Dear Francis,
You can visualize SPOT.XDS with adxv.
Since column 3 of SPOT.XDS is the image number of spot centroid,
you can extract spots near frame 4 like this:
awk '{if (int($3+0.5) == 4) print $1, $2;}' SPOT.XDS > spots_04.adx
Then you can load "spots_04.adx" into adxv.
(you must load the image into adxv before reading the spot list)
Best regards,
Takanori Nakane
On 2014-04-15 10:30, Harry Powell wrote:
> Hi Francis
>
> At the risk of offending Wolfgang and Kay, why not try using other
> software to index & visualize spots found on the images? Mosflm is the
> one that comes to my mind straight away, but there are others that
> could probably do the job...
>
> It would certainly be possible to write a jiffy that would read a
> SPOT.XDS and write it in Mosflm .spt format, which could then be read
> directly into iMosflm.
>
> On 15 Apr 2014, at 02:24, Francis Reyes wrote:
>
>> Hi all,
>>
>> I'm trying to diagnose a tricky indexing issue and I suspect the
>> spot picking is poor. Any jiffy's for analyzing the spot.xds file
>> (prior to running IDXREF) ? (like an overlay onto the actual image)?
>>
>> Thanks,
>>
>> F
>>
>> ---------------------------------------------
>> Francis E. Reyes PhD
>> 215 UCB
>> University of Colorado at Boulder
>>
>> ----------------------------------------------
>
> Harry
> --** note change of address **
>
> Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick
> Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH
> Chairman of European Crystallographic Association SIG9
> (Crystallographic Computing)
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