Dear Dusan,
Following up on Gerard's comment, we also read your nice paper with great
interest. Your method appears most useful for cases with a limited number of
reflections (e.g., small unit cell and/or low resolution) resulting in 5% test
sets with less than 1000 reflections in total. It imp
Dear Derek,
I suggest you try 10% for the test set. You should still be able to judge the
effect of
various restraints (or constraints) as long as you keep the same test set. If
you switch test sets, and re-refine, Rfree
might change as much as 2% for a test set consisting of 200 reflections
We just had a chance to read this most interesting discussion. We would agree
with Ian that jiggling or SA refinement may not be needed if refinement can in
fact be run to convergence. However, this will be difficult to achieve for
large
structures, especially when only moderate to low resoluti
Chris,
First, I would try NCS restraints even at ~ 2 A.
Second, any outliers in your diffraction data set that might skew the R values?
Third, have you checked that your refined bulk solvent model is reasonable?
Axel
On Feb 21, 2014, at 6:13 PM, Chris Fage wrote:
> Thanks for the assista
השב: [ccp4bb] Why nobody comments about the Nobel
>> committee decision?
>>
>> Levitt also contributed to DEN refinement (Schroder et al. 2007, 2010).
>>
>> -Nat
>>
>>
>> On Wed, Oct 9, 2013 at 2:29 PM, Boaz Shaanan
>> mailto:bsh
ion?
>>
>> Levitt also contributed to DEN refinement (Schroder et al. 2007, 2010).
>>
>> -Nat
>>
>>
>> On Wed, Oct 9, 2013 at 2:29 PM, Boaz Shaanan
>> mailto:bshaa...@bgu.ac.il>> wrote:
>> Good point. Now since you mentioned contri
Begin forwarded message:
> From: "Randy Schekman"
> Subject: The eLife journal is now online.
> Date: December 13, 2012 10:00:09 AM PST
> To: Axel Brunger
> Reply-To: "Randy Schekman"
>
> Dear Axel,
>
> In June 2011, three of the most pres
characterization, novel sample delivery systems, data processing, experimental
phasing, and refinement at low resolution.
Extensive experience in computational or experimental crystallography is
desirable. Candidates should submit a resume and a list of three references to
Axel Brunger, Chair of the
I performed DEN-refinement with CNS using the same data and starting model, and
obtained
similar "twinned" R values and maps. The twin fraction is 0.5.
Axel
On Feb 9, 2011, at 3:29 PM, Jon Schuermann wrote:
> According to the paper, the data was refined in REFMAC in 'twin mode' which,
> I
We defined "super-resolution" in our DEN paper as
achieving coordinate accuracy better than the resolution
limit d_min of the diffraction data. We proposed this
definition in analogy to its use wide-spread use in optical microscopy:
"super-resolution" methods such as STORM, PALM, and STED achi
Dear Gerard,
Actually, for some of the tests we turned off the DEN network restraints
for the last two refinement macrocycles, so, at least for these
particular cases, the DEN method truly found a better minimum
rather than forcing the system to the higher resolution structure.
Cheers,
Axel
O
==
Announcing version 1.3 (general release) of the software:
Crystallography & NMR System (CNS)
(copyright 1997-2010, Yale University)
==
Inf
-linux to
> cns_solve_1.21/instlib/machine/supported/intel-x86_64bit-linux. Compile with
> 'make install compiler=gfortran', making sure that /usr/local/path is in
> $PATH.
>
> With the Intel 11.1 compilers (and I used the evaluation version here), CNS
> compiles succ
he problem, but so far there have been no
updates of the Intel compilers to fix the problem with Xcode.
Axel Brunger
On Jun 9, 2010, at 11:35 AM, Ethan Merritt wrote:
> On Wednesday 09 June 2010 10:45:07 am James Holton wrote:
>> I have often wondered how it is that one can actually
I suggest you explicitly define the heterocompound as a rigid
body for torsion dynamics. There are sometimes situations involving closed
ring systems that cause this topology generation error.
Axel Brunger
On Mar 20, 2010, at 3:46 AM, Suman Tapryal wrote:
> Hi all,
>
> I am
Begin forwarded message:
From: Charles Wolfus
Subject: Memorial Service for Warren DeLano
In case you have not already heard, the DeLano family is having a
memorial service for Warren:
Sunday, February 7th @ 10am
The Lucie Stern Center
1305 Middlefield Road
Palo Alto, 94301
Please join
not see the [ccp4bb] tag on
it, so I pass it on. I think that this is important, since Warren
has done so much for us all. I'll see how I can contribute (I hope
it is easily done from abroad).
Fred.
Message du 15/11/09 01:09
De : "Axel Brunger"
A : undisclosed-recip
Dear Linda,
NSMB asked me and Jim Wells to write an obit for Warren.
With your permission we would like to include a
quote of your CCP4 posting (or a reference to it -
depending what NSMB decides to do). Warren's
words summarize so much how we call remember him.
I hope you are doing well.
All
more information as I receive it.
Please join me in extending our condolences to Warren's family.
Sincerely yours,
Axel Brunger
Axel T. Brunger
Investigator, Howard Hughes Medical Institute
Professor of Molecular and Cellular Physiology
Stanford University
Web:http://atbweb.stanford
Dear Ian,
I totally agree with your observations and recommendations. If one is
concerned about "instability" of the optimizer (minimization
and/or simulated annealing) I suggest to also monitor the value
of the total energy function (X-ray maximum likelihood term
plus all restraints).
Another
.
The pre-publication manuscript is available on my website,
publication section.
Axel Brunger
On Nov 14, 2008, at 3:13 PM, Boaz Shaanan wrote:
oops, I forgot to give the reference:
Science (1992), vol. 257, p. 961
Boaz
Axel T. Brunger
Web:http://atbweb.stanford.edu
Email:
Brian,
There is one disadvantage with using AFP rather than wide open
(potentially
insecure) NFS mounts. Remote login via "ssh" into a client computer
won't by default mount the
user's AFP home directory. While it is possible to manually
mount the AFP home directory it may preclude other
dependent
on the particular case. Thus, it's useful to compute both
types of maps. I don't see the need to compute a composite annealed
omit map every time you make a change in model, though.
Axel Brunger
On Nov 15, 2008, at 10:34 AM, Priya Mudgal wrote:
Dear All,
I have a general qu
You might find this review useful:
X-ray Crystallography and NMR: Complementary Views of
Structure and Dynamics, Nature Structural Biology 4, 862-865 (1997).
The pre-publication manuscript is available on my website,
publication section.
Axel Brunger
On Nov 14, 2008, at 3:13 PM, Boaz Shaanan
This sounds to me like a compiler problem on your machine. Try using
the latest Intel Ifort, Portland Group pgf95, or GFORTRAN compiler.
Axel Brunger
On Sep 12, 2008, at 2:56 AM, jxqi wrote:
Dear ccp4bbs,
When I was refining a protein structure using the rigid.inp in
CNS(Version 1.21
,
so there will be some small differences between the single and multi-
processor versions.
The only changes compared to the single processor version of CNS 1.21
are in a few
source files, the Makefile compilation files, the test output files,
and the executable cns file.
Axel Brunger
Axel
CNS 1.21 is now available. A particular highlight is automatic
dimensioning
of torsion angle dynamics arrays (e.g., MAXTREE), so no user
intervention
is needed anymore. There are many bug fixes in source code, modules,
and input files.
I would like to thank Joe Krahn, Ben Eisenbraun, and m
There is an operating system bug in mac osx 10.5.x that may cause
this problem if you
are running the program with input redirection, but without output
redirection, i.e.,
cns < test.inp
and the input file contains one ore more blank lines.
try:
cns < test.inp > test.out
Axe
I certainly have not experienced this problem with our pre-compiled
Intel version for mac os X that is
available when downloading CNS 1.2 from the CNS website.
Axel
On Apr 23, 2008, at 7:59 AM, William Scott wrote:
Could one or both of you try this with the pre-compiled intel
version that
In such cases, we always define the test set first in the high-symmetry
space group choice. Then, if it is warranted to lower the
crystallographic
symmetry and replace with NCS symmetry, we expand the test set
to the lower symmetry space group. In other words, the test set itself
will be inva
t low resolution, for
example).
Axel Brunger
On Feb 7, 2008, at 9:57 AM, Dean Madden wrote:
Hi Dirk,
I disagree with your final sentence. Even if you don't apply NCS
restraints/constraints during refinement, there is a serious risk of
NCS "contaminating" your Rfree. Consider
wrote:
No, we have been using version 1.1 so far. Thanks for the suggestion,
we'll use version 1.2 from now on and try Phenix as well.
Bert
-Original Message-
From: Axel Brunger [mailto:[EMAIL PROTECTED]
Sent: Thu 1/24/2008 7:35 PM
To: Van Den Berg, Bert
Cc: CCP4BB@JISCMAIL.
Are you using CNS 1.2? This version has a robust bulk solvent model and
anisotropic correction
that is much improved compared to CNS 1.1. It is similarly robust as
that of Phenix (although
different in detail).
Axel Brunger
Van Den Berg, Bert wrote:
Hi all,
during refinement of our
test set while keeping your original test set
selection.
If you continue to have trouble, please contact me directly with more
details.
Axel Brunger
Florian Brückner wrote:
Dear colleagues,
I have a dataset form a protein-ligand complex. I want to use the same
Rfree test set for r
Make sure there is an END statement at the end of your coordinate file.
Axel Brunger
C. Ainsley Davis wrote:
Hello all,
I have been having major issues with CNS that I havent been able to figure out.
My protein has 2 molecules in the asu, ds DNA, ions, and a ligand. I have been
using refmac
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