Hi Rui, for some reasons, I also always encounter problems when building new
ligand by CCP4 Sketcher. You can try PRODRUG (
http://davapc1.bioch.dundee.ac.uk/prodrg/index.html) to build your new
ligand and get the cif from the server, it always works for me.
HTH,
Matt
2009/11/27 rui
> Hi,
>
> I
David had developed an empirical theory to model the air, solvent,
Compton & acoustic contributions and correct the integrated data for
these, without background correction of course since the optic DS
background was ultimately to be our data!
...
Hi Ian, did David publish this theory somewhere
this doesnt exactly go to the detail i was looking for...
but thanks, i do know where the pages are.
tommi
On Nov 26, 2009, at 9:52 PM, Jacques-Philippe Colletier wrote:
Hi Tommi
You will find all the information you need on the following web page:
http://www.phenix-online.org/documentation/
Dear colleagues!
I would like to draw your attention to two new job opportunities that have
opened up at the Protein Data Bank in Europe (PDBe) at the EBI (Hinxton, UK)
and that will hopefully interest some of you:
- Software Engineer/Scientific Programmer - to work on database integration
a
Hi Tommi
You will find all the information you need on the following web page:
http://www.phenix-online.org/documentation/refinement.htm
as per your question, you could try :
phenix.refine yourdataset.mtz yourmodel.pdb strategy=rigid_body
rigid_body.number_of_zones=1 sites.rigid_body="chain
Hi,
I found this old post in ccp4 and it's very useful. I used the same
procedure Scott described to add a ligand into pdb file. What I did, is in
coot, search for the ligand in the library and find the ligand and then
merge. However, when I tried to refine in refmac, it has some problems, it
comp
Apologies, i know this is not phenix bb but since i am here (and not
subscr. there), does anyone
know how to control rigid body ref positions in phenix.refine, i am
trying to do very low res check
(6 Å) with quite many molecules, and they start landing on each other
while the MR solution from
Please unsubsribe me for all the listings from CCP4b.
Thanks
Sapna
Ian
Surely the Bragg peaks, acoustic and optic components of the diffuse
scatter all occupy a finite volume in reciprocal space. In x-ray
scattering/diffraction the area they occupy on a detector therefore
expands as the detector is moved further away. However, one will not
always see this. If the
Postdoctoral/Research Associate in Structural Biology - Division of Molecular
Biosciences - Imperial College - London
Applications are invited for a Cancer Research UK funded Research Associate
position investigating structure and mechanism of cell signalling systems
involved in ER stress. The
Hi Colin
Yes I know, I worked with David Moss at Birkbeck for many years to
develop software to process the DS data. I think the point of using
finely collimated SRS X-rays (from the Daresbury SRS of course!) was to
scale down the spot size of both the Bragg & acoustic peaks by the same
factor, s
Ian
Maybe - maybe not.
Investigations of acoustic and optical components of diffuse scatter
from proteins were carried out in the 80s and 90s including of course
work at Birkbeck (which I am sure you are aware of)
Refs can be found in Glover et. al. Acta Cryst. (1991). B47, 960-968.
This paper i
Hmm - I dont understand that.
I ran structure idealisation on both examples and that tidies up the
geometry perfectly..
Are there some clashes with pre-existing water molecules or other
indicators in the log file that one conformation is suspect?(Look for
warnings..)
Eleanor
John Pasca
> The source for the X-ray background are points along the air path
> post-collimator including the sample with loop and cryoprotecdant (or
> capillary and mother liquor). So the 1/r^2 falloff is
> noticable going from
> 100 mm to 200 mm. The same counts in a 2x2 pixel area is now
> seen in a 4
hello
this is not a new question i was searching this in archives but i
did'nt get .
just send me link for this .
i want to link AMP covalently with lysine in my structure (phosphoamide
bond)how i will do this in coot and refmac .
in turbo there is option make bond but in this n
I think you have a found a supercell and dont really need to run any MR
program to find the solution - just reposition the molecule
Your P422 point group cell is
126.514 126.514 76.766 90.00 90.00 90.00
Your I422 point group cellis:
180.096 180.096 152.530 90.00 90.00 90.00
Note c
Dear Users,
The PDBe site is scheduled for hardware maintenance on Thursday 26th
November starting at 2pm. This will effect all web resources until 10am
on the 27th.
Additionally all deposition and annotation services of new entries will
not available.
We shall update the status on the PDBe m
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