The program that does the indexing in HKL is Denzo. Denzo doesn't care
about the space group. It cares about the point group (cf. Ethan's
point) and the cell dimensions, because it integrates the data without
regard to the symmetry expressed in the intensities - however it does
take notice of the restrictions placed on cell dimensions by point
groups. Denzo therefore picks primitive orthorhombic cells in a<b<c.
Scalepack scales the integrated data but does not reindex the data if
you tell it the space group is P22121. Therefore unit cell choice in
HKL is by default driven by cell edge size. Scalepack has the ability
to reindex the data, for those of us that like to work in P21212 rather
than P22121.
On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt
> Scaling is done in a point group, not a space group.
My quibble with this statement is that the output reflection data from
Scalepack differs depending on what space group you tell it, since
systematic absences along h00, 0k0 and 00l in P2x2x2x are not written
out. The number of reflections affected is quite small, of course.
Phil Jeffrey
Princeton
On 5/7/12 4:48 PM, Jacob Keller wrote:
Is it true that HKL adopts the naming convention of putting the screw
axes first and then naming a<b<c if possible, whereas CCP4 just makes
the cell a<b<c? E.g., would HKL ever output by default a p22121 dataset,
or would it automatically be p21212?
JPK
On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt <merr...@u.washington.edu
<mailto:merr...@u.washington.edu>> wrote:
On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote:
> Hi all,
> I was wondering if anyone knows how to convert the P21221 to P21212
> spacegroup in HKL2000. I scaled the data set in P21212 in HKL
2000 but I
> got a correct MR solution in P21221 spacegroup.
Shya:
Scaling is done in a point group, not a space group.
The point group P222 contains both space groups P2(1)22(1) and
P2(1)2(1)2,
so your original scaling is correct in either case.
It is not clear from your query which of two things happened:
1) The MR solution kept the same a, b, and c axis assignments but made a
different call on whether each axis did or did not correspond to a
2(1) screw.
In this case you don't need to do anything to your files. Just make sure
that you keep the new space group as you go forward into refinement.
2) The MR solution kept the orginal screw-axis identifications but
permuted the axes to the standard setting (non-screw axis is
labelled "c").
In this case you will need to construct a file containing the permuted
indices. For example, the reflection originally labeled (h=1 k=2
l=3) is now
(h=3 k=1 l=2). There are several programs that can help you do this,
including the HKL2000 GUI. But you do not need to go back into HKL
if you don't want to. You could, for example, use the ccp4i GUI to
select
-> Reflection Data Utilities
-> Reindex Reflections
Define Transformation Matrix by entering reflection transformation
h=l k=h l=k
Ethan
> I have a script file that
> runs with scalepack but was wondering if there is an easier way
to do it
> with HKL2000 gui mode.
> thanks,
> Shya
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu <mailto:j-kell...@northwestern.edu>
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