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Hi Ralf,<br>
<br>
The log files are attached.<br>
They are same regardless of the version of phenix.<br>
<div class="moz-signature"><br>
<font color="#000099" face="Times">
Thanks, <br>
Abhinav </font>
<p><font color="#000099" face="Times">
</font>
<font color="#0099AA" face="Verdana" size="-1">
JCSG@SSRL, SLAC <br>
(650) 926-2992 <br>
</font></p>
</div>
<br>
On 05/01/2012 10:31 PM, Ralf Grosse-Kunstleve wrote:
<blockquote
cite="mid:CAPbyqJG3uyHFegBDXQ+uGivhRPwtXW9UA3o0c+xsAaZN1sm6JA@mail.gmail.com"
type="cite">Could you send me (not the list) the outputs of:
<div><br>
</div>
<div>phenix.mtz.dump junk.mtz</div>
<div>iotbx.reflection_file_reader junk.mtz</div>
<div><br>
</div>
<div>from both versions of phenix?</div>
<div><br>
</div>
<div>Ralf</div>
<div><br>
</div>
<div><br>
<div class="gmail_quote">On Tue, May 1, 2012 at 3:22 PM, Abhinav
Kumar <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:abhinavk@slac.stanford.edu" target="_blank">abhinavk@slac.stanford.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000099"> Hi,<br>
<br>
When I try to do R vs R analysis for calculated data using
xtriage, it has a problem accepting calc labels.<br>
<br>
source
/home/sw/rhel5/x86_64/phenix/phenix-1.7.3-928/phenix_env <br>
phenix.xtriage_1.7.3-928 junk.mtz calc_labels=FC<br>
<br>
==> Sorry: No matching array:
scaling.input.xray_data.calc_labels=FC<br>
<br>
Howevere, it works fine with an earlier version:<br>
<br>
source
/home/sw/rhel5/x86_64/phenix/phenix-1.6.4-486/phenix_env <br>
phenix.xtriage_1.6.4-486 junk.mtz calc_labels=FC
<div> <br>
<font color="#000099" face="Times"> Thanks, <br>
Abhinav </font>
<p><font color="#000099" face="Times"> </font> <font
color="#0099AA" face="Verdana" size="-1"> JCSG@SSRL,
SLAC <br>
<a moz-do-not-send="true"
href="tel:%28650%29%20926-2992"
value="+16509262992" target="_blank">(650)
926-2992</a> <br>
</font></p>
</div>
<br>
<br>
-------- Original Message --------
<table border="0" cellpadding="0" cellspacing="0">
<tbody>
<tr>
<th nowrap="nowrap" valign="BASELINE" align="RIGHT">Subject:
</th>
<td>RE: SP16569N-180314</td>
</tr>
<tr>
<th nowrap="nowrap" valign="BASELINE" align="RIGHT">Date:
</th>
<td>Tue, 1 May 2012 15:09:00 -0700</td>
</tr>
<tr>
<th nowrap="nowrap" valign="BASELINE" align="RIGHT">From:
</th>
<td>Miller, Mitchell D. <a moz-do-not-send="true"
href="mailto:mmiller@slac.stanford.edu"
target="_blank"><mmiller@slac.stanford.edu></a></td>
</tr>
<tr>
<th nowrap="nowrap" valign="BASELINE" align="RIGHT">To:
</th>
<td>Kumar, Abhinav <a moz-do-not-send="true"
href="mailto:abhinavk@slac.stanford.edu"
target="_blank"><abhinavk@slac.stanford.edu></a></td>
</tr>
</tbody>
</table>
<br>
<br>
<pre>Hmm, it seems like it may be a bug introduced into phenix.
(or else they changed they syntax and did not update the
documentation)
Can you report it? I get it to do the RvR analysis for calculated
data if I use
source /home/sw/rhel5/x86_64/phenix/phenix-1.6.4-486/phenix_env
phenix.xtriage_1.6.4-486 junk.mtz calc_labels=FC
but if I use
source /home/sw/rhel5/x86_64/phenix/phenix-1.7.1-743/phenix_env
phenix.xtriage_1.7.1-743 junk.mtz calc_labels=FC
or
source /home/sw/rhel5/x86_64/phenix/phenix-1.7.3-928/phenix_env
phenix.xtriage_1.7.3-928 junk.mtz calc_labels=FC
then I get the error
Sorry: No matching array: scaling.input.xray_data.calc_labels=FC
Thanks,
Mitch
P.S. the results I got were:
R vs R statistic:
R_abs_twin = <|I1-I2|>/<|I1+I2|>
Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95
R_abs_twin observed data : 0.451
R_abs_twin calculated data : 0.502
R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2>
R_sq_twin observed data : 0.279
R_sq_twin calculated data : 0.335
The analyses of the Patterson function reveals a significant off-origin
peak that is 44.82 % of the origin peak, indicating pseudo translational symmetry.
The chance of finding a peak of this or larger height by random in a
structure without pseudo translational symmetry is equal to the 1.4447e-04.
See the relevant section of the logfile for more details.
The results of the L-test indicate that the intensity statistics
behave as expected. No twinning is suspected.
Even though no twinning is suspected, it might be worthwhile carrying out
a refinement using a dedicated twin target anyway, as twinned structures with
low twin fractions are difficult to distinguish from non-twinned structures.
-----Original Message-----
From: Kumar, Abhinav
Sent: Tuesday, May 01, 2012 1:30 PM
To: Miller, Mitchell D.
Subject: Re: SP16569N-180314
I am having trouble inputting Calc labels to xtriage:
My mtz file has the following columns: FreeR_flag FP SIGFP FC PHIC FC_ALL PHIC_ALL FWT PHWT DELFWT PHDELWT FOM PHCOMB
I tried "FC,PHIC" and "FC" for calc labels but xtriage does not like it.
It writes:
No matching array: scaling.input.xray_data.calc_labels=FC
Possible choices:
/mnt/exdsstaff/abhinavk/Refine/SP16569N-180314/RESULTS/current.mtz:FP,SIGFP
/mnt/exdsstaff/abhinavk/Refine/SP16569N-180314/RESULTS/current.mtz:FOM
/mnt/exdsstaff/abhinavk/Refine/SP16569N-180314/RESULTS/current.mtz:PHCOMB
Thanks,
Abhinav
JCSG@SSRL, SLAC
<a moz-do-not-send="true" href="tel:%28650%29%20926-2992" value="+16509262992" target="_blank">(650) 926-2992</a>
On 05/01/2012 12:51 PM, Miller, Mitchell D. wrote:
Also, you could try running xtriage with FC's from the untwined refinement
to look at the R vs R stats for Fc vs Fobs.
</pre>
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