Dear CCP4
I wish to crystalise a transcription factor in complex with DNA. Are there any
good papers you can recommend on protein-DNA crystallisation?
Also any helpful tips on protein:DNA ratios, protein concentrations or buffer
conditions that have worked for any of you would be most helpful
Th
Hi, it would be nice if you highlight different type of R-factors used in
the literature. I like to understand various kind of R-Factors, their
mathematical formula, and relations among them.
Thank you.
Teri
Thanks a lot!
Wei
At 2013-01-17 17:02:12,"Randy Read" wrote:
This means that the unit cell in the MTZ file obtained from the density is
non-orthogonal, i.e. the angles are not all 90 degrees. Although in principle
we could have made it possible to use non-orthogonal unit cells, it would m
Hi Theresa,
The overexpression of any MP may depend on 100 factors and what you listed
below are just a few!
toufic
On Thu, Jan 17, 2013 at 9:50 PM, Theresa Hsu wrote:
> Dear all
>
> I have a general question on membrane protein overexpression in E. coli.
> Are E. coli proteins expressed in E
If you change it in the def.site file, when you start HKL2000 and select the
detector type, it has to be the one with the name of the directory of the
def.site file that you corrected. If it doesn't have the values that you
entered into the def.site file then you are either not choosing the corr
Dear all
I have a general question on membrane protein overexpression in E. coli. Are E.
coli proteins expressed in E. coli always better in terms of yield, lipid
preservation and so on than another homologous protein?
I am aware that it is different for *crystallization* because of flexible lo
Niu,
Could you give me some information about when you came to NE-CAT and
I will tell you the beam center. We can do this off the CCP4BB. My email
is schue...@anl.gov
Thanks,
Jon
On 01/17/2013 03:19 PM, Niu Tou wrote:
Hi colleagues,
We have collected several datasets at APS with det
Hello Niu,
Have you tried adding the following line to appropriate areas in the macro tab
(indexing, refinement and integration I believe they're called?):
x beam 156 y beam 157
Sincerely,
Scott Classen
On Jan 17, 2013, at 1:19 PM, Niu Tou wrote:
> Hi colleagues,
>
> We have collected seve
Hi colleagues,
We have collected several datasets at APS with detector 24IDE, while
processing date, the beam center is obviously not in position. But no
matter what values we set in "Site Configuration" or "def.site", it remains
about (156, 165). Based on the image, the estimated correct center s
I guess you may have to decide whether you want to modify your current
conditions or just start over to find new conditions, to get around this
"ultra-fast" crystallization. I don't know if you have played around all
parameters of current condition, such as lower temperature, protein
concentration
A year or two ago we switched from Fedora to Scientific Linux 6. It is a
free repackaging of Red Hat Enterprise, so it should be a
straightforward shift from Fedora. It is supported long term, and has
backing from several large labs (fermilab, CERN, etc)
CCP4, Coot, etc. seem to be well-suppor
Thanks Eleanor, your tip has got me there. I was attempting the problem
the wrong way round.
To get it to work
I had to reindex the P212121 h=-l k=k l=h
Then rigid body refinement of the P213 symmetry generated trimer dropped
it to 40% and NCS refinement to around 25%
My reasoning for avoid
Dear Nicholas,
Why do you want to do the same rebuilding twice? Once in the P212121 map
and once guided by the rotated P212121 map?
What I usually do in these cases, and which seems more efficient to me,
is to first complete rebuilding and refinement of the better defined
p212121 structure and t
Polymorphs are another possibility. The packing could be very similar but
the space
group could be different.
Enrico.
On Thu, 17 Jan 2013 15:30:20 +0100, Eleanor Dodson
wrote:
Hard to say without data - but I would generate the 3 symmetry copies of
the molecule you would have in P213,
Hard to say without data - but I would generate the 3 symmetry copies of the
molecule you would have in P213,
then do rigid refinement of those coordinates with the P212121 cell
dimensions and symmetry. There are so many possibilities for origin shifts
But you don't say how non-equivalent the
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Dear Nicholas,
not sure whether it will work - learning by doing:
You might integrate the P213 data set in the subgroup P212121 with the
real P212121 data as reference data set. At least XDS will then choose
consistent indexing.
As last step you repea
I have a structure which normally crystallises in P213 but one data set
the edges became slightly non-equivalent in length by a couple of
angstroms and the data process in P212121
P212121 symmetry operators appears to be a subset of P213
http://img.chem.ucl.ac.uk/sgp/large/019az1.htm
http://img.
That may be the "CALBIOCHEM Buffers Booklet," which is free online as a PDF.
On 01/17/2013 12:38 AM, Mike John wrote:
Hello,
Shameful and sorry for asking this simple question, it looks like this
when first starting a new setup in
so-called structural biology.
I remmeber a book of, probably,
Tim & Eugene
node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-58> which ccp4um
./ccp4um
node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-59> cd
node066:~-60> which ccp4um
ccp4um: Command not found.
node066:~-61> echo $PATH
/software/virtualenv/python2.7/64/cluster/bin: ...
:/software/CCP4-6.3.0/ccp4-6.3.
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Dear Ian,
I am not sure, but maybe the error is caused by $PWD being part of
your path variable so that when you call 'ccp4um' while your cwd is
/software/CCP4-6.3.0/ccp4-6.3.0/bin, python make 'sys.argv[0]' (line
10 in $CBIN/ccp4um) "./ccp4um". This
Yes it's my .login so it's always set up:
node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-47> echo $CCP4
/software/CCP4-6.3.0/ccp4-6.3.0
Cheers
-- Ian
On 17 January 2013 12:51, Tim Gruene wrote:
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> Dear Ian,
>
> did you source the ccp4 input scr
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Dear Ian,
did you source the ccp4 input script so that variables like CCP4 are set?
IOError: [Errno 2] No such file or directory: '/libexec/ccp4um'
looks like CCP4 is an empty string.
Best,
Tim
On 01/17/2013 01:44 PM, Ian Tickle wrote:
> Dea
Dear Eugene
ccp4um doesn't work for me at all (update worked fine up until #012).
node066:/software/CCP4-6.3.0/ccp4-6.3.0/bin-45> ccp4um
Traceback (most recent call last):
File "ccp4um", line 17, in
shutil.copy2 ( fname,fname1 )
File "/software/python/python_v2.7.3_64/lib/python2.7/shuti
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Dear Mike,
I'd be surprised if the book was from Hampton: The pH-value of Hampton
solutions refers to the stock solution of the buffer before setting up
the final solution, and can differ a lot from your drop's pH - e.g. in
the presence of Imidazole o
These days I always ask people to send me the XDS_ASCII.HKL file if they
used XDS, then I can be sure that it is really UNMERGED, which has many
advantages (and I can read it into hkl2map, shelxc or xprep directly).
George
On 01/17/2013 10:37 AM, Graeme Winter wrote:
> Hi Sebastiano,
>
> If the
Thanks Graeme.
Long live and prosper to the unmerged files, then.
ciao,
s
On Jan 17, 2013, at 10:37 AM, Graeme Winter wrote:
> Hi Sebastiano,
>
> If they hand you an *unmerged* mtz file containing scaled data you can
> do this, by remerging the data with Scala or Aimless. Equivalently the
> un
Hi Sebastiano,
If they hand you an *unmerged* mtz file containing scaled data you can
do this, by remerging the data with Scala or Aimless. Equivalently the
unmerged output of scalepack or XSCALE (or XDS CORRECT)
If however you have merged data then you have lost this information,
though complete
Hi all,
maybe a silly question, but I can't figure this out.
Is there a piece of software to calculate "Table I statistics" such as Rsym,
Mn(I/sigI), Multiplicity, Completeness, from a structure factors file already
containing merged structure factors?
That is, if somebody hands me an mtz fil
This means that the unit cell in the MTZ file obtained from the density is
non-orthogonal, i.e. the angles are not all 90 degrees. Although in principle
we could have made it possible to use non-orthogonal unit cells, it would make
things more difficult for us and, since the density has to be c
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