A mixture between mathematical significance and biological significance
as a part of the reply:
you should also take into account the thermal vibrations of the atoms
present in that domain, i.e. the "thermal ellipsoids" when you have one
of the representations of anisotropic temperature factor
> If the difference in likelihood is quite small then you cannot distinguish
between a RB shifted model and one w/o the shift and that shift must be
insignificant (in a statistical sense.) If the likelihood is better when
the shift is allowed then the shift is significant.
That of course is corre
On Nov 21, 2011, at 6:34 PM, Jacob Keller wrote:
> I am curious how all of this can be more than splitting hairs, i.e.,
> under what conditions can this 1Ang domain motion mean something
> biologically significant?
To engage in the discussion, I think we had to accept this:
On Nov 21, 2011, at 3
I am curious how all of this can be more than splitting hairs, i.e.,
under what conditions can this 1Ang domain motion mean something
biologically significant? Proteins are pretty flexible, after all,
especially between domains.
JPK
On Mon, Nov 21, 2011 at 6:41 PM, James Stroud wrote:
> On Nov 2
Hi,
I'm not sure if that is what you are looking for, but if you want to use
the "real space refine zone" function in coot with sugars that is possible.
For a monosaccharide you will need a cif dictionary with the restraint
definitions - in some cases present in the refmac monomer database, but
On Nov 21, 2011, at 5:23 PM, James Stroud wrote:
> except that you use Euclid's formula to calculate the distances in higher
> dimensions
I meant to say "Euclidian distance". "Euclid's formula" has a specific meaning
that is different.
I just installed CCP4-6.2.0 and COOT on a Red Hat v6.1, x86, linux
workstation. Some of the menus, along the right edge, are gray buttons on
gray background. Where is the preferences file to change the colors of the
menu buttons? The menus across the top of the window are fine.
Also, idiffdisp is
On Nov 21, 2011, at 3:52 PM, Filip Van Petegem wrote:
> As mentioned for X-ray structures, a Luzzati analysis may give information
> about the positional errors, but there should be an increased resolution when
> comparing domain movements, because it's unlikely for all atoms to have an
> erro
Hi everyone!
Does anyone know if there is a way of auto-refining a sugar in Coot?
Jan
This is a subtle problem and performing an analysis of this type
of error is confusing. Most of the tools we use to analyze errors
begin with the assumption that the "errors" are random and uncorrelated.
These include Luzzati and Fo-Fc maps.
My solution is to perform a null hypothesis test.
I'll jump in here, and avoid the question entirely.
Since running MR on an isomorphous crystal gives the same answer as just
stuffing in the model and running some rigid body refinement, however you decide
to handle your R free flags, you should do the same thing in both cases. The
model is
Hi Mike,
Often, I generate independent freeR set (especially in cases where "soak"
dataset is of different resolution (usually worse) compared to the native
dataset and do following two things to get rid-off the bias: 1. add a noise
to the coordinates (this can be done using PDBSET). 2. set the Bv
On Nov 21, 2011, at 3:04 PM, Filip Van Petegem wrote:
> So the question is: how you can state that a particular movement was
> 'significantly large' compared to the resolution limit?
I can think of a different but related question. How significant is a
particular movement compared to a measure
Hello Jacob,
that's correct, I'm only looking at the mathematical significance, not the
biological one. I follow the same reasoning - it is highly improbably for
all atoms to be skewed in the same direction.
In a case I'm currently looking at, I'm particularly dealing with cryo-EM
data, not X-ra
- Forwarded Message -
From: "Michael Thompson"
To: "e dodson"
Sent: Monday, November 21, 2011 11:30:17 AM GMT -08:00 US/Canada Pacific
Subject: Re: [ccp4bb] LESS MR pleae.. 1.95A, different phase
A question regarding the plea for less MR (which I support):
There have been several recent
Just to clarify: I think the question is about the mathematical sense
of "significance," and not the functional or physiological
significance, right? If I understand the question correctly, wouldn't
the reasoning be that admittedly each atom in the model has a certain
positional error, but all toge
I believe ESCET was designed to answer your kind of question
Best
Roberto
On 21 Nov 2011, at 22:03, "Filip Van Petegem"
mailto:filip.vanpete...@gmail.com>> wrote:
Dear crystallographers,
I have a general question concerning the comparison of different structures.
Suppose you have a crystal
Dear crystallographers,
I have a general question concerning the comparison of different
structures. Suppose you have a crystal structure containing a few
domains. You also have another structure of the same, but in a different
condition (with a bound ligand, a mutation, or simply a different
c
The problem was resolved with your help, and in fact there was no
problem, except that I was unaware of the alternative origins. I promise
I'm reading more about it. :$
A side note: I collected another crystal, different crystallization
condition but same cell parameters, and followed Eleanor
What is Kd?
Also, in reply to earlier posts: it is sadly common in crystallizing large
protein-DNA complexes to go through a couple dozen different duplexes and
several dismally-diffracting crystal forms before finding a good one.
Phoebe
>From: CCP4 bulletin board (on behalf of umar faroo
Sent from my Verizon Wireless Phone
- Reply message -
From: "umar farook"
Date: Mon, Nov 21, 2011 10:59 am
Subject: [ccp4bb] Protein-DNA complex crystallization
To:
Dear All,
I have been trying to crystallize protein DNA complex, but all the time i
end up with DNA crystals. Even i ch
yum install lesstif ?
but wouldn't the motif stuff be required for the X-server, i.e. your terminal, not for the
server running adxv?
Rajesh kumar wrote:
Dear Mark,
$ locate XKeysymDB - didnt come with any thing suggests probably openmotif lib
is not
installed.
I linux server has Fedora and
Curious, how did you assess that your crystals only have DNA?
F
On Nov 21, 2011, at 8:59 AM, umar farook wrote:
> Dear All,
>
> I have been trying to crystallize protein DNA complex, but all the time i end
> up with DNA crystals. Even i changed the length of DNA many times but still
> no comp
Greiner Bio One is an alternative with distributors in various
different countries worldwide
http://www.greinerbioone.com/en/france/articles/catalogue/article-groups/11_5/
On Fri, 18 Nov 2011 12:40:56 -0500, Poorva Dharkar wrote:
Hi,
I need to buy 24-well crystallization plates. I want to kno
Dear All,
I have been trying to crystallize protein DNA complex, but all the time i
end up with DNA crystals. Even i changed the length of DNA many times but
still no complex, DNA only crystallizes! Does anybody has idea, why do DNA
crystallize by itself ? My protein behaves very nicely, Dynamic L
my DNA contains a 9-1-9 palindromic sequence,i tried different blunt end
DNA,and got two kind of crystal with different lenght DNA.both don't
diffract.
2011/11/21 Michael Murphy
> Deng, could you tell us a bit more about the DNA that you used? I think
> you may want to try to optimize the DNA
Dear Mark,
$ locate XKeysymDB - didnt come with any thing suggests probably openmotif lib
is not installed.
I linux server has Fedora and I am using latest version of Adxv so details on
the sbgrid suggest its same problem.
So how would I fix this.
Thanks for your time.
Regards
Rajesh
>
I think you are proving yet again that refinement at 3.3A is not easy.
Indeed there are probably multiple conformations for parts of the
structure and that may well be why your data is at low resolution and
anisotropic. Maybe this is the best you can do..
I think I would make sure the apo str
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Wei,
you could use coot "Calculate->Model/Fit/Refine->Simple Mutate" also for
nucleic acids.
It may be worth running geometry idealisation in coot or refmac5 before
using the model in MR.
Tim
On 11/19/2011 09:44 PM, Wei Shi wrote:
> Hi all,
> I
Or use Kevin's csymmatch which does wonders on scrambled oligomers that (nearly
always, at least in my hands) come out of Phaser in cases like those mentioned
by Ian and which do need MR.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84
Dear All,
I posted some odd diffraction late last year consisting of Bragg
diffraction spots with a diffuse ring or halo. Along with Richard
Welberry at ANU we have now published an explanation for this diffuse
scattering. For those that are interested the reference is:-
Acta Cryst. (2011).
On Mon, Nov 21, 2011 at 10:23 AM, Eleanor Dodson wrote:
> Just a plea for less molecular replacement.
>
> If you get a new crystal of a known protein with the same cell dimension as
> youur old crystal, the most likely scenario is that it has the same group,
> and you really should not try MR - u
Just a plea for less molecular replacement.
If you get a new crystal of a known protein with the same cell
dimension as youur old crystal, the most likely scenario is that it has
the same group, and you really should not try MR - use the previous
solution as input to do rigid body refinement,
Do note that all the Pointless 1.5.x versions had a serious bug and should not
be used
Phil
On 19 Nov 2011, at 09:49, Rajesh kumar wrote:
> Thanks to Harry Powell, Phil Evans, De-Feng Li for suggestions and special
> thanks to Charles Ballard looking in to my data.
>
> The summary is
>
> Har
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