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Hi Peter,<br>
<br>
one more question... What is "Z absent: mean normalized intensity for
absent reflections"? I mean:<br>
<br>
- what this values is supposed to tell?<br>
- one can normalize things in many various ways. What is the
normalization procedure in this particular case?<br>
<br>
Thanks!<br>
Pavel.<br>
<br>
<br>
On 4/20/09 9:00 PM, Pavel Afonine wrote:
<blockquote cite="mid:49ED44CB.5010005@lbl.gov" type="cite">
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
Hi Peter,<br>
<br>
what does "score: a likelihood based score combining all info" exactly
mean? What is the "good value" (and why), what is "so-so value", and
what is the "bad value" (and why)? Could you please give a reference to
where this score is defined and its use is evaluated?<br>
<br>
I asked myself all these questions when I read this phrase in your
reply below and, sorry for my ignorance, I failed to find the answers.<br>
<br>
Thanks!<br>
Pavel.<br>
<br>
<br>
On 4/20/09 12:06 PM, Peter Zwart wrote:
<blockquote
cite="mid:bbd5677f0904201206u27dcc5d6y139b7e97df12a38f@mail.gmail.com"
type="cite">
<pre wrap="">2009/4/20 <a moz-do-not-send="true"
class="moz-txt-link-rfc2396E" href="mailto:sbiswas2@ncsu.edu"><sbiswas2@ncsu.edu></a>:
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
I tried running phenix xtriage with a scaled data in P4322 space group. I
got the following output:
-----------------------------------------------------------------------------------
| space group | n absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- |
score |
-----------------------------------------------------------------------------------
| P 4 2 2 | 0 | 0.00 | 0.00 | 0 | 5 |
0.000e+00 |
| P 41 2 2 | 0 | 0.00 | 0.00 | 0 | 5 |
0.000e+00 |
| P 42 2 2 | 0 | 0.00 | 0.00 | 0 | 5 |
0.000e+00 |
| P 43 2 2 | 0 | 0.00 | 0.00 | 0 | 5 |
0.000e+00 |
| P 4 21 2 | 8 | 1.71 | 8.07 | 6 | 3 |
4.817e+00 |
| P 41 21 2 | 8 | 1.71 | 8.07 | 6 | 3 |
4.817e+00 |
| P 42 21 2 | 8 | 1.71 | 8.07 | 6 | 3 |
4.817e+00 |
| P 43 21 2 | 8 | 1.71 | 8.07 | 6 | 3 |
4.817e+00 |
Can anyone explain what these numbers mean? It seems all enantiomorphic
space groups have the same score (which is the last column)
</pre>
</blockquote>
<pre wrap=""><!---->
n absent: number of absent intensities according to spacegroup
Z absent: mean normalized intensity for absent reflections
Z/sigZ: 'signal to noise' of absent reflections
+++ : reflections that seem present that should be absent
---- : reflections that seem absent but should be present
score: a likelihood based score combining all info
If you want, you can send me your sca file and I can have look to make
sure that nothing is messed up.
Cheers
Peter
</pre>
<blockquote type="cite">
<pre wrap="">The documentation in phenix does not explain this in detail.
I scaled the data in HKL2000 and there was no systematic absences with
P43222.
Thanks,
Shya
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