[phenixbb] Space group
mohamed noor
mohamed.noor34 at gmail.com
Fri Sep 4 06:28:01 PDT 2015
Dear all
I processed my images in point group P 3 2 1. After running Phaser and
building it, the space group was P 3(2) 2 1. However, the refinement is
stuck with Rfree at around 35-38 % (data extending to 3.3 A). As I believe
the R factor is a bit high, and I have a different crystal form in P4(2)
2(1) 2 with R free at 25 % for data to 3.8 A, I expanded it to P 1, redid
Phaser searching for 48 copies. After refinement, the R free is at 38 %.
For some reason, Zanuda/Refmac is not able to read my files. So I ran
Xtriage instead:
A summary of R values for various possible point groups follow.
-------------------------------------------------------------------------------------------------------
| Point group | mean R_used | max R_used | mean R_unused | min
R_unused | BIC | choice |
-------------------------------------------------------------------------------------------------------
| P 3 | 0.000 | 0.000 | 0.271 |
0.000 | 3.521e+05 | |
| C 1 2 1 (2*y,-x+y,z) | 0.423 | 0.423 | 0.200 |
0.000 | 1.763e+06 | |
| P 1 | None | None | 0.219 |
0.000 | 1.056e+06 | |
| P 6 | 0.242 | 0.423 | 0.200 |
0.000 | 1.365e+06 | |
| C 2 2 2 (x+y,2*y,z) | 0.271 | 0.423 | 0.200 |
0.000 | 1.464e+06 | |
| P 3 2 1 | 0.000 | 0.000 | 0.423 |
0.423 | 1.761e+05 | |
| P 3 1 2 | 0.242 | 0.423 | 0.200 |
0.000 | 1.365e+06 | |
| C 2 2 2 (2*x,x+y,z) | 0.271 | 0.423 | 0.200 |
0.000 | 1.464e+06 | |
| P 1 1 2 | 0.423 | 0.423 | 0.200 |
0.000 | 1.763e+06 | |
| P 6 2 2 | 0.219 | 0.423 | None |
None | 1.265e+06 | |
| C 1 2 1 (x+y,-x+y,z) | 0.000 | 0.000 | 0.242 |
0.000 | 5.282e+05 | |
| C 1 2 1 (x+y,2*y,z) | 0.423 | 0.423 | 0.200 |
0.000 | 1.763e+06 | |
| C 1 2 1 (x-y,2*x,z) | 0.000 | 0.000 | 0.242 |
0.000 | 5.282e+05 | |
| C 2 2 2 (x-y,x+y,z) | 0.271 | 0.423 | 0.200 |
0.000 | 1.464e+06 | |
| C 1 2 1 (2*x,x+y,z) | 0.000 | 0.000 | 0.242 |
0.000 | 5.282e+05 | |
| C 1 2 1 (x-y,x+y,z) | 0.423 | 0.423 | 0.200 |
0.000 | 1.763e+06 | |
-------------------------------------------------------------------------------------------------------
R_used: mean and maximum R value for symmetry operators *used* in this
point group
R_unused: mean and minimum R value for symmetry operators *not used* in
this point group
Looking at the R values, it is possible that it is actually C 1 2 1.
My questions:
1. What is the difference between the C 1 2 1 lines? What do the values in
brackets mean?
2. Since Xtriage did indicate a possible NCS axis parallel to
crystallographic axis (and it looks almost like that in my P321 model), do
I reintegrate in one of those C121 and then redo Phaser/refinement? I can
post a screenshot of model if that will help.
Thanks.
Mohamed
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