Dear Niu,
concerning XDS: there is no way, using just XDS.INP, to force the IDXREF step
to use a cell that is not compatible with the reflections that COLSPOT found.
But I can think of two ways to reach your goal (even if I believe that
crystallographically it makes no sense to ignore every second existing
reflection).
a) stop after the IDXREF step that uses all reflections, and gives you the 40A
axis that you want to halve (suppose it is the "a" axis). Next, edit SPOT.XDS
and remove
all lines which have (in this example) odd h. This can be accomplished with
mv SPOT.XDS SPOT.XDS.all
awk '{if ($5%2==0) print $0}' SPOT.XDS.all > SPOT.XDS
Then, run IDXREF and subsequent steps - they will use the short a axis.
b) stop after the IDXREF step that uses all reflections, and gives you the 40A
axis that you want to halve (suppose it is the "a" axis). Next, edit two lines
in XPARM.XDS: line 4, which has the cell parameters (halve a in this line), and
line 5, which has the direction of the a axis in space (halve all 3 values).
Then, run DEFPIX and subsequent steps - they will use the short a axis.
Hope this helps,
Kay
On Mon, 18 Nov 2013 17:03:06 -0500, Niu Tou <niutou2...@gmail.com> wrote:
>Dear Andrew,
>
>As previously I posted a MR case which has a significant 95% off origin
>peak, some experts suggested to reprocess the data with cutting one axis to
>half, from 40A to 20A. I tried HKL2000 and XDS, none of them is willing to
>give a solution with 20A, even I specify it in XDS script. So I wonder is
>there any way to force this work to be done. Thanks!
>
>Best,
>Niu
>
>
>On Mon, Nov 18, 2013 at 4:56 PM, Andrew Leslie <and...@mrc-lmb.cam.ac.uk>wrote:
>
>> Dear Niu,
>>
>> It depends on which part of processing you are referring
>> to, i.e. the indexing step or the integration step. In MOSFLM there is no
>> way to enforce cell dimensions during indexing, but providing there is an
>> indexing solution that has cell dimensions close to the ones you want, you
>> can enforce a (slightly) different set of cell dimensions during the
>> integration step. Normally other refined parameters will ensure that you
>> still get a good prediction of spot positions.
>>
>> I suspect that this can be done in other programs too.
>>
>> Without knowing why you want to do this, I cannot comment on whether this
>> is the best procedure to follow.
>>
>> Best wishes,
>>
>> Andrew
>>
>>
>>
>> On 18 Nov 2013, at 21:48, Niu Tou <niutou2...@gmail.com> wrote:
>>
>> > Dear All,
>> >
>> > Does any one know how to strictly fix the cell dimensions during data
>> processing? In HKL2000 there is only a keyword to define the longest
>> vector. In XDS there is a option to input cell parameters, but sometimes
>> the program would not follow the input values
>> > and switch back to the one it thinks best. Any suggestions will be
>> appreciated. Thanks!
>> >
>> > Best,
>> > Niu
>>
>>
>
