Indexing involves storing all the reflection positions in orthogonal
reciprocal space and then finding a reciprocal lattice that fits most of
them.
For a 10 degree frame all we know is that a reflection lies somewhere on
a sort of 10 degree arc; only two of the three coordinates are
precisely known, which makes indexing difficult. For 0.1 degree frames
all three coordinates of each reflection are known. For the
purpose of indexing, the number of reflections per frame is irrelevant.
Unless one is using a detector like an image plate with a long
read-out time, there is no advantage in using frames significantly wider
than the reflections, they also have a higher background noise level.
This applies equally for small molecules and macromolecules, though for
a strongly diffracting small molecule a higher background can be
tolerated.
George
On 03/25/2014 09:55 AM, Tim Gruene wrote:
Dear Felix,
as far as I understand we are talking about the frame width, not the
total data range for indexing ("10 degree rotations to get enough spots
per frame"). I have used 180degrees of data for indexing. At least XDS
places the reflection at the centre of the frame so that with a 10deg
frame width the position is know within +/-5 degree - it is not
surprising indexing fails here.
Regards,
Tim
On 03/25/2014 09:41 AM, Felix Frolow wrote:
Dear Tim,
I am sure your statement is too general and is not very precise.
10 deg oscillation range is as precise as 0.1 deg. Positions of diffraction
spots on the area detector have
defined position on rotation axis within the precision/accuracy of the stepping
motor and the spacial resolution of the area detector
and NOT defined by oscillation range. If it does, change your setup. We need
sometimes 10 deg to have enough reflections for indexing. Obviously we
need some reflections to define the orientational matrix and cell dimensions.
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular
Microbiology and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail: [email protected]
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Mar 25, 2014, at 10:26 , Tim Gruene<[email protected]> wrote:
Dear David,
I dare claim that rather you do not know how to use the listed programs
in the case for small molecule data rather than none of them were
optimised. E.g. 10degree frames loose all the possible accuracy in the
phi-direction so I am not surprised you had trouble indexing. There is
no reason for that, if you know which parameters to modify.
In addition to that, concluding from one single data set that programs
are not optimised may be a little overinterpreted. In my experience,
this interpretation does not hold.
Best,
Tim
On 03/24/2014 10:03 PM, David Schuller wrote:
Coincidentally, I just spent my day trying to index a lattice of ~ 10 x
10 x 11 A.
Mounting samples: if the compound is stable, just glue it to the end of
a steel pin. No muss, no fuss.
We had to attenuate our synchrotron beam heavily to make it work; motors
can only turn so fast.
We did 10 degree rotations to get enough spots per frame per imaging.
Detector setup allowed for ~ 1 A resolution.
Indexing was a challenge for many of the samples, heavily overloaded
spots and streaks seemed to be causing the most problems.
We tried various of the usual macromolecular programs for indexing;
HKL2000, iMosFlm, XDS, DPS. None of them seem to be optimised for this,
but some of them actually worked in some instances.
On 03/24/14 14:04, Andreas Förster wrote:
Dear all,
I've been approached by a materials student with a petri dish full of
big, sturdy, salty, yellow crystals. He claims I have the best kit
for single-crystal diffraction on campus.
I would very much appreciate advice on how to deal with this, anything
in the range from "won't work" to "use software X to analyze data in
space group P-43N" would be welcome.
Thanks.
Andreas
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582
