Your suspiciously low spread between R and Rfree might be because your
free flags might not have been chosen considering the twinning law.
Twin-related reflections should have the same flag value. You can get
phenix's reflection file utility to pick free flags for you while taking
the twinning
It is in general matter for debate what to do in these extreme cases.
When NCS rotation is parallel to the potential twin operator even if
twin is present electron density does not change much (at least not as
much as we would like). There are many cases where because of this
twinning was
Dear all,
I posted here recently regarding a potential twinning problem I had
and got some very useful feedback.
The summary of what happened is I had a crystal that appeared to be
P42212 from systematic absences after scaling in SCALA (a,b,c;
118,118,192). Interestingly POINTLESS suggeste
Dear Dr. Murshudov,
Thank in advance.
I will try the version 5.6 to fix this problem.
Best wishes.
On Tue, Jun 23, 2009 at 6:05 AM, Garib Murshudov wrote:
> This case would happen if the program first decides that the number of twin
> operators are several. But them to be twin cell should be def
Hello All,
I cannot imagine that crystallographers will not find the following link
astonishing...
http://ngm.nationalgeographic.com/2008/11/crystal-giants/shea-text/1
JPK
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Prog
This case would happen if the program first decides that the number of
twin operators are several. But them to be twin cell should be
deformed. This deformation makes some of the reflections to be
equivalent to higher resolution reflections than they are.
After calculating Rmerge and twin fra
The X-ray Crystallography Laboratory in the Department of Structural Biology
and Computational Chemistry at Wyeth Pharmaceuticals has an opening for a
Senior Research Scientist who is interested in structure-based drug design.
This position is located in Cambridge, Massachusetts. The research w
Ok, now we can perhaps debate of another problem.
With a multiple choice question that has more than one acceptably good
answer,
is it "convergent", or rather "independent", evolution?
This multiple choice question is open for discussion.
Greetings,
Nadir
Pr. Nadir T. Mrabet
Cellular & Mo
Many thanks to everyone who replied. Once again a proof of this community!
I am sure I will find what I am looking for in the cited publications.
Thanks,
justin
--
Justin Lecher
Institute for Neuroscience and Biophysics
ISB3 - structural biochemistry
Research Centre Juelich GmbH,
52425 Juelic
For a classic example, how about going back to the very dawn of enzyme
crystallography and the avian lysozymes? e.g. chicken (128aa??? alpha+beta) and
Embden goose lysozymes (196aa?? all alpha) but with a conserved active site.
Again probably convergent evolution.
However, great examples of whe
How about five (!) convergently evolved proteins?
The carbonic anhydrases are a well-known family of proteins which (to
date) have 5 independently convergently evolved forms: alpha, beta,
gamma, delta, and zeta. (Epsilon got folded into beta after
crystallography revealed it to be a beta-form.)
Some years ago, I produced a short computer-animated video (complete
with music and narration) for Jon Clardy's group on chorismate
mutase. The e. coli and b. subtilis forms of chorismate mutase
catalyze the same claisen rearrangement but have completely different
folds and hydrogen bond ne
Hello everxone,
I am looking for an example of two proteins where the primary sequence
does not show any significant similarities, but which have the same
function due their structure? I want to use it to demonstrate that
function could not always deduced from sequence alignments, but from
structu
I observe the same oddity for linux refmac 5.5.0092
Boaz
- Original Message -
From: Jiamu Du
Date: Monday, June 22, 2009 7:11
Subject: Re: [ccp4bb] problem of Refmac refinement on twinning data
To: CCP4BB@JISCMAIL.AC.UK
> I am using Refmac on a windows xp system.
>
> On Mon, J
Dear Sunjian,
what is important is the structural similarity of your model to the
unsolved structure, for instance in r.m.s.d - of course, this cannot
be determined until you have solved the structure!
The % identity is only an indication of how similar the structures may
be, sometimes 100%
My structure has a Cys that is solvent-exposed and an unidentified
'blob' of density which is connected to the sulfur of the Cys. The
protein was crystallized in presence of DTT, and DTT does fit the
density. However, I do not know if it is oxidized or not, as the density
does not appear to acc
孙建 wrote:
Dear all:
Recently,I have a problem about molecular replacement with
identity 30% model. There are two moleculars in AU.Through
self-rotation analyze,there are a two-fold axis in AU along X axis or
Z axis.Then I rotate and translate the model with CNS MR module.
several model
If you extend the R32 data set to R3 or C2 you will keep the same FreeeR
flags..
You can do this using cad or sftools I think..
Then add those f;lags to your reintegrated data sets..
Eleanor
Francis E Reyes wrote:
I have an R-free set for R32, I want to try scaling the data into say
R3 or C2.
Have you tried ACORN starting from a random atom?
Eleanor
Sickmier, Allen wrote:
I should have added we are currently getting licenses for direct methods
software but right now I do not have that option.
Allen
From: CCP4 bulletin board [mailto:ccp...@jiscmail.a
19 matches
Mail list logo
