acta Crystallogr D Biol Crystallogr. 2006 Aug;62(Pt 8):923-32. Epub 2006
Jul 18.
Considerations for the refinement of low-resolution crystal structures.
DeLaBarre B, Brunger AT.
Hope that helps,
Tomas
On Mon, Nov 17, 2014 at
Dear all
can anyone help me with literatures references to B-factor blurring as a
technique to reveal low resolution features in an electron density map? I have
seen the poster from Andrea Thorn at
http://shelx.uni-ac.gwdg.de/~athorn/pdf/thorn_iucr2014_poster.pdf
but was wondering if there wer
Dear all,
I received a few replies to my request, all but Pavel's privately.
Those included suggestions of using moleman2, pymol, baverage (from ccp4).
Several required manual intervention like visual selection of the
responding atoms, which made them less appealing to me.
I used Robbie Joosten'
Hi Tim,
a non-ccp4 solution (since you haven't gotten any suggestion yet)..
1) Get atom selection of atoms involved into ion coordination:
phenix.metal_coordination model.pdb
2) Using atom selection from above extract portion of PDB that contains
atoms in question:
phenix.pdb_atom_selection mode
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear all,
could anyone suggest a way to get the average B-factor from a PDB-file
of those atoms a specific ion binds to (e.g. as judged by header LINK
records or a distance interval)?
I would like to get this number for all K-ions from a set of
PDB-f
Indeed! If the B factors are rather large compared to the globular protein
core (assuming there is a globular core being that the protein
crystallized), one can make the assumption, especially within a loop
region, that this is an indirect measurement of flexibility. However,
as Jürgen pointed out,
yes - but keep in mind your protein is in the context of the crystal lattice,
so flexible regions in solution are likely to be stabilized in the crystal
lattice. So if you color by B also look at the symmetry mates.
And you should also submit both structures to the TLSMD server and look at
those
Dear all
Can B factor in the crystal structure be the criteria to look into the
flexibility of a region or domain.? Also if two structures are at
different resolutions.
Faisal
--
Hi Amit,
you can manually define the range of a spectrum in PyMol:
spectrum [parameter], [spectrum type], minimum=[min], maximum=[max]
--> if you want to color according to B-factor this will translate to
e.g. :
spectrum b, blue_white_red, minimum=0, maximum=50
hth, Arjen
On May 12, 2011,
Hi Amit,
you can manually define the range of a spectrum in PyMol:
spectrum [parameter], [spectrum type], minimum=[min], maximum=[max]
--> if you want to color according to B-factor this will translate to
e.g. :
spectrum b, blue_white_red, minimum=0, maximum=50
hth, Arjen
On May 12, 2011,
hello sir ,
in chimera its available in module Render by Attribute. go
through this link
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html
.
regards
On Fri, May 13, 2011 at 12:01 AM, Luthra,Amit wrote:
> Hey all,
>
> I would like to make one ribbon dia
Hey all,
I would like to make one ribbon diagram of the structure showing the B
factor in different colors (contour levels).
I am using pymol but it is not representing the perfect contour level of B
factor. Is any other program where I can change the color according to B factor?
Thanks
Ami
Dear Crystallographers,
do any of the commonly-used superposing algorithms weight
superpositions by b-factors? Seems like it would be a good idea, so I
assume it is implemented somewhere?
Jacob Keller
--
***
Jacob Pearson Keller
Northwestern University
Me
Hi All
Seems Roberts suggestion has worked.
Thank you Robert
Best Gina
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Clayton, Gina Martyn
Sent: Wednesday, March 31, 2010 4:34 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] B factor
Subject: Re: [ccp4bb] B factor Coloring in Pymol
Hi Gina,
On Wed, 31 Mar 2010 15:00:34 -0400 "Clayton, Gina Martyn"
wrote:
> I am trying to colour a structure by B factor in Pymol. More
> specifically I am colouring conserved residues (value in b factor). I
> want to use 4
b Nicholls
Sent: Wednesday, March 31, 2010 3:14 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] B factor Coloring in Pymol
Hi,
I'm aware of two ways to do this:
by writing the colour as a word, e.g:
color white, (mypdbfile//A/*/*)
which will colour a whole chain.
Or by using rgb colours,
Hi Gina,
On Wed, 31 Mar 2010 15:00:34 -0400 "Clayton, Gina Martyn"
wrote:
> I am trying to colour a structure by B factor in Pymol. More
> specifically I am colouring conserved residues (value in b factor). I
> want to use 4 colours - say white, yellow, orange, red. However it
> seems that Pymo
Hi,
I'm aware of two ways to do this:
by writing the colour as a word, e.g:
color white, (mypdbfile//A/*/*)
which will colour a whole chain.
Or by using rgb colours, e.g:
set_color newcolor0 = [1,1,1]; color newcolor0, (mypdbfile//A/2/*)
which will colour individual residues (residue 2 in this
Dear Everyone
Slightly off topic...
I am trying to colour a structure by B factor in Pymol. More
specifically I am colouring conserved residues (value in b factor). I
want to use 4 colours - say white, yellow, orange, red. However it
seems that Pymol now only allows 3 colours to be used - I t
Sampath Natarajan wrote:
Dear All,
I am refining a structure with 2.5A resolution by refmac5. I
could find the solution by MR using molrep. After fitting the model, I
refined the structure again with 0.3 weighting term, but the output PDB file
shows many splits in the residues. So I us
Hi,
What is the lower limit of the weighting term one can use. If the data is
around 2A can one use 0.04 or less and which type of refinement is more useful
when one is doing the initial refinement (isotropic, aisotropic, overall or
mixed).
sincerely
Debajyoti
On Tue, 17 Jun 2008 Roger R
On Tuesday 17 June 2008 09:08:24 am Sampath Natarajan wrote:
> Dear All,
>I am refining a structure with 2.5A resolution by refmac5. I
> could find the solution by MR using molrep. After fitting the model, I
> refined the structure again with 0.3 weighting term, but the output PDB file
On 17 Jun 2008, at 19:56, Roger Rowlett wrote:
Sampath Natarajan wrote:
Dear All,
I am refining a structure with 2.5A resolution by
refmac5. I could find the solution by MR using molrep. After
fitting the model, I refined the structure again with 0.3
weighting term, but the ou
Sampath Natarajan wrote:
Dear All,
I am refining a structure with 2.5A resolution by refmac5.
I could find the solution by MR using molrep. After fitting the model,
I refined the structure again with 0.3 weighting term, but the output
PDB file shows many splits in the residues. So I
Dear All,
I am refining a structure with 2.5A resolution by refmac5. I
could find the solution by MR using molrep. After fitting the model, I
refined the structure again with 0.3 weighting term, but the output PDB file
shows many splits in the residues. So I used 'auto' as a weighting te
in ccp4, "baverage" does the job.
Mark
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
On 4 Jun 2008, at 21:40, xu zhen wrote:
Hi, everyone,
I am preparing the table of data collection and ref
xu zhen wrote:
> Hi, everyone,
>
> I am preparing the table of data collection and refinement statics. In this
> table, I need to list the average B factor of protein, ligand and water
> seperately, can you tell me how to calculate thoes numbers?
>
> Zhen
> __
For example,
this will show you complete statistics about B-factors:
phenix.pbdtools your_model.pdb --show-adp-statistics
this will show you complete statistics about stereochemistry:
phenix.pbdtools your_model.pdb --show-geometry-statistics
For more information:
http://www.phenix-online.org/
Hi, everyone,
I am preparing the table of data collection and refinement statics. In this
table, I need to list the average B factor of protein, ligand and water
seperately, can you tell me how to calculate thoes numbers?
Zhen
_
Hi all,
I know this was most addressed by Eleanor back on June 14, 2007... and
I've had no problems making such "sharpened" maps. But I'm confused as
to why FFT decides to put "SCALE 2.0 -100.0" in the command file by
default, and not "SCALE 1.0 -100.0"; I've been correcting this manually.
Any th
There is a CAD option to apply a scale and B factor to any set of data,
and an FFT option to apply a scale and B factor to any column in the map.
Check the documentation for whether you need SCALE 1 -10.0 or SCALE 1
+10.0 !
Eleanor
Jeff Lee wrote:
Hi,
I have a question for everyone. I want
:23 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] B-factor sharpening in CCP4 or Coot
Eleanor was kind enough to modify truncate years ago for me to do this -
I would guess the feature is still there.
Thanks again Eleanor!
Steve
-Original Message-
From: CCP4 bulletin board [mailto
@JISCMAIL.AC.UK
Subject: [ccp4bb] B-factor sharpening in CCP4 or Coot
Hi,
I have a question for everyone. I wanted to up-weight my high
resolution terms in my electron density map by applying a B-factor
sharpening term. I have mtz files produced from DM and I usually use
Coot to generate my
Hi,
I have a question for everyone. I wanted to up-weight my high
resolution terms in my electron density map by applying a B-factor
sharpening term. I have mtz files produced from DM and I usually use
Coot to generate my electron density maps. I was wondering is there
an easy way to a
On Tuesday 05 June 2007 12:19, Edward A Berry wrote:
> You have a good point there and I would be interested in hearing
> some other opinions, so I take the liberty of reposting-
>
> My instinctive preference is that each structure should be
> supported solely by the data that is deposited with it
I think the relevant point in this discussion is that the original paper
discussed the apo and substrate complexes of the protein. For the
structure with lower resolution data you may indeed get a better model
by taking the high resolution model and just applying rigid body
refinement to it. Af
Wouldn't the desirability of this depend on the extent to which the
molecule has moved between the high-resolution and low-resolution
datasets ? I would have thought that there was an effective information
transfer between R-work and R-free once the rigid body movements became
too large, which
You have a good point there and I would be interested in hearing
some other opinions, so I take the liberty of reposting-
My instinctive preference is that each structure should be
supported solely by the data that is deposited with it -
(one dataset one structure) but in terms of good science
we
Hi All,
Thanks a lot for all reply with valuable inputs. In my original
post: I meant a = b "does not equal" c. I used # for "does not equal".
Many asked where is that paper published! Actually the paper is
under revision. When reading, I assumed the unit cell dimensions (or
the space g
Yes; a==b for P6i - prob. a typo..
B factors at 3.2A are hard to fix - it will depend on scaling convention
to some extent..
Can you download the data and re-run refinement for your own satisfaction.
If R ==Rfree for the complex then I suspect they did not transfer the
FreeR flags from the a
Hi Ibrahim,
On 04/06/07, Ibrahim M. Moustafa <[EMAIL PROTECTED]> wrote:
Hi all,
While reading a crystallographic paper describing the structure
of an apo-protein and its complex I noticed that
the authors described the space goup as P6122 for the unit cell:
a=141.9, b=143.9, c=380.4
Ibrahim M. Moustafa wrote:
The last question: In the same paper, for the complex structure R and
Rfree are equal (30%) is that an indication for improper refinement in
these published structure? I'd love to hear your comments on that too.
Several times I solved low resolution structures using
Hi all,
While reading a crystallographic paper describing the structure
of an apo-protein and its complex I noticed that
the authors described the space goup as P6122 for the unit cell:
a=141.9, b=143.9, c=380.4 !
Could this be considered as a typo or I'm missing something here!
the
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