On Tuesday, November 16, 2010, James Stroud wrote:
> I was reading the PNAS author guidelines and I came across this gem:
>
> Datasets: Supply Excel (.xls), RTF, or PDF files. This file type will be
> published in raw format and will not be edited or composed.
>
> Did I read those last two file
I was reading the PNAS author guidelines and I came across this gem:
Datasets: Supply Excel (.xls), RTF, or PDF files. This file type will be
published in raw format and will not be edited or composed.
Did I read those last two file formats correctly? I have actually came across a
dataset in su
Take any protein where a helix moves as a rigid body and look at your results.
Then fix the alpha helix and superimpose the rest of the structure on that
moving helix and compare both results.
If you want to give it a shot try 2pc4 and the unliganded structure.
You see the difference in both meth
There was a thread about this topic--dyes--a little while back. It
seemed that many many dyes work, not just methylene blue. I believe
there was even an over-the-counter mercury-bromine compound
(merbromin?) which was suggested by Artem, as it would provide a nice
derivative as well.
JPK
On Tue,
One problem with a dye like methylene blue is that it tends to crystallize
in certain conditions commonly found in crystallization screens (e.g. some
that are high in PEG) making them less useful in such conditions. Has
anybody systematically tested alternative dyes and found one that is more
solu
I strongly agree with Eric Larson’s suggestion on trying to see the diffraction
of your crystal. The most straightforward solution. Other suggestions may work
too, but there are chances they will still give you false positives.
If you need bigger crystals, try to slow down the nucleation (use lo
With Izit or other dyes, you might wish to do a positive control with bona
fide protein crystals and a negative control with bona fide salt crystals.
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Matthew Bratkowski
Sent: Tuesday, November 16, 2010 7:58 PM
To: CC
I like using Izit dye from Hampton (
http://hamptonresearch.com/product_detail.aspx?cid=4&sid=41&pid=33) to check
if crystals are protein or salt. If the crystals are protein, the dye
should absorb rather readily into the crystals and turn them blue, while the
rest of the drop will eventually turn
>>The lowest rmsd might not be the biological relevant one
True, however the least square fit using the right residues (thus producing the
lowest rmsd possible) can really tell you the most significant differences (or
not signifcant ones) that cause biological changes. Human eyes are often not
Dear all,
We are investigating the possibility to upgrade from an old 35mm film
camera to a digital camera for taking crystal pictures through a
microscope (Olympus CH30 already equipped with a trinocular port.)
To avoid overpriced cameras from optics companies (at least $900 not
including ad
Hi Bryan
If it's an odd image here and there, that's right. If there's
something weird about part of an individual frame, I'd more than half
expect there to be other inconsistencies about the image as well - so
it might be the right thing to exclude it from processing in any case.
On 16
If you have a polarizer on your microscope you could see if they are extremely
dichroic, in which case they may be salt. You could also open the well up and
see if they are heavy - do they sink immediately when you lift them to the top
of the drop? This could also indicate salt. But I agree with
Hi Raspudin,
you can use plotmtv for the *.mtv files. If you have a running fink
install, than you can install it quiet easily with "fink install plotmtv".
Cheers,
Georg
Am 16.11.10 20:52, schrieb Raspudin:
Dear all,
Could anyone please suggest me a program to open scatter plots (" .mtv " f
Dear all,
Could anyone please suggest me a program to open scatter plots (" .mtv " file
format) from SHELXD/autoSHARP run in OS X Platform.
Thank you,
Raspudin
Hi Yibin,
MiTeGen offers different loops that make it easier to pick really tiny crystals
which can be diffracted at the synchrotron.
If you would like to optimize small needles or rod shaped crystals, you may try
an additive screen.
You may also try to lower the rate of crystal growth.
Perha
Hi Yibin,
I cannot tell the actual scale of your crystals but judging by the curve of the
drop outline, these crystals look to be plenty big enough to mount in a loop to
stick in the beam and test diffraction. If indeed they are too small to mount a
single crystal, and you are mainly intereste
[ mosflm 7.0.6 ]
[ imosflm 1.0.4 ]
wondering if users can define a mask to associate with specific frames.
e.g. if theres something weird on one region of frame 23, make a mask
to block that part out only, and for all other frames, use the default
mask for beamstop shadow.
AFAIK the only way to
Dear Laurie,
your cysteines might all be cytines, i.e. all paired and not really be the
reason for the aggregation. Since you have soluble protein as long as MBP is
tagged to it, why don't you test a large number of conditions for solubility?
I'd probably start with a 3-D screen testing 2-4 diffe
Hi Laurie,
What E. coli strain did you use? As you describe about your protein, I guest
your protein may required disulfide bonds to be folded correctly. E. coli
cytoplasm is a reduced environment, which is not suitable to make disulfide
bonded proteins. to solve this problem it is recommended to
All -
We are trying to express for structural studies a 257 AA eukaryotic
intracellular (also possibly nuclear) protein (predicted to be single domain
all-helical) that has 12 Cysteines. No known metal-binding function not
that it couldn't happen. So far (E. coli) it expressed solubly as MBP
fus
Dear Fulvio,
Mosflm attempts to read the phi start and end
angles from the image header, but on some synchrotron beamlines this
information is not written correctly to the header, which would
explain the error message. Alternatively, if you have really collected
a "st
Dear all,
I received this error message from ipmosflm. I started ipmosflm from
terminal, entered the detector (detector marccd) loaded the image and
then press go. Can anyone help me?
"Phi values have not been specified on AUTOINDEX keyword, and
oscillation range from image header is zero. Supply
Hi,
Can you explain what you want to do?
Do you just want more of some tRNA corresponding to a codon that is rare in E.
coli you can use the pRare2 plasmid that you can easily isolate from the
Rosetta2 strain (or use Rosetta2 directly if you don't mind).
If you just want some extra tRNA produ
My favorite tools for doing this are:
http://webapps.embl-hamburg.de/rapido/
and/or
http://www.theseus3d.org/
Reading some of the associated papers will not hurt inchoosing when to
apply which one!
A>
On Nov 14, 2010, at 22:52, E rajakumar wrote:
Dear All
I have two structures of homo-d
Well - I usually use the COOT ncs map generation first.
You place waters into good peaks in the 3 fold averaged map -say it is A
B C - check that there are reasonable peaks in the other rotated maps -
then once the waters are generated for A, fit those coordinates A to B
and save them, then A t
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