Dear all crystallographers,
Recently I have collected two data sets from two different crystals, first data
at 2.6A and second is at 1.9A, the datasets were isomorphous. I tried to merge
the two dataset as a single MTZ file using CAD (CCP4i), but it is unsucces
Dear all
I use scala 6.1
Even though I scale my native data, scala outputs anamolous data
statistics in these columns:
Nmeas Nref Ncent %poss C%poss Mlplct AnoCmp AnoFrc AnoMlt Rmeas
Rmeas0 (Rsym) Rpim RpimO PCV PCV0
I use "anamolous off" for scala and "anamolous no" for ctruncate. My
co
Dear Atul,
you mention the anomalous statistics in the log-file. Is this what bothers you?
There is nothing wrong with it, and you should check whether or not your final
data set has merged Friedel pairs or not. It probably has, and that's what you
want, isn't it?
Tim
On Thu, Sep 30, 2010 at 0
You don't have to. The anomalous values (F+, F-, Dano) are included in the file
in case you need them later. You can just ignore them
Phil
On 30 Sep 2010, at 08:33, atul kumar wrote:
>
> Dear all
>
> I use scala 6.1
>
> Even though I scale my native data, scala outputs anamolous data
> stat
If you want to merge them into a single dataset, you need to go back to the
unmerged intensities (ie the output of eg Mosflm), combine them together, best
done with Pointless (ccp4i task "Find or match Laue group") and scale them
together in eg Scala (task "Scale and merge intensities" )
Phil
Different numbers of columns wont stop CAD working, but if you have the
any occurence of the same labels in either file this will produce an
error mesage - eg Label FreeRflag found twice..
And if you have labelled both data sets as Fnew or some such
uninformative label, then again you will hav
Hello,
we are currently preparing a tutorial for a practical from lysozyme data.
pointless picked the spacegroup P41212 and phaser should show the students that
P43212 is the correct spacegroup. How do I best change the scala-mtz-file to
that spacegroup? Can I tell pointless (and eventually rerun
Hi Tim,
Is it as easy as
reindex hklin a.mtz hklout b.mtz << eof
symm P43212
eof
This will simply (and correctly) reassign the symmetry operations. Is
this what you meant?
Best wishes,
Graeme
On 30 September 2010 10:49, Tim Gruene wrote:
> Hello,
>
> we are currently preparing a tutorial for
This recent discussion does tend towards the ideal scenario: of identifying ones
best-diffracting crystals... before embarking on the synchrotron trip.
The established Oxford Diffraction PX Scanner home laboratory instrument can
therefore be most useful. This enables the direct X-ray scree
Marcus,
May I ask the following: assuming 8 A is obtained from a single
crystal on the home source, what diffraction limit would one expect
on the PX scanner?
Best regards,
Klaus
===
Klaus Fütterer,
Or
mtzutils hklin1 a.mtz hklout b.mtz <
Hi Tim,
Is it as easy as
reindex hklin a.mtz hklout b.mtz << eof
symm P43212
eof
This will simply (and correctly) reassign the symmetry operations. Is
this what you meant?
Best wishes,
Graeme
On 30 September 2010 10:49, Tim Gruene wrote:
Hello,
we a
Does any one have T H Bhats email - He was at RSCB I think but is
probably retired.
Eleanor
Thanks for everyone who replied (and so quickly)
The space group can be changed with
PROG hklin in.mtz hklout out.mtz << eof
symm P43212
eof
where PROG is 'reindex' (Graeme Winter), 'mtzutils' (Eleanor Dodson), 'cad'
(Phil Evans, Manfred Weiss), or 'sortmtz' (Manfred Weiss), all of which are also
Another possibility is with sftools, set spacegroup option
Fred.
PS not in ccp4i
Graeme Winter wrote:
Hi Tim,
Is it as easy as
reindex hklin a.mtz hklout b.mtz << eof
symm P43212
eof
This will simply (and correctly) reassign the symmetry operations. Is
this what you meant?
Best wishes,
Gr
Here is the link to his home page at NIST
http://www.nist.gov/cstl/biochemical/cell_systems/talapady_n_bhat.cfm
Frances
=
Bernstein + Sons
* * Information Systems Consultants
5 Brewster
Dear all,
i have a 30 kDa protein that crystallize so far in three different conditions
but with the same space group. It initially looks like tetragonal (I4, a=141,
b=141, c=208) and then results triclinic (P1, a=141, b=141 c=144, alpha=119,
beta=119, gamma=90), hosting about 24 mol. in the uni
Mario,
beside what you were mentioning, I would definitely try a quick soak (10-30
seconds) of the crystals in cryo conditions supplemented with halides such as
NaBr, or NaI, at pretty high concentrations (say 0.5 M), then directly freezing
without backsoak.
If the crystals survive the treatment
Dear Mario,
what is the resolution of the data? Could you try SeMet-MAD/SAD or some other
phasing method to overcome the MR-problem?
Tim
On Thu, Sep 30, 2010 at 12:54:36PM +0100, Mario Milani wrote:
> Dear all,
> i have a 30 kDa protein that crystallize so far in three different conditions
> b
Thank you for the suggestions. The data resolution is 1.9 so i can try
different heavy atoms techniques ... anyway i am really puzzled by the
peculiar assembly in the crystal and on the possible causes... does anyone
know about similar cases?
mario
>
> Mario,
> beside what you were mentioning, I w
What does this mean?
You index what looks to be tetragonal, do your collection, and then it
integrates/scales only in P1?
F
On Sep 30, 2010, at 5:54 AM, Mario Milani wrote:
> It initially looks like tetragonal (I4, a=141, b=141, c=208) and then
> results triclinic (P1, a=141, b=141 c=144, al
Hello Mario,
at 1.9A you might even give S-SAD a try, especially if you have access to an
inhouse source with the flexibility to collect data with a (real) high
multiplicity.
Tim
On Thu, Sep 30, 2010 at 02:40:26PM +0200, Mario Milani wrote:
> Thank you for the suggestions. The data resolution is
Yes, this sort of thing happens a lot more often than one might think,
but people who have crystals with such "high-copy asymmetric units" tend
to not solve them. Hence, they don't end up in the PDB. In cases where
the structure is eventually solved, it is usually done by finding an
alternati
Hi James,
Can you, or anybody else, point me to a publication where "...not that
uncommon for one or more crystal symmetry operators to "collapse" upon
cryo-cooling..."
Thanks,
Nukri
Ruslan Sanishvili (Nukri), Ph.D.
GM/CA-CAT
Biosciences Division, ANL
9700 S. Cass Ave.
Argonne, IL 60439
Tel: (63
no publication springs to mind immediately (often apparently of non scientific
relevance) but I have seen it on numerous occasions so fully support James'
comment.
All you need to do is read the IUCr tables (yes, boring, but occaisionally
useful) to see how simple it actually is.
Liz
__
Folks,
I am not questioning James - I just would like to see some papers if
there are any so I can use them as reference.
Cheers,
N.
Ruslan Sanishvili (Nukri), Ph.D.
GM/CA-CAT
Biosciences Division, ANL
9700 S. Cass Ave.
Argonne, IL 60439
Tel: (630)252-0665
Fax: (630)252-0667
rsanishv...@anl.gov
@R.Brown
Resolution 3.2A
DENZO suggests P6.
Angles are 90,90,120
Data completeness ~95%
R-merge-0.06
Wilson B-factor 42.0
There are a couple of papers...
Acta Cryst. (2010). F66, 346-351
Crystallization and X-ray diffraction studies of cellobiose phosphorylase from
Cellulomonas uda
The space group was originally P21. During collection the crystal moved out of
the beam (and possibly the cyrostream). Upon recenter
To Eleanor,
I changed the column label for two data sets, FreeR_Flag for the first data and
F_x for the second data.
Now CAD compiled the data successfully.
The merged MTZ file contains column label like this
H K L FreeR_Flag F_x
I conclude to use this file fo
Nukri poses a very good question. Fortunately for me, I think others
are answering it:
Daniel Bonsor has emailed me a couple of relevant references, which I
reproduce here:
-
Acta Cryst. (2010). F66, 346-351=20
Crystallization and X-ray diffraction studies of cellobiose
phos
Mario,
As others have asked, why/how did you decide on P1? You mentioned
pseudo-translation being present. Depending on the location in the
Patterson map this could be a pseudo-centering operator showing an
apparent I4 space group. If this is the case you may want to reindex in
the P4 cell
we had a P1 case with 12 mols/au, about 30% sequence id, 2.4A
resolution, which was solved after a lot of trials with phaser. Other
problems of these crystals were that they took months to grow and
invariable presented multiple lattices (we did not try microbeam).
See:
Crystallization of t
Here is an example that is is not cryocongelation but spacegroup change
upon cooling :
Garavito RM, Jenkins J, Jansonius JN, Karlsson R, Rosenbusch JP. X-ray
diffraction analysis of matrix porin, an integral membrane protein from
Escherichia coli outer membranes. J Mol Biol. 1983 Feb 25;164(2):31
We had a P1 case with 8 molecules/asu and the crystal diffracted to 2A
resolution. Initial indexing showed that the data could be indexed in P212121
space group but the data could not be merged in this space group (Rsym 60%). P1
was the only space group that we could merge the data (Rsym 10%).
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