Dear all,
The MALLS instruments on-line with an FPLC and with an RI detector,
should provide an 'absolute MW', shape independent,
and indeed in our hands they do well. Until yesterday, where a 21kD
protein pretends to be 25 kD. We did the mass spec
anyway, and its 21kD as we expected to the r
Hi Tim,
thankyou very much for the fast reply.
Dear colleagues,
Tim suggested:
>Hi Klaas
...
>Actually, you don't need to install arpwarp through the ccp4i interface.
>Once you setup your ccp4 environment, you can just run the install.sh (or
>install.csh in your case) which is in the arp-wa
Thanks all for the suggestion. I have ordered the additional salts from
Hampton. I still have about 600uL of the original solution in the block. BTW,
the hits obtained were in two different conditions with the two salts.
They were PEG/Ion HT screen A7 and D6.
I am keeping my fingers crossed.
Sin
Jacob
Have you seen the Crystal Catcher system, developed in Japan?
http://adsabs.harvard.edu/abs/2008APExp...1c7002K
Some of us saw it at a recent IUCr meeting, but I don't know anyone who
has tried it with their own proteins
Patrick
--
For information and discussion about
Pretty cool, but the examples shown are all gigantic. Having just
spent a frustrating several hours chasing 5 um crystals, I'd give
half my kingdom for a simple way to catch THOSE little buggers (damn
you, surface tension!).
Begin forwarded message:
From: Patrick Shaw Stewart
Date: March
Tassos,
The most obvious answer (and possibly incorrect) is that DNA itself has a
different dn/dc value and when you say that you have a DNA binding protein,
chances are that some or all of it may be bound to DNA, which would change the
nature of the beast (and the MW). Perhaps you can delibe
Dear all,
Not a CCP4 question.
We seem unable to process with XDS a set of images collected at ESRF
ID23-1.
Images can be open and processed by other software (adxv, mosflm...)
They have appropriate read permissions and so has the directory where
we run XDS. We use the latest XDS binaries
This might be a bit too obvious, but have you checked that the path to
the images is correct? The path written in the input files generated
on the beamline reflects where the images were located in the file
tree there. Does it match where you have the files on your own computer?
Cheers,
Ron
I have seen this when the actual size of the image is different from
what
XDS expects. If you have now:
NX=6144 NY=6144 QX=0.0513 QY=0.0513
try
NX=3072 NY=3072 QX=0.10259 QY=0.10259
or the other way around.
If the auto-generated input file doesn't match your images it might be
because the binnin
Hi Klaas,
I had exactly the same problem with opensuse 11.1. I installed the precompiled
version of ccp4 6.1.1, so I don't think the problem is related to the compiler.
I resolved the problem in a dirty way, simply copying the ccp4i configuration
files for arp/warp from another installation of cc
Hi Ronnie and others,
Le 27 mars 09 à 15:02, Ronnie Berntsson a écrit :
This might be a bit too obvious, but have you checked that the path
to the images is correct? The path written in the input files
generated on the beamline reflects where the images were located in
the file tree there.
Dear Tassos,
Your assumptions are right, if (1) your dn/dc is accurate, or (2) your
machine is calibrated. We recently measured a protein of a similar size
to yours, and when a 700 Da ligand was added to the buffer, the measured
protein mass was increased accordingly. So MALS can be pretty acc
Dear List,
I am trying to install the latest CCP4 6.1.1 binaries on Linux and
running into sourcing problem. I could source the ccp4.setup file as
root (c-shell) and ccp4 ran just fine. But as a user, with the same
shell, I could not source the setup file. The error is "setenv: Too many
arguments"
I think Dr. Loll has expressed my reasons for my original suggestion. When
there are skins, evaporation, etc., "crystal catching" can be a real pain, and
then you break your best crystal...
What if you could just go up to your intended crystal and vacuum it up, and
whisk it away to the dewar?
Hi Jason
Type 'set verbose' (without the apostrophes) and trying sourcing again,
it should stop just before the offending line.
Cheers
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Phan, Jason
> Sent: 27 March 2009 16
Is it possible, as I have heard about some DNA-binding proteins, that it is
at least partially intrinsically disordered (ID), which might change the
Stokes radius? You could cross-check by SDS-PAGE or SEC (ID's run larger).
CD, with careful protein quantification, might also do the trick. ID its
Does your system eliminate the need for cryoprotection? Also, how do you
time the buffer-removal/freezing steps?
JPK
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Ev
Hello,
There are available spots remaining for the 2009 SBGrid Computing
School, please see below for more information.
Please Note: SBGCS registration fees will increase for any attendee
who registers after Friday, April 3, 2009. Starting April 4th
Nanocourses will increase to $119.00, a
As an undergrad late in the last century, I used a micromanipulator,
quartz capillaries, and a device similar to a patch pipet (manually
operated via a screw) to do just this. It was just about the time that
nylon loops were coming into wide use, though, and I gladly abandoned he
capillary method
Dear Ian,
I got bumped out at this line:
Setenv PATH ${PATH}:${XIA2CORE_ROOT}/Test
Could you shed some light on this? I'm using C shell. It can't be the
syntax since I could source as root.
Thanks,
Jason
-Original Message-
From: Ian Tickle [mailto:i.tic...@astex-therapeutics.com]
Se
Jacob,
Although the use of patch-clamp pipettes and micromanipulators come to
mind, I just wonder about what would happen to the pipette and the
fluid in it when you flash-froze it. Nonetheless, the idea of a means
to transfer small crystals easily and quickly has some merit. In
another
Dear All,
I'd like to add substitute a natural base (adenine) for a non-natural
base (2-aminopurine), in a molecular model of an RNA molecule.
I'd like to do this with CCP4 and Coot. Could I ask for some help
please?
Thanks! and all the best,
--Buz
Hello all,
I have a structure that has been solved by MR and now have experimental SAD
phases that I hope will improve the map.
I used Phaser for this from within the CCP4i suite but I would like to take
the solution and work with it further in CNS.
Is there a way to generate a .hkl file from the
The CCP4 mtz2various will do this. A sample script
and instructions for using the CCP4i GUI can be found at
http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Phase+Solution#File_preparation.
The example cited is for preparing a file for EPMR, which is a simple
hklF listing.
Cheers,
--
Dear Kelly-Anne
2009/3/27 Kelly-Anne Twist :
> Hello all,
>
> I have a structure that has been solved by MR and now have experimental SAD
> phases that I hope will improve the map.
> I used Phaser for this from within the CCP4i suite but I would like to take
> the solution and work with it further
Hi Jason
Nothing obviously wrong there (I assume that the capital 'S' in 'Setenv'
is just your mail client being silly?). Is that the last line printed?
(sorry I got it wrong before, I just checked & the source will stop
*after* the offending line, not before as I said, so it's the last line
you
On Fri, Mar 27, 2009 at 02:52:10PM -0400, Phan, Jason wrote:
> I got bumped out at this line:
>
> Setenv PATH ${PATH}:${XIA2CORE_ROOT}/Test
What does $PATH expand to? If you had a directory with a space in it,
that would generate the error you're seeing.
> Could you shed some light on this? I'
On Mar 27, 2009, at 11:52 AM, Phan, Jason wrote:
Setenv PATH ${PATH}:${XIA2CORE_ROOT}/Test
try replacing this with
setenv PATH "${PATH}":"${XIA2CORE_ROOT}/Test"
setenv needs to be all lower case, and the double quotes permit spaces
in the path (assuming that is the problem)
Thank you, Ian, Ben and Bill.
My apology for the S in setenv, a typo.
I expanded the variables in $PATH and found the culprit: set PATH =
(/usr/lib /usr/lib64 /usr/local/lib /usr/local/lib64) in my /etc/cshrc
file. I have the line "source /etc/cshrc" at the top of my ~/.cshrc
file. After commentin
Dear Jason:
Glad to hear it is working now. If you really want to have a fun
weekend, try the z-shell: zsh.
zsh combines the user-friendliness of tcsh with the power of bash and
ksh.
It can do all sorts of cool stuff, like user and host completions,
remote file name completion (with sc
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