Dear Tim,
My most experience is with HKL2000 which during the index doing something quite
mysterious and not very well described
such as a brute search for the correct reciprocal lattice. I do not know where
initially the reflections are placed by HKL2000,
but finally it converges. In the moment we know our orientational matrix (for
small molecules we need get enough reflections for that doing 5-10 deg
oscillation, again if we intend to use HKL2000), nothing matters (oscillation
range etc.) but
only stepping motors, stability of goniostat, detector spatial resolution and
refinement of parameters. However I will be very glad to be corrected if I am
wrong.
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: mbfro...@post.tau.ac.il
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Mar 25, 2014, at 10:55 , Tim Gruene <t...@shelx.uni-ac.gwdg.de> 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: mbfro...@post.tau.ac.il
>> Tel: ++972-3640-8723
>> Fax: ++972-3640-9407
>> Cellular: 0547 459 608
>>
>> On Mar 25, 2014, at 10:26 , Tim Gruene <t...@shelx.uni-ac.gwdg.de> 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
>>>
>>
>>
>
> --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
