Clearly, the code can change without anyone knowing!
For this reason, and others, I try to remember to do it manually and to
check. In cases of pseudo-symmetry, for example P21 with a 90.2 deg
beta angle and high tNCS, the software may or may not decide it should
pick free flags in the P222 setting, but it probably "should".
To do it manually, you want to re-index to the higher space group using
"reindex"
Then pick your free flags
Use "cad" with "outlim" feature to symmetry-expand the data
Use "cad" again to change the space group back
One final run through "cad" to clean things up and make sure you have
the right asymmetric unit.
That's what I do, anyway,
-James Holton
MAD Scientist
On 8/31/2021 3:04 AM, Eleanor Dodson wrote:
Espec. Jan & Kay,
I had better check this out - ville wrote the code I believe, and I
have never actually checked the distribution!
Cheers Eleanor
On Tue, 31 Aug 2021 at 08:01, Jan Dohnalek <dohnalek...@gmail.com
<mailto:dohnalek...@gmail.com>> wrote:
This is good to know indeed.
Will improve my teaching now, I also did not know this is now done
automatically. Thanks for pointing it out.
Jan
On Mon, Aug 30, 2021 at 9:44 PM Kay Diederichs
<kay.diederi...@uni-konstanz.de
<mailto:kay.diederi...@uni-konstanz.de>> wrote:
Dear Eleanor,
Thanks for pointing out that CCP4 FreeRflag selects the test
set in the highest possible symmetry for the crystal class! I
didn't know that.
The following sentences (which are somewhat difficult to
understand for me) in
https://www.ccp4.ac.uk/html/freerflag.html
<https://www.ccp4.ac.uk/html/freerflag.html> appear to
document that:
"The FreeR_flag is randomly and uniformly distributed
reflexion-by-reflexion, but, additionally, if the keyword
NOSYM is not set, all reflections that are equivalent by the
symmetry of the point group of the twin lattice (assuming the
data is twinned), obtain the same flag. This includes both the
possibility of merohedral and pseudomerohedral twinning. In
the latter case, the obliquity parameter can be set using the
keyword OBL."
I wonder since which CCP4 version (or date) this is the
default behaviour.
best wishes,
Kay
On Mon, 30 Aug 2021 18:28:23 +0100, Eleanor Dodson
<eleanor.dod...@york.ac.uk <mailto:eleanor.dod...@york.ac.uk>>
wrote:
>Back to FreeR factors - Phenix, and I believe FreeRflag now
select FreeRs
>in the highest possible symmetry for the crystal class - eh
P6/mmm for a
>trigonal crystal, and expand the set to fill the actual space
group. This
>means the Free R assignment is suitable if later the crystal
symmetry is
>reassigned. But this was not always done in the past so if
you are trying
>to reuse free/work assignments from an old project there are
possibilities
>of not getting this. Maybe the best solution is to just
generate a new Free
>R set ?
>Eleanor
>
...
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