Hi
I don't think Phil or I are saying that HKL is not a good tool to use
in this case - but
(*) I develop Mosflm, so I have a certain bias.
(*) As far as Pointless and Aimless are concerned, to get the best
out of them you need to have some geometrical information that the
authors of HKL have not included in the reflection output files.
Mosflm (and XDS & Saint...) do give this information. So if you want
to use Pointless and Aimless at any point, it may be better to use a
different integration package than HKL (bearing in mind Phil's point
about checking your symmetry with Pointless)...
On 1 Aug 2012, at 16:16, Uma Ratu wrote:
Please correct me if I am wrong:
The HKL is not good to combine multiple data sets, even they are
come from the same crystal?
With HKL, I also tried this way:
Index, integrate each data set individually, they all have the same
space group.
Then scale them together.
Still, the graph from scale of the whole set look very wired
compared with those of individuals.
Uma
On Wed, Aug 1, 2012 at 9:55 AM, Phil Evans <p...@mrc-lmb.cam.ac.uk>
wrote:
Note that neither Aimless nor Scala will do a particularly good job
at scaling data from Denzo or Scalepack, since the output files
from Scalepack are missing essential geometrical information. They
work well with data from Mosflm or XDS (or Saint) (although AFAIK
the XDS & Saint scaling programs work perfectly well)
However, Pointless may still be useful to check that you have
indexed them consistently
Phil
On 1 Aug 2012, at 14:36, Harry Powell wrote:
> Hi
>
> I'd process (i.e. index, refine, integrate) each data set
individually, check that (at least) they all have the same crystal
system, then combine the datasets using Pointless. Then scale with
Aimless.
>
> Of course, I'd use Mosflm/Pointless/Aimless rather than HKL, but
that's another question (pace, ZO, WM, MM!)
>
> On 1 Aug 2012, at 14:08, Uma Ratu wrote:
>
>> The data sets were collected from the same crystal by "scan"
collecting 40 frames from each section. The space group of this
crystal is P2.
>>
>> My guess that I may have to index and integrate each set
indivadually, and then scale them together.
>>
>> Thanks
>>
>> Uma
>>
>> On Wed, Aug 1, 2012 at 9:01 AM, Machius, Mischa Christian
<mischa_mach...@med.unc.edu> wrote:
>> Not much info to go by...
>>
>> Anyway, if the program 'goes crazy' you either have very
different exposure levels, radiation damage leading to non-
isomorphism, or you have a trigonal space group (P3xxx or P6xxx)
and forgot to make sure all batches are indexed the same way.
>>
>> If you have translated your crystal between batches, HKL2000
won't of course be able to process all batches in one go. If you
haven't touched the crystals at all, and alln-in-one processing
doesn't work, the parameters at the end of one batch may not be
accurate to start off a new batch, which is mostly due to
inaccurate goniostats. In that case, you will need to process the
batches individually and them combine them during scaling.
>>
>> Hope that helps.
>>
>> MM
>>
>>
>> On Aug 1, 2012, at 8:50 AM, Uma Ratu wrote:
>>
>> > Dear All:
>> >
>> > I collected 5 data sets from one crystal and would like to
process them together.
>> >
>> > Here is how I did:
>> >
>> > In HKL2000, load the all data sets. "Index" each set. When I
try "Intergrate", the program automatically go through the whole
data sets there, and do not go through.
>> >
>> > I then process data sets by loading one at each time. Index,
intergrate and scale all go through very smoothly. But when I put
them together, the program just goes crazy.
>> >
>> > Thank you for advice
>> >
>> > Uma
>>
>>
>
> Harry
> --
> Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,
Hills Road, Cambridge, CB2 0QH
>
>
>
Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,
Hills Road, Cambridge, CB2 0QH
