[phenixbb] Re: 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 *Sent:* Wednesday, December 24, 2025 10:58 PM *To:* [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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