Subhendu
I wonder if you approached this issue by molecular replacement using the
antigen-binding fragment (Fab) of any antibody (e.g. 1FVD). You can separate
the Fab into the two domains; Variable and Constant, delete the loops from
each, and use them as models in Molecular replacement.
Please l
Can we have a moratorium on plugs for books please?
James
--
Dr. James W. Murray
David Phillips Research Fellow
Division on Molecular Biosciences
Imperial College, LONDON
Tel: +44 (0)20 759 48895
From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behal
Hi everyone,
I am currently in the process of solving some antigen-antibody complex
structures. I was wondering if people here have used Modeller and Rosetta
for homology modeling and have any recommendations.I would like to build the
model of the antigen/antibody to the known structure of the anti
page 682 :-)
BR
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Pavel
Afonine
Sent: Monday, December 14, 2009 9:24 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] When can I say the refinement is done?
This is pointed out (in absolutely unobvious way - I wish I can
thanks to all for the replies. the protein of interest is a membrane
associated (lipoprotein) but i express this without the signal sequence in
the cytoplasmic context. also it is not his-tagged, to address the debate of
protein crystallize with or without the tag i presume as one reason. also
the
I saw something like this once that turned out to be CAT
(chloramphenicol acetyltransferase) denatured and entangled with a
massive amount of RNA (which was yellow). I was not using
chloramphenicol, but an examination of the vector lineage reminded me
that the gene was in there. This aggregat
Hi Rafael,
If you really want to diffract your crystals frozen, I have two more
suggestions for cryo-procedures which can be tried:
a) annealing
e.g.
Harp, J.; Timm, D. & Bunick, G. Macromolecular crystal annealing:
overcoming increased mosaicity associated with cryocrystallography.
Acta Crystallo
This is generally the result of strain upon cooling. I. E. the outside
of the crystal is shrinking and the inside is expanding. The trick is
to match the density of the stuff in the solvent channels upon cooling
to the preferred final density of the lattice (Juers and Matthews,
(2004) Acta D6
Hi, I apologize immediately that this question is not directly related to
crystallography but the protein i am trying to overexpress is eventually for
that purpose. i understand the huge knowledge-base of people here
experienced in protein expression/purification and would appreciate any
insight in
The electron density snapshots I can understand on some level - after
all, picture is sometimes worth thousand words. But it does take a
"windows person" to post Mb-sized picture instead of a one-line error
message.
On the substance, you should probably do what the program suggests -
check the m
I appreciate learning that the R32/H32 tangle was based on a wwPDB
recommendation. For some reason, I find it calming to view this as a PDB issue
and not a ccp4 one. Ron
On Tue, 15 Dec 2009, Eleanor Dodson wrote:
Just a correction - ccp4 had NOTHING to do with H32 definitions - just followe
Also try growing them in the presence of the cryoprotectants...
Jacob
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9
Kay Diederichs wrote:
Kevin Cowtan schrieb:
Emsley P, Lohkamp B, Scott W, Cowtan K (2010)
"Features and Development of Coot" Acta Cryst D66 (in press)
Sorry, I wouldn't like to cite a paper whose contents I don't know.
Excellent!
I think the corresponding author may be able to provide y
With salt-based conditions sodium malonate is your friend:
Acta Cryst D59: 2356
On Tue, 2009-12-15 at 12:20 +, Natalie Zhao wrote:
> -Original Message-
> From: owner-c...@dl.ac.uk [mailto:owner-c...@dl.ac.uk] On Behalf Of Rafael
> Couñago
> Sent: 14 December 2009 20:22
> To: c...@ccp
You could try conditioning your crystals in a dehydration device (such
as the FMS (proteros) or the HC1 (EMBL)). Even if you crystals don't
improve from dehydration they can often be cryocooled without any
cryoprotectant after the mother liquor has been removed. We offer the
HC1b at the ESRF
Did you also try a cryo salt (e.g. Li+)? In the best case the xtals might even
grow in there.
GL
Jan
--- Natalie Zhao schrieb am Di, 15.12.2009:
Von: Natalie Zhao
Betreff: [ccp4bb] FW: [ccp4]: TDS upon flashcooling
An: CCP4BB@JISCMAIL.AC.UK
Datum: Dienstag, 15. Dezember 2009, 13:20
-Orig
We are offering RapiData 2010, the twelvth offering of our popular course:
Rapid Data Collection and Structure Solving at the NSLS: A Practical
Course in Macromolecular X-Ray Diffraction Measurement
The course will be held 11-16 April 2010. Students could be at any level
from adva
Kevin Cowtan schrieb:
> Two things
> for Coot users...
>
> Firstly, I have just uplaoded the remaining Linux binaries for Coot 0.6,
> i.e. Fedora 8, Fedora 10 and Ubuntu 6.06 (with python and gtk2 gui).
> You can find them on the Coot website here:
> http://www.biop.ox.ac.uk/coot/software/binarie
You can also set your cryostream to something like 253K... or even lower
with high salt. Better than RT and still no freezing. You need to use
one of these new loop covers to prevent drying out.
Flip
mjvanraaij wrote:
why not stay with room temp?
many structures have been solved at RT...
Ma
why not stay with room temp?
many structures have been solved at RT...
Mark J. van Raaij
Dpto de Bioquimica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
researcherID: B-3678-2009
On 15 Dec 2009, at 13:20, Natalie Zhao wrote:
-Original Message-
From: owner-c...@dl.ac.uk [mailto:owner-c...@dl.ac.uk] On Behalf Of Rafael
Couñago
Sent: 14 December 2009 20:22
To: c...@ccp4.ac.uk
Subject: [ccp4]: TDS upon flashcooling
Dear all,
I got these beautiful looking crystals that grow in high salt (1.8M) and
diffract under
I think that we have been here before. It is a lot less confusing for
users if the program checks the cell dimensions to see which setting
is being used. For example SHELXC will interpret both "R 3 2" and "h32"
correctly for either hexagonal or primitive rhombohedral axes. There is
really no exc
I think SPASM by Gerard Kleywegt is a great tool for this sort of thing - you
can set the similarity matrix threshold to make it more or less sequence
independent (it still calculates the sequence match which is good for looking
for key residues in the motif like structurally required GLYs). You
I have no opinion on what should be written (such debates are a world of
pain) but I tried to make csymlib accept anything.
I tried ncont (as an example of a C++ program) and contact (as an
example of a Fortran program) and both seemed happy with such a CRYST1
line. CCP4 is pretty heterogenous, so
On Tue, Dec 15, 2009 at 9:40 AM, Eleanor Dodson wrote:
> Yes, the PDB required format is H 32 - but the xHM symbol is: 'R 3 2 :H'
>
> I guess the PHENIX group are trying to pressurise the wwwPDB to change..
>
You'd have to ask Ralf. Besides, it isn't just PHENIX/CCTBX that uses this
notation:
h
Just a correction - ccp4 had NOTHING to do with H32 definitions - just
followed the wwwPDB requirements.. there were bitter arguments over
accepting it from many!
E
Peter Zwart wrote:
Hi Stephen,
R32
H32
R32 :H
Correct. These are all hexagonal setting. As far as I know, the
hexagonal set
Yes, the PDB required format is H 32 - but the xHM symbol is: 'R 3 2 :H'
I guess the PHENIX group are trying to pressurise the wwwPDB to change..
symbol Hall ' R 3 2"'
symbol xHM 'R 3 2 :H'
symbol old 'H 3 2'
Anyway as a mere user compromise is probably the simplest solution!
Eleanor
Ja
We are pleased to announce the release of TARDIS v2 at http://tardis.edu.au
TARDIS v2 provides a central, searchable index for federated raw
crystallography data.
If you are interested in the safe storage and simple annotation of your
diffraction data (eg as soon as it comes off the detector),
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