Hello,
After several years of offering the molecular biology software VectorNTI
free to the academic community (their open access program) and building
up a huge user base, Invitrogen have suddenly announced that they will no
longer renew these free licences and the existing ones will be left to
Hi Darren,
much much easier than VectorNTI is ApE (http://www.biology.utah.edu/jorgensen/wayned/ape/
), which is multi-platform and very easy to use for simple tasks.
Please, could you post a summary of the answers?
Thanks,
ciao
Sebastiano
On Jan 28, 2009, at 9:47 AM, Darren Hart wrote:
A PhD student position is available to develop new protein modelling methods
which can be applied to drug design. The successful candidate will work in
collaboration with the Blundell and Hyvonen groups in the Cambridge
University Biochemistry Department and industrial CASE award sponsors Eli
I've used serial cloner (http://serialbasics.free.fr/
Serial_Cloner.html) but not ApE, which I hope to try now that I know
of it. One thing that serial cloner has going for it is a nice
assembly tool that makes construct design much easier. Otherwise it
could be a little less clunky in its
Hi Darren,
My favourite program for editing sequences (apart from
Vector NTI, which I suppose I'm going to have to delete soon), is
BioEdit:
http://www.mbio.ncsu.edu/BioEdit/bioedit.html
It has an old fashioned cluttered interface, but does do sequence
editing, translation into
I am looking for a reagent (and vendor) that will irreversible put a
raher bulky substituent on a free SH group and that does not react with
free amines (or other potential reactive groups present on a protein
surface). The connection with crystallography is that it is required for
an
I am looking for a reagent (and vendor) that will irreversible put a raher
bulky substituent on a free SH group and that does not react with free
amines (or other potential reactive groups present on a protein surface).
The connection with crystallography is that it is required for an
Dear Remy,
Iodoacetamide might be a good candidate as it alkylates thiol groups and
is also used as cysteine protease inhibitor.
good luck,
hannes
-
Hannes Uchtenhagen, Ph.D student
Karolinska Institutet
Center for Infectious Medicine (CIM)
Karolinska University Hospital Huddinge, F59
SE-141
I like BioEdit too. It is PC based, downloadable, and very easy to use. It
allows copy-paste of a word or text file, and does alignment, translation,
back translation, etc, and more. Fabulous program.
I also use Lasergene which has the long standing DNA Star, Megalign, but you
have to buy a
Hi
Anybody have suggestions for Mac OsX alternatives?
Thanks in advance,
Mark
Hi everyone,
Thanks for answer my question. Just to add some more notes regarding to
my expression system. The insert-vector (pET28) has been sequenced and
the his-tag is N-terminal. The anti his-tag WB is positive and the
binding buffer's pH is 8.2 (double-checked).
I had already experienced
On Wed, 28 Jan 2009, Jovine Luca wrote:
On 28 Jan 2009, at 16:02, Mark Collins wrote:
Hi
Anybody have suggestions for Mac OsX alternatives?
Thanks in advance,
Mark
Hi Mark,
The latest version of DNA Strider (1.4) runs just fine on both Tiger and
Leopard. For more info, you can contact the
Hi all,
I've recently come across the program PlasmaDNA which seems pretty good
for the basics - http://research.med.helsinki.fi/plasmadna/ . It works
under Mac OS X and Windows... and probably Wine on Linux too.
Cheers,
Roger
Original Message
Subject: Re: [ccp4bb] OT:
Hello,
Thanks for all the emails (only some of which reached the bb). It is clear
that I am not alone in feeling aggrieved by Invitrogen suddenly introducing
licence fees, having first persuaded us to put our files and time into their
free product over several years.
Once the thread goes quiet,
Margriet
This looks like stacking or shift disorder which can occur when perfect
3 dimensional order breaks down. For example one can have a situation
where the lattice is preserved in 2 dimensions but the planes can slide
with respect to one another destroying the order in the 3rd dimension,
Hi Darren,
I can recommend another free tool: pDRAW32 ( http://www.acaclone.com/ ).
It runs natively under Windows but I am using it with the emulator wine
on Linux.
Cheers,
christian
Darren Hart wrote:
Hello,
After several years of offering the molecular biology software VectorNTI
free to
There is GENtle which has a whole slew of tools associated with it.
There are versions for several platforms.
http://gentle.magnusmanske.de/
If you're used to Vector NTI, it is pretty similar (and open source
for the ambitious).
_
Cynthia Kinsland, Ph. D.
Director,
Hi Savvas,
If the very good suggestions you have already got from the ccp4bb do not
help, try crystallization with agarose as an additive. Crystals form
inside the very soft gel and they are hold in place by this meshwork.
So, they are mechanically protected and do not fall down onto the bottom
of
Hi all,
Geneouis also runs on OS X. From my experience (past two years), the
program works just fine. You can download the trial at http://www.apple.com/downloads/macosx/math_science/index1.html
(second page).
Cheers,
Yann
ir. Yann Sterckx
Pre-doctoral student
Structural Biology
Hi Margriet
It's almost certainly due to diffuse scattering as a result of
correlated atomic displacements. See this:
http://www.nature.com/nsmb/journal/v1/n2/pdf/nsb0294-124.pdf .
Are they lines or sheets, in other words do they appear only on one
image, or are they also on adjacent images,
I second Chris's suggestions. These have worked well for me in the
past. You only need a very thin layer of the grease (i.e. keep
wiping until its almost completely gone) and it usually has no affect
on the crystallization.
Jeff
On Jan 27, 2009, at 3:51 PM, Christopher Colbert wrote:
Two things to be mentioned.
* IDA columns bear an overall negative charge. I expect this behavior
holds true with NTA gels. Hence salt, (= 0.5 M NaCl) must be present in
your adsoprtion buffer to quench possible repulsive electrostatic
interactions.
* You are dealing with protein adsoption by
Couldn't the lines be explained most simply by extreme mosaicity, perhaps
severely anisotropic? If not, why not? What were the values obtained in
integration?
Jacob
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Hello All,
I'm trying to use BALBES locally to perform molecular replacement on data of
a two protein complex.
Protein 1 is a truncated version of a two domain protein of known
structure.
Protein 2 has a homologous protein of known structure and ~50% identity.
I'm having two related problems -
I recommend you have a look at a book from OUP called Diffuse X-Ray
Scattering and Models of Disorder by T. R. Welberry. The first chapter
explains quite well (I think) where all these streaky things come from.
It will also make you feel better about having it when you see all the
small
Jacob
Traditional mosaic spread (ordered mosaic blocks imperfectly aligned with
respect to one another) gives spherical caps in reciprocal space. These would
appear as arcs on a single crystal rotation photograph. If anisotropic, the
arcs would be more extensive in some directions. The
Hi, it's clearly not a detector problem (at least not an obvious one!),
since the 'lines' clearly follow the *curved* path of the reciprocal
lattice lines as they are projected from the Ewald sphere onto the
detector. A saturated pixel would presumably affect other pixels only
in the same row and
Re: [ccp4bb] small lines in diffraction patternI had thought that in a previous
thread, we had all come to a consensus that actually the largest source of what
is normally explained as mosaicity is really differences in unit cell size,
due perhaps to uneven shrinkage in crystals upon freezing
Re: [ccp4bb] small lines in diffraction patternActa Cryst. (1998). D54, 848-853
[ doi:10.1107/S0907444998001875 ]
A Description of Imperfections in Protein Crystals
C. Nave
Abstract: An analysis is given of the contribution of various crystal
imperfections to the rocking widths of
From: Darren Hart
After several years of offering the molecular biology software VectorNTI
free to the academic community (their open access program) and building
up a huge user base, Invitrogen have suddenly announced that they will no
longer renew these free licences and the existing ones
Just to let you know. No way, Talon also don't work. I am gonna try the
GE His-trap column.
Fred wrote:
Hi everyone,
Thanks for answer my question. Just to add some more notes regarding
to my expression system. The insert-vector (pET28) has been sequenced
and the his-tag is N-terminal. The
Hi Fred,
I am not sure if this has been brought up already. Another possibility might
be to generously pipet your Ni- or Co-matrix of choice directly to buffered
solubilized inclusion bodies, incubate for some time (even overnight if you
feel its necessary), and then use the slurry to pack a
Hi Fred,
I doubt His-trap column be any better. I never found much a difference
between these resins or columns. If you want to try, use His-Trap HP, not
His-Trap FF.
Doing batch binding may help you figure out the problem. In some cases,
protein binds better in batch mode. You can take beads
Dear colleagues,
I would like to thank all of you who responded so generously (either
privately or publically on the ccp4bb) to my question on how to deal with
'sticky crystals'. I provide below a consensus of all the many answers
grouped according to the proposed solution.
Best wishes
Savvas
For basic analysis, editing, etc, i really like ApE, A Plasmid
Editor. Versions are available for OS X, linux and Windows.
http://www.biology.utah.edu/jorgensen/wayned/ape/
i find it does most everything MacVector does, and a few things
MacVector does not do.
What VectorNTI functionality are
There is something in the unit cell, aligned with the long axis of the cell,
with a periodicity corresponding to ~1/5 of the long axis. This can be seen
as greater intensities along the long axis every fifth spot. Without knowing
the unit cell parameters, I would guess it is either the
I'm coming in late here, having only now found time to look at the images.
It's facinating, isn't it?
Since the lines are not arcs centered on the origin, this isn't mosaic
spread.
For those who haven't seen the image and the zoom, the diffraction pattern
clearly shows one very long axis
Hi James,
what your descriptions aims at is I think shown in this publication
Borgstahl, G. E. O. Incommensurate Crystallography by Sander van
Smaalen Crystallography reviews 14 , 259-260 (2008).
Or am I misunderstanding something here ?
Jürgen
On 28 Jan 2009, at 12:39, James Holton
I'm coming in late here, having only now found time to look at the images.
It's facinating, isn't it?
Since the lines are not arcs centered on the origin, this isn't mosaic
spread.
For those who haven't seen the image and the zoom, the diffraction pattern
clearly shows one very long axis
I'm coming in late here, having only now found time to look at the images. It's
facinating, isn't it?
Since the lines are not arcs centered on the origin, this isn't mosaic spread.
For those who haven't seen the image and the zoom, the diffraction pattern
clearly shows one very long axis and
I'm sure Gloria would be delighted if that were the case, but I don't
think this is an incommensurate lattice. These actually don't so much
give you diffuse scattering as little satellite spots near the main
spots at spacings that don't make any sense given the lattice repeat.
My
Hi Bob et al:
I think that this is the convolution of the helical transform with the
Bragg diffraction, which you often see in nucleic acid diffraction
patters. I think I first saw it, in fact, at your beam-line in 1994,
with ribozyme crystals. (Aaron Klug had to explain it to me.)
The
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