[cctbxbb] Conversion from symmetry operation to matrix

[lesser at helix.nih.gov]

Hi Ralf,

  as a big fan of phenix, I still wonder if there is a way to improve the
output of xtriage. Even after looking at it for a number of years now, I
manage to confuse myself. I for one would prefer clear statements over
probability scores. I never know whether a high number is good or bad (or
what the scale is!) because sometimes a score reflects the probability
whether something is true or whether an assumption is wrong. Would it not be
possible to print likelihood of a space group scaled to 100% ? I realize
that it involves a bit of judgment and you have to evaluate absent
violations and weak violations with different number of occurrences etc.But
still...
 Also what surprises me is that when I run phenix.xtriage or phenix and then
"reflection tools" xtriage, I get different results.

For instance in one test case I get in phenix.xtriage logfile.log:

Analyses of the absences table indicates a number of likely space group
candidates, which are listed below. For each space group, the number of
absent violations are listed under the '+++' column. The number of present
violations (weak reflections) are listed under '---'. The last column is a
likelihood based score for the particular space group.  Note that
enantiomorphic spacegroups will have equal scores. Also, if absences were
removed while processing the data, they will be regarded as missing
information, rather then as enforcing that absence in the space group choices.


------------------------------------------------------------------------------------
| space group | n absent | <Z>_absent | <Z/sigZ>_absent | +++ | ---  | score  
    |
------------------------------------------------------------------------------------
| P 2 2 2     | 0        |     0.00   |     0.00        |  0  |  13  | 
0.000e+00  |
| P 2 21 2    | 0        |     0.00   |     0.00        |  0  |  13  | 
0.000e+00  |
| P 2 2 21    | 11       |     0.09   |     2.03        |  3  |  5   | 
2.413e-01  |
| P 2 21 21   | 11       |     0.09   |     2.03        |  3  |  5   | 
2.413e-01  |
| P 21 2 2    | 9        |     0.21   |     7.53        |  6  |  10  | 
9.251e+00  |
| P 21 21 2   | 9        |     0.21   |     7.53        |  6  |  10  | 
9.251e+00  |
| P 21 2 21   | 20       |     0.15   |     4.51        |  9  |  2   | 
9.492e+00  |
| P 21 21 21  | 20       |     0.15   |     4.51        |  9  |  2   | 
9.492e+00  |
------------------------------------------------------------------------------------


Whereas phenix (gui) gives me negative scores. (see screenshot in attachment).
(View log shows the table as in the logfile.log)

I also attach the output.sca if you want to try it yourself.

I was using phenix 1.7.1-743 on a 64 bit linux system.

Again a clearer output of a list of spacegroups that one could try I think
would be very helpful.

Thanks,

   Lothar





-------------- next part --------------
A non-text attachment was scrubbed...
Name: phenix-gui.png
Type: image/png
Size: 139500 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20110712/1b730cdb/attachment-0001.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: output.sca
Type: application/octet-stream
Size: 394257 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20110712/1b730cdb/attachment-0001.obj>