Hi,
Elongation factor Tu was one of the first E. coli proteins that was
identified as being phosphorylated given certain conditions (early
90s).
What I find interesting is the fact that EF-Tu becomes
hyperphosphorylated if the cells grow at 20 degrees.
Maybe this is also true for other pro
Hi Yangming,
If you change the HETATM records of the ligand to ATOM records in the PDB
file, you can replace the spheres for a surface representation, for which
you can set the transparancy to make it less visible, that might help.
Flip
-Original Message-
From: CCP4 bulletin board [mail
The Fifth International Workshop on X-ray Radiation Damage to Biological
Crystalline Samples will be held at the Swiss Light Source from 13:00
March 3rd to 13:00 March 5th 2008.
This series of workshops was originally concerned with the effects of
radiation damage during investigation of protein s
Dear Yanming,
To show "pretty" density of a model you have to import a ccp4 density
map and display it around your ligand. The simplest solution is using
ccp4 and tick the box "Generate weighted difference maps files in CCP4
format" when running Refmac5 (one or two cycles are enough). Speci
I'd be curious to know if there is any consensus in the community with using
the "carve" command for showing maps. I have never felt comfortable showing
density within a cutoff radius of a particular residue or--even worse--a
ligand, and felt the figures should display the extraneous bits as well.
Dear all,
Sorry I did not make it clear in my first email. Now my question can boil
down to:
IS IT POSSIBLE TO ONLY ZOOM ONE OBJECT AND KEEP ALL THE OTHER OBJECTS
UN-ZOOMED IN PYMOL?
thanks
Yanming
On Mon, 29 Oct 2007, Yanming Zhang wrote:
Hi, all,
I want to make a pymol figure wich can
Dear Rebecca,
a good microscope is very difficult to beat. The reason for this is the
larger numerical aperture (= the maximum cone of light that can enter
the lens) when compared to long and small-diameter tubes with a camera
on top. The resolution of the camera is less important here and it
Just my two cents with a bit of a delay ...
1. I have tried the 'cheap' solution and simply lost not so much
money since it was damped to the junk yard at the end. We now have an
'expensive' solution (Crystal Farm) but - guess what - it works. Our
cheap solution was the BioTom robot, from a
Dear Andrew,
Thank you for that posting; I would like to simply agree with the
Bobscript manual and your suggested practice.
I think the 'carve' commands should not be there; if you wonder why,
take a ligand, put it wherever you want in space,
set the map sigma to -0.5, display a map with c
Anastassis Perrakis wrote:
Dear Andrew,
Thank you for that posting; I would like to simply agree with the
Bobscript manual and your suggested practice.
I think the 'carve' commands should not be there; if you wonder why,
take a ligand, put it wherever you want in space,
set the map sigma to
Thanks very much for all the suggestions so far.
While I am pursuing all the checks and balances for twinning here are
the Wilson plots I forgot to attach before..I am not sure what is going
on, especially in B !
best,
Iain
On Oct 25 2007, Iain Kerr wrote:
Dear all,
I find myself pose
If you put the coordinates into COOT it will give you a validation score.
If you use the CCP$i map correlation procedures it will also give you a
CC for the density match.
The input in each case is the reflection file with appropriate amplitude
and phase terms.
What you use depends on what p
Hi,I just installed the OSX leopard on my Macbook. Tried to run COOT
0.3.3for intel
10.4 which I downloaded from CCP4 webpage. The installation proceeds without
any problem. But, once I try to start it, it fails to start and give the
following error message:
'Dyld Error Message: Symbol not found:
Wilson plots are not very informative for the detection of twinning.
The spikes you see in your Wilson plots, could be due to ise ring
issues (both 3.89 and 2.24 A are at ice ring related d scapings.) The
very large mean intensity in those resolution shells could be due to
the fact that only str
This is not such a problem when using the old "Map-cover" command
in O, because the cut-offs are flat planes, you would get cubic
density around each atom which would raise the suspicion of even
the most gullible reader.
But a better solution would be to not contour the carved surface-
leave a ga
I don't like using 'carve' options but I can see where it may come useful.
On the positive side, in the age where deposition of coordinates and
structure factors is almost mandatory, there shouldn't be a question of how
your map looks because presumably the skeptical reader can go and calculate
on
> contour the real density, but only display the contours within
> certain radius of selected atoms.
That is exactly what PyMOL does.
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Edward Berry
Sent: Monday, October 29, 2007 4:33 PM
To: CCP4BB@JISCMAIL
Hello All!
I have a problem with the output there from CCP4 into the log files on a
dual-Core Intel Mac with Os X Server 10.4 and CCP4 6.0.1.
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
ATOM13 Ano 0.147 -0.001 0.7232.055 BFAC 20.000
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
Hello All!
I have a problem with the output there from CCP4 into the log files on a
dual-Core Intel Mac with Os X Server 10.4 and CCP4 6.0.1.
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
ATOM13 Ano 0.147 -0.001 0.7232.055 BFAC 20.000
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
Hello All!
I have a problem with the output there from CCP4 into the log files on a
dual-Core Intel Mac with Os X Server 10.4 and CCP4 6.0.1.
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
ATOM13 Ano 0.147 -0.001 0.7232.055 BFAC 20.000
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL B ALL
> the Nz test says no twinning
and the intensity stats say this as well.
> but the Britton and H-plots give a twin fraction of
> 0.46-0.47 !
The britton and H test give an estimate of the twin fraction IF THE
DATA IS WOULD BE TWINNED. The fact it gives a non zero value does not
indicate the pres
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