Dear all,
I received a few replies to my request, all but Pavel's privately.
Those included suggestions of using moleman2, pymol, baverage (from ccp4).
Several required manual intervention like visual selection of the
responding atoms, which made them less appealing to me.
I used Robbie
In the case of F1-ATPase they are not biologically independent copies in the
a.u. though, rather subunits of a biological complex...
(but perhaps I interpreted the question to narrowly)
Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin
Dear Shane,
Human antithrombin III (code 1ath) is a dimer of an active and latent
conformation.
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Shane
Caldwell
Gesendet: Montag, 27. Januar 2014 19:09
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Examples of
Dear Shane,
To add a bit of detail to Frank von Delft's suggestion,
perhaps the best example is the structure of the yeast F1-ATPase that has 3
copies in the asu, from David Mueller's lab in Chicago. Two of these are very
similar, but the third is rather different and
Hi there,
another nice kinase example might be IRAK-4. there are several pdbs,
the one I have in mind is 2OIB. The alphaC helix that takes on
different conformations in active and inactive conformations in
kinases ('in' and 'out') is in four different positions in the four
different
If you are including two copies in a single biological complex, then the two
halves of the reverse transcriptase heterodimer have dramatically different
domain organizations (OK, one copy is truncated - losing one whole domain out
of five; PDB codes ad nauseam). Indeed one stretch of sequence
Dear Shane,
the others have already given very good examples of high impact
biology structures; I would still like to add the structure PDB:1J49
(Razeto et al. (2002). JMB 318, 109).
Its a structure of a D-Lactate dehydrogenase, a two-domain enzyme, where
one ASU subunit adopts an open and
Dear All,
Does anyone have experience with the FreezerMill for lysing E coli?
see:
http://www.spexsampleprep.com/products_by_category.aspx?cat=2
It seems to be more for tissues, but perhaps it could also be used for lysing
reasnoble quantities of E coli - the reason for asking is that I have to
Hi Shane,
One example that comes to mind is aquaporin-z. Two protomers were found in the
ASU, one contained the water channel in an open conformation while the other in
a closed conformation. The structural differences are not “large” but the
functional implication is.
Here is the primary
We do not have experience with this product. We use a BeadBeater. Can
handle up to 25-30 g of wet packed cells in the medium beater jar. The
large jar will handle maybe 3-5x that, but I've never had to go to that
scale.
___
Roger Rowlett
Gordon Dorothy Kline
Another interesting example might be a structure of Mad2, protein essential
in the process of chromosome segregation. Protein has 2 different secondary
structure topologies and both of them are part of the AU in 2V64. There are
other X-ray structures where only one of the conformations is captured
Hi all,
I am trying to generate a high resolution figure of a molecule together
with its symmetry mates (250 A readius) for a poster. If I try to ray it,
the pymol session crashes (perhaps too many molecules are open). Using png
xxx.png, dpi=300 or dpi=600 command doesn't make any difference; the
CCP4MG?
On 28 Jan 2014, at 15:27, A K wrote:
Hi all,
I am trying to generate a high resolution figure of a molecule together with
its symmetry mates (250 A readius) for a poster. If I try to ray it, the
pymol session crashes (perhaps too many molecules are open). Using png
xxx.png,
The Industrial Special Interest Group and Young Scientists Special Interest
Group of the American Crystallographic Association will be hosting a scientific
session on Sunday, May 25, 2014 during the ACA Meeting in Albuquerque, New
Mexico which will highlight research by young scientists
Hi Alex -
I'm not surprised you're having memory issues. I just tried this test
with one of my molecules. Simply generating and displaying the symmetry
mates in a 250 A radius required 4 G of memory, and the raytracing would
have needed a lot more (I only have 8 G on this computer, so I
Hi Alex -
You can also try reducing the value of
`hash_max`http://www.pymolwiki.org/index.php/Hash_max (e.g. `set hash_max,
50`). The default value is 130; a lower number reduces the memory PyMOL tries
to obtain for ray tracing. The trace will take longer, but hopefully will get
you through
Dear all,
I recently collected several datasets for a protein that needs experimental
phasing.
The crystals are hexagonal plates, and (automatic) data processing suggests
with high confidence that the space group is P622. This is where the fun begins.
For some datasets (processed in P622), the
Hi Alex,
If you don't mind forgoing the ray tracing, you may try the draw command to
specifically set the resolution (and antialiasing) to your needs, and then save
the image.
Yong
--
Dear Bert Van-Den-Berg,
as far as I understand this, if you have true P622, process the data in
P6 and then test for twinning, both the Britton-test and H-test will
indicate perfect merohedral twinning.
This is because the Britton-test checks for a sudden increase of
negative intensities
Dear Crystallographers,
Your are invited to submit your abstract for the Exciting Structures session
at the upcoming ACA meeting (Albuquerque May 24-28. 2014).
The focus of this session is to provide young scientists an opportunity to
present highly relevant structures of biological
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