A post-doctoral position is available to study the molecular
mechanism for self vs. non-self discrimination by the innate immune
system. We use a combination of X-ray crystallography, biochemistry
and computer simulation to characterize structures and functions of
key host molecules that r
Dear colleagues,
How do I get from scalepack the average I/sigma for the higher resolution
shell?
Mike Colaneri
A post-doctoral position is available in Dr. Choi laboratory at University
of Texas Medical Branch (UTMB) at Galveston to study the structure and
mechanism of virus infection. We use a combination of cryo-electron
microscopy, X-ray crystallography, protein chemistry, and bioinformatics
to dete
it was there for some time. Info about this and some other new and
not so new features can be found here:
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html
Some of the features like n mfo-l dfc map was there for 5.3 and may
be even earlier.
regards
Garib
On 8 Jul 2008, at
Is this something new in refmac, or something undocumented (or am I looking in
the wrong place by checking LABOUT)?
-Original Message-
From: CCP4 bulletin board on behalf of Kevin Cowtan
Sent: Tue 7/8/2008 4:06 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Definition of Fourier coe
We have been thinking of buying Malvern Zetasizer Nano. We were given
a proper demonstration by the friendly Malvern staff, and it was
satisfactory.
I also had RiNA Spectroscatter 201 demonstrated to me and it seems
a reasonable alternative to Malvern.
I am just looking at the brochures and th
I've used variations of the Malvern instrument at two positions now,
and I have to say I've never had a problem with them.
Yes, I believe it was designed to be a non-biological instrument, but
I have to say it does a good job of DLS and SLS on proteins from
7-200KDa (in my experience) in a cuvette
Why not get an in-line, flow-cell LS detector for use with your
chromatography system? We once had a great system, set up with a good SEC
column, UV detection at three wavelengths on an akta, followed by SLS and
DLS, and refractive index detector. The data were beautiful, as the SEC made
the ba
Hmmm...
we had a demo of the Malvern Zetasizer instrument here, and to be honest: It
did not convince us at all (it is obviously built for non-biological
particle analysis)
The Viscotek is also a plug&play device, every pc with a USB is suitable.
..in the end... Viscotek and Malvern are the
I'll second the recommendation for the Malvern Zetasizer. They are
rock-simple and interface with a computer through USB which makes future
computer upgrades relatively simple. The are however, not cheap--oops,
inexpensive.
Cheers,
--
-
Dear colleagues,
manual editing suggested by Martyn Winn worked and I can process the
data further now. I was not able to process the file with readmtz, most
probably because of my low experience with this. Thanks to all of you,
for discussion and goodwill to help me.
Best Regards,
Petr
Petr
Dear All,
I had initially got some clusters of needles for one of my proteins. I then
tried to streak seed them. However, I still seem to get quite a large number
of nucleations, hence smaller xtals. I have tried streak seeding in in drops
carrying additives such as ethanol, isopropanol, ethylene g
Dear All,
Thanks to many of you who posted comments and suggestions.
The review process concluded on our paper.
I will try to distil the suggestions I found useful with some comments from
my own experience.
1 Do not be put off by editor, argue for a technical review in advance of
Dear Petr
In your $CCP4/src/dev_tools_ directory there is a small utility named
readmtz.cpp which I created for use in a situation like this. You will
need to compile it by typing
g++ -o readmtz readmtz.cpp
Then type
./readmtz .mtz
The data will be written out as an ascii file called output.tx
"env | grep SYMINFO" shows nothing. But there was a "Logical Name:
SYMINFO Filename: /protein/ccp4-6.0.2/ccp4-6.0.2/lib/data/syminfo.lib"
line in logfile of all runs. Is it what you mean?
Petr
Partha Chakrabarti wrote:
what happens if you type:
env | grep SYMINFO
Does it show the path? Ei
Dobre den,
If all else fails, use a text editor! I use emacs for this ...
Most of the file will look like garbage, but the header at the end of
the file can be edited. Be very very careful not to change the number of
characters just do replacements.
Send the file to me if you want (and tell
Hey Thomas,
also consider Malvern instruments. Their Zetasizers are really sweet
and work with volumes smaller than 15ul if you use the smallest cuvette.
http://www.malvern.com/LabEng/products/zetasizer/zetasizer.htm
The last DynaPro that I've used, half as old as the universe but
equipped w
Hi Ed,
We are using a Viscotek DLS902. It seems to be robust against all types of
user- and sample-unfriendliness
. So were quite happy at the moment.
The advantage of the system is, that you can use standard cuvettes e.g.
fluorescence 3-window-cuvettes from Hellma with standard window heights.
Hi ,Haitao ,
If I were you ,the first thing I will do is to check xtal using MS and
N-terminal sequencing to know what it is . These need to be done anyway.
At the same time ,try to use the ways describe by other people to
handle the data and search for solution using truncated model without
what happens if you type:
env | grep SYMINFO
Does it show the path? Either Solve or CCP4?
On Tue, Jul 8, 2008 at 10:15 AM, Petr Kolenko <[EMAIL PROTECTED]> wrote:
> Unfortunately, it also failed:
>
> Failed to find spacegroup in SYMINFO!
> MTZTONA4: Fatal error in ccp4spg_register_by_symops
>
>
Dear BB,
Sorry for the off topic question:
I would like to buy a Dynamic Light Scattering system.
Could people suggest which they like the best and/or which is best
value?
I have in the past used a Protein Solutions Dyna Pro with micro cuvette
(I would like a micro cuvette option).
Unfortunately, it also failed:
Failed to find spacegroup in SYMINFO!
MTZTONA4: Fatal error in ccp4spg_register_by_symops
Does anybody know how to fix it?
Petr
Hi!
The interesting thing is that it works on other systems. So there is
something odd about your ubuntu system.
Ah - maybe I have it. You are from Switzerland? What is your locale set
to? Could the commas in the symops be being interpreted as decimal points?
Does it make a difference if yo
When all else fails you can dump the file as an ASCII format using
mtztona4, edit that file to correct the spacegroup and reconvert it to
mtz using na4tomtz.
Eleanor
Petr Kolenko wrote:
Dear colleagues,
I have a ?.mtz file from integration with missing info about the space
group in the SYMINF
Yup, refmac too.
Pavel Afonine wrote:
Not sure for other software, but in phenix.refine you can request to
output I*mFo-J*DFc map, where I and J are any user specified values.
Pavel.
On 7/7/2008 6:00 PM, Meyer, Peter wrote:
It is redundant, but it adds an additional step if someone wanted to
Dear colleagues,
I have a ?.mtz file from integration with missing info about the space
group in the SYMINFO. I tried to modify the file with combat and
mtzutils, but it always ends up in reading the original file with this
message:
Failed to find spacegroup in SYMINFO!
MTZUTILS: Fatal error
If the structure factors are available for the original protein you can
use ALMN to check if there is an agreement between
the two data sets.
(Very old technology but a useful trick)
Other things to check - Does the crystallographic 2fold in P43212
generate a tight dimer?
is there a non-crys
Dear All,
many thanks for all the replies. I have gone with the most
suggested option which was to loosen the sigmas in the dictionary file:
this has worked very well. Other options were to refine in SHELXL
(although George Shedrick cautioned against this - see below) or
phenix.refine.
Florian,
You can use additional planarity restraints for individual base pairs
for low resolution refinement. Easiest way to do this is to define
explicitly individual base pairs and use appropriate weights. You can
include the definitions in the 'dna-rna_restraints.def' file after the
'
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