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Postdoctoral Research Assistant – Ref: 10082
School of Crystallography, Faculty of Science
Full time, fixed term appointment for up to five years
The School of Crystallography/Institute of
I have a structure with an unsaturated lipid in the active site, which
according to the chemists has one cis and one trans double bond. I
would expect these to be controlled by the torsion angles in the cif
files. However altering torsions between 0 and 180 makes no difference
to the
Dear Nic(holas),
Nicholas Keep wrote:
I have a structure with an unsaturated lipid in the active site, which
according to the chemists has one cis and one trans double bond. I
would expect these to be controlled by the torsion angles in the cif
files.
Yes, and a planar restraint (which is
Greetings.
I'm wondering if anyone has ever seen something like this. I have a 2.1 A
data set (synchrotron data) that is nearing completion. I see density that
appears to join a cysteine side chain to a lysine (30 residues away from
each other in primary sequence). There is a picture of the
Hi Andrew
You don't say what your protein is crystallised in, or has seen during
purification, but maybe S- MERCAPTOCYSTEINE might fit?
(search for CSS in MSD CHEM)
Do you have lower wavelength data that you might get a sulphur
anomalous signal to check this?
S-methyl Cysteine might fit as well -
...by lower wavelength, I mean longer wavelength... or lower energy.
Take your pick.
Dave
2008/5/22 David Briggs [EMAIL PROTECTED]:
Hi Andrew
You don't say what your protein is crystallised in, or has seen during
purification, but maybe S- MERCAPTOCYSTEINE might fit?
(search for CSS in MSD
Dear All
I am processing data from a crystal for a large macromolecular complex
with mosflm. Cell dimensions are around 120 x 150 x 650, with a p222
spacegroup. To avoid overlaps, we have collected data with a oscillation
of 0.1 degrees.
When I try to process the data with mosflm, mosaicity
Dear All,
We are in the process of buying a new microscope with
digital camera. Currently we are using MOTIC Digital Stereo Microscope
(Model DMW-143-FBGG)
with built-in CCD camera, but the quality of the crystal pictures is very
poor.
Furthermore the halogen light is quite hot.
I would
Perhaps it should also be noted here that the long crystal axis should be
oriented close to parallel to phi, in order to minimize overlaps. I have
heard anecdotal evidence (anyone else?) that this long axis, in plate
crystals, is usually normal to the surface of the plates.
Dear Francisco,
With a c axis of 650 Angs your phi-overlap problem is severe. When this
axis is close to being parallel to the beam, the angular distance in radians
between h,k,l and h,k,l+1 for a reflection hkl close to the top or bottom of
an image is the angle spanned by c* viewed at a
Hi Francisco,
you could try using these keywords in Mosflm:
POSTREF WIDTH 3
#since you have 0.1 degree oscillation and Mosflm can only handle 30
images at once, the default I believe is 5 images if I'm not mistaken
SEPARATION CLOSE
PROFILE RMSBG 25
POSTREF USEBEAM
Then I would start indexing
Hi,
On Thu, May 22, 2008 at 11:22:19AM -0700, Juergen Bosch wrote:
You can also scratch your head and look at the selfrotation function
of your dataset.
Some of that scratching can be done using GETAX for you - it's in CCP4
(for years), but hasn't got a CCP4i interface (yet: next release will
Hi Partha,
ncs6d did really great things to me a while ago. Similar case as yours, only
one Met site in each of the 4 monomers, pretty horrible maps. I was amazed
how ncs6d could sort its way through the maps and find the ncs operators. As
a simple approach I just took a spherical map around the
This almost does what you want, but not quite.
To quote from the NCS6D manual:
NCS6D uses a set of BONES or PDB atoms as input and tries to find a set
of rotations and translations which maximise the correlation coefficient
between the density at the (BONES) atoms and those at the same atoms
Hi all,
... tried on the ccp4mg bb before ...
ccp4mg is such a nice program, yet it is so slow in my hands. An average
sized map calculated from a mtz file takes about 30s to display, while coot
displays both 2FoFc and FoFc maps in about 5s.
Is there anything I can do to speed things up?
I use:
-
Hello,
Does anyone know if any of these graphical softwares: COOT, UCSF
Chimera, ccp4mg, PyMOL, accepts input from a sgi dialbox? And how to
setup?
We have just got one old SGI 8-dial box working on our linux PC
(Fedora 8, x86_64). But it seems that only O responses to the input...
Sorry for this non-CCP4 question, but I know no better venue to ask this:
Do people see detergent spherulites or other artifacts in crystal screens in
the presence of dodecyl-maltoside or other detergents? Are there any papers
about this? I have seen some papers talking about the relationships
Dear All,
I have a 3 minor questions re refmac internals:
1) does refmac use angle values directly or restrain 1-3
distances for angle restraint setup?
2) the ML coefficients FWT and DELFWT - are they the complete
Fourier coefficients including the exponential, i.e. for example
FWT =
On 23 May 2008, at 02:03, Bernhard Rupp wrote:
Dear All,
I have a 3 minor questions re refmac internals:
1) does refmac use angle values directly or restrain 1-3
distances for angle restraint setup?
Yes. Angles are angles in degrees.
2) the ML coefficients FWT and DELFWT - are they the
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