Hi guys,
I was trying to view the simulated annealing omit map generated by Phenix
in Coot. When I opened resolve_composite_map.mtz and *_ed.pdb in Coot, I
could only see one monomer of the protein. It should be two dimers of the
protein plus two pieces of DNA. And when I opened the *_ed.pdb in pym
*Dear All
*In case we have more than one molecule per asymmetric unit, how to look
for the results of the self-rotation function calculation and translation
peak in the native patterson.
--
Regards
Faisal
School of Life Sciences
JNU
I found a fix, but not an explanation. I scaled the same data with
scalepack and had no problem with loosing reflections. I am not sure what
happened in HKL2000.
Ursula
On Fri, Jul 5, 2013 at 12:38 PM, Phil Jeffrey wrote:
> Ursula,
>
> I/sigI of -3 as I recall.
>
> Are you sure that the downstre
Well, the output.sca file contains only 64000 lines ( reflections)
while the logfile lists ~ 73000 reflections, corresponding to about
100% completeness. So I don't understand why only 64000 are written
out.
The sigma cutoff was just a guess, but may not be the reason.
Ursula
On 7/5/13, Phil Jeff
Ursula,
I/sigI of -3 as I recall.
Are you sure that the downstream programs you are using aren't the ones
applying the cutoff ? Scalepack is, in general, perfectly happy to
write negative intensities to output.sca and certainly is doing so as of
HKL3000. Perhaps you need to use the TRUNCATE
Sorry for the non-CCP4 question.
I am confused about the sigma cutoff used by HKL2000 for scaling. I
scaled a data set to 3.0 A resolution. I collected a complete dataset
to 2.8A, but the I/sigma is about 1.0 at 3.0 A. The scaling logfile in
HKL2000 shows 100% completeness in the highest resolutio
Right-click on the shortcut on your desktop, select "properties", and see what
folder
it has for "start in". Try changing it to C:/CCP4/6.3/bin/ if it is not.
Or add that folder to your path.
Perhaps windows has a notion of "current directory" and
includes that in the search path, and when you st
Dear all,
I have a strange behavior of the ccp4 interface.
I have a shortcut icon for my ccp4i on my windows7 desktop, when I open it
and try to open the shelxcde module in the program list it complains about
the missing path for the shelx.
But, but,
when I go to the installation directory C:/CCP
Hi Careina,
Yes it does. I have run ethidium bromide-containing agarose gels of samples
containing poly(dI-dC) and they light up under UV, just like any other
regular DNA does on agarose gels.
Cheers,
Raji
On Fri, Jul 5, 2013 at 9:11 AM, Careina Edgooms wrote:
> Just a quick question, does any
With that translational vector the data set is approximately I centred.
If you integrate it in I centred lattice then you must consider space
groups I 4 or I41.
In point P4 you might need to consider SGs P4, P41, P42, P43
Eleanor
On 1 July 2013 11:19, rajakumara eerappa wrote:
> Dear Fulvio Sa
You have obviously solved this problem, but one thing that can change
apparent Rfactors is the number of reflections accepted..
If one gives you 5% more very weak reflections say, then those will
inevitably have high Rfactors and this can increase the apparent Rfactor
without changing the map appea
Just a quick question, does anybody know if ethidium bromide binds to
poly(dI-dC)?
Careina
Dear Rain Field,
A new xia2 release is now available please see:
http://xia2.blogspot.com
for details. This version should be included in the next CCP4 update.
Once again apologies for the inconvenience.
Best wishes,
Graeme
On 4 July 2013 08:18, Graeme Winter wrote:
> Dear Rain Field,
>
>
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Dear Fei,
are you familiar with the small molecules section at the XDS wiki at
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Small_molecules
?
If you see many warning messages during the INTEGRATE step of unstable
refinement, the too sma
Dear XDSGUI users,
new XDSGUI binaries with new functionality and bugfixes may be
downloaded; the download links are in the XDSGUI article (which has been
improved over the last weeks) in XDSwiki.
Being an acronym, the name of the program has now been decided to be
XDSGUI; on the commandline
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