Dear Hubing,
since your crystal is smaller than the beam, the shape of your spots
will be the shape of your crystal as viewed from the spot position on
the detector. This means that if your crystal has a rod shape, spots at
certain detector positions will have a rod shape. If your crystal has
Dear Hubing,
Thankyou for the extra details.
The MARCCD to my experience does not show 'bleeding' from pixels at strong
spots. Such effects on a CCD anyway are in a line not like the 'ears' you
have here.
It also does not look like diffuse scattering.
So, since it seems to be an effect visible on
Dear all
Herman might be correct in this case but spot shapes can be affected by
imperfactions in the crystal rather than the crystal shape.
Some types of imperfections (e.g. strain) manifest themselves more for
higher resolution data. They are still there for the low resolution
data, but buried
Hi folks
I'm wondering if the ears may be due to hollow ends of the rod-shaped
crystals? Hollow ends are more common than you might imagine (especially in
rods), and it's fairly easy to see how they could give rise to these ears...
On 25 Nov 2010, at 09:09, Colin Nave wrote:
Dear all
Herman
In the past I've collected data on crystals with hollow ends and the
spots were round and had no ears. As it was 15years ago, collecting on
the old SRS my recollection of beam and crystal relative size is a
little hazy but I think they were fairly well matched (both 200um).
Dr. Liz Duke
Oh dear - Yes you are right
There is an old program called compar
See http://www.ccp4.ac.uk/dist/html/compar.html
Here is the example script. You need the same residue numbering in each,
so if the sequence of the 2 coordinate files is different you will need
to run CHAINSAW to renumber one
Dear Hubing,
please don't discard a structure just because the Rfree 30%, or approve a
structure just because the Rfree 30%. Other quality parameters like relative
absence of clashes and Ramachandran outliers are much more important. Perhaps
even more important is whether the structure gives
I have had excellent service from Mike Weldon (m.a.wel...@bioc.cam.ac.uk) at
PNAC University of Cambridge Biochemistry. He will accept outside orders
subject to capacity being available.
http://www.bioc.cam.ac.uk/pnac/
Cheers
Martyn
Martyn Symmons
EBI - Cambridge
On 24/09/2010 4:46,
I would second that suggestion, I just had some bands sequenced to
identify internal cleavage sites within a protein and got very clear
sequence back.
Cheers
Tom
On Thu, Nov 25, 2010 at 11:20 AM, MARTYN SYMMONS
martainn_oshioma...@btinternet.com wrote:
I have had excellent service from Mike
Jeff Keen is good, but just to add to the list Cambridge Peptides
http://www.cambridgepeptides.com/proteinsequencing.html based in Birmingham
(!), is fast and efficient from either membrane or directly from gel slices.
Yours,
Mark
On 24 September 2010 16:46, Rex Palmer rex.pal...@btinternet.com
Dear CCP4
I looped a v.thin rod emerging from a cluster of v.thin rods that grew in
29%PEG1500 and 0.1M SPG buffer at pH7.5 (succinic acid, sodium dihydrogen
orthophospate and glycine). The loop i used had been washed more than 10 times
with deionised water (so assumed as 'clean'). The
Hi,
You're working with a very 'rich' crystallization condition. It probably was
supersaturated or close to super-saturated with respect to something, and
that something crashed out on the surface (where liquid contacted air)
forming a crust. Your loop (while perfectly clean) can also be the
The shell may be denatured protein. Remove the protein from the
experiment and the problem will likely go away.
On 11/25/10 09:45, Rick wrote:
Dear CCP4
I looped a v.thin rod emerging from a cluster of v.thin rods that grew in
29%PEG1500 and 0.1M SPG buffer at pH7.5 (succinic acid, sodium
Hi,
In our hands, the crystallisation droplets of glycosomal pyruvate phosphate
dikinase had a 'skin' of what I thought was denatured protein at the surface of
every crystallisation droplet. We had to learn to use the crystal microtools
(such as a microknife, or a micro-needle can't remember
Dear All,
Possibly a trivial question but your experience would be much appreciated:
I recently submitted a structure to PDB containing 3 DTT (dithiothreitol)
molecules, or so I thought. The molecules had been imported and fitted with
Coot using the Get Monomer... instruction with the code
Hi Emmanuel,
it is hard for me to imagine that Coot has the wrong stereoisomer. So what
I think might have happend is the following:
You have imported the correct DTT, but when you have fitted the molecule
into the map you might have distorted the sterochemistry at the C3 atom.
And then it was
If it's on a glass coverslip, another good trick is to (carefully) cut
through the skin around the crystal with a razor blade. With some
practice, one manages not to get the crystal entangled in the skin.
On Thu, 2010-11-25 at 16:03 +, Frederic VELLIEUX wrote:
Hi,
In our hands, the
Credit where it's due, Coot's Get Monomer is just a wrapper for LIBCHECK.
If you look at the restraints for DTT after Get Monomer, you will notice
that chiral centres are both marked as both. Using the restraints
editor (or otherwise) change them to positive (C2) and negative (C3)
and
DTT.cif in $CLIBD_MON has explicit chiralities, assuming these are right
DTT chir_01 C2 C1 O2 C3positiv
DTT chir_02 C3 C2 O3 C4negativ
On 25 Nov 2010, at 17:11, Paul Emsley wrote:
Credit where it's due, Coot's Get Monomer is just a
Often you can also avoid this skin formation by adding a bit of your reservoir
solution first to make it a larger droplet.
Then the microtools as mentioned earlier or just two loops
Jürgen
..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of
Hi Emmanuel,
The monomer library is great, but it is also created by scientists (and
computers) that can err. I remember a few cases (some reported on the
ccp4bb) where mistakes were revealed and later fixed. Just because
something is in the monomer library that does absolve anyone from not
21 matches
Mail list logo
