Hello Jorge,
If it is a pseudo two fold, then the reflections relating the pseudo two fold are not identical, so should not be scaled and merged together. Even if they are very close in value/ intensity, these intensities should not be merged (under almost all circumstances). The programs are pretty good about picking a fairly random set of free R reflections and setting the space group to P1 should allow everything to work as it should. There is nothing that should be done if it is a pseudo two fold.
If it is a crystallographic two fold, then you do need to process in the monoclinic space group to make sure everything works properly and an appropriate set of free R reflections are chosen.
I hope that helps, Tom
________________________________
From: Jorge Iulek
Sent: Thursday, December 25, 2025 8:57 AM
To: Tom Peat ; [email protected]
Subject: Re: [phenixbb] transform C2 to P1 and the R-free set
Hi, Tom,
Thanks for your input.
Hello Jorge,
I'm not sure I understand your question, so this answer may not be appropriate, but: if you think the two fold is pseudo, why not just run with the P1 space group?
Setting the space group to P1 will allow the program you use to get an appropriate set of reflections for your free R set and your working set.
But I think in this case it would not know about the pseudo 2 so it will not care to include reflections related by this "nearly" 2 fold in the R-free set.
Well, one question here might be how much the 2 fold should depart from crystallographic to pseudo-crystallographic such that a (free) random free set would not be influenced by the pseudo 2 fold.
Cheers,
Jorge
Happy holidays, Tom
________________________________
From: Jorge Iulek mailto:[email protected]
Sent: Wednesday, December 24, 2025 10:58 PM
To: [email protected]mailto:[email protected] mailto:[email protected]
Subject: [phenixbb] transform C2 to P1 and the R-free set
Dear all,
I got a set of images (very recently) . Dials gives me:
+------------+--------------+--------+--------------+----------+-----------+-------------------------------------------+----------+-----------+
| Solution | Metric fit | rmsd | min/max cc | #spots |
lattice | unit_cell | volume |
cb_op |
|------------+--------------+--------+--------------+----------+-----------+-------------------------------------------+----------+-----------|
| * 2 | 0.3001 | 0.066 | 0.272/0.272 | 10685 | mC
| 212.43 81.92 133.04 90.00 113.12 90.00 | 2129290 | a-2*b,a,c |
| * 1 | 0 | 0.052 | -/- | 10559 | aP
| 81.95 113.64 133.10 68.50 89.98 69.13 | 1065523 | a,b,c |
+------------+--------------+--------+--------------+----------+-----------+-------------------------------------------+----------+-----------+
Many indications are that the 2-fold axis is not really
crystallographic, but a pseudo one. My point in this case is that
reflections related by this "almost" 2-fold axis should go into the same
set, free and work, this in the (new) P1 setting.
I could not devise clearly how to get a program to do this
automatically (say, flag reflections with this pseudo 2 related for
free -set ) . Is there? I understand cb_op is the real space operation,
possibly out of a crystallography package I can get that, but easier if
there is a crystallographic tool.
Any thoughts?
Thanks,
Jorge
(Season's Greetings)
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