<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Tatyana,<br>
<br>
could you please send me the data and model files (off-list) so I
can investigate? I will post the summary on phenixbb once we know
what's going on.<br>
<br>
I see a number of potential issues but I don't want to waste time
guessing, since it's much more efficient if you send me the files
then I run some tests and tell you how to proceed.<br>
<br>
I'm pretty confident there is a quick fix.<br>
<br>
Thanks!<br>
Pavel.<br>
<br>
On 7/30/11 11:35 AM, Tatyana Sysoeva wrote:
<blockquote
cite="mid:CAGikDO7iCFgb=fP=LyM1mGQzZ1++HY=FVoJT5SfAbE-166SbYg@mail.gmail.com"
type="cite">I ran the same commands with the build dev-833.<br>
Below are the results. <br>
These parameters are obtained by running phenix.ramalyze, cbetdev,
and clashscore.<br>
I am almost done repeating fix-rotamers run. First time it gave a
way worse validation results then before running phenix without
fix_rotamers=true. <br>
I don't understand what I am doing wrong in the runs and would
appreciate your help!<br>
<br>
Thanks,<br>
Tanya<br>
<br>
<br>
<p class="MsoNormalCxSpFirst" style="text-align: justify;"><span
style="font-size: 12pt; font-family:
"Arial","sans-serif";">I used
phenix-dev-833 to test the
riding hydrogens refinement at 3.6A.</span></p>
<p class="MsoNormalCxSpLast" style="text-align: justify;"><span
style="font-size: 12pt; font-family:
"Arial","sans-serif";">I ran two
indentical commands:</span></p>
<p class="MsoPlainText" style="text-align: justify;"><span
style="font-size: 12pt; font-family:
"Arial","sans-serif";">Command line
arguments: "model.pdb"
"data.mtz" "main.ncs=true"
"ncs.find_automatically=false" "ncs_groups.params"
"refinement.input.xray_data.high_resolution=3.6"
"mgadpbef.cif"
"refinement.ncs.excessive_distance_limit=None"
"strategy=individual_sites+individual_sites_real_space+group_adp+occupancies"</span></p>
<p class="MsoNormalCxSpFirst" style="text-align: justify;"><span
style="font-size: 12pt; font-family:
"Arial","sans-serif";"><span style="">�</span>with
the only difference in the input files �
ncs.params and model.pdb</span></p>
<p class="MsoNormalCxSpMiddle" style="text-align: justify;"><span
style="font-size: 12pt; font-family:
"Arial","sans-serif";">Model pdb contained
the model
identical to the control run but with added H atoms. I have
not add H to the
ADP molecules since I did not know how to write a correct CIF
file for it. NCS
definitions were changed by addition of �and not (element H)�
to each line. It
was done to exclude H from the NCS groups.</span></p>
<table class="MsoTableGrid" style="border-collapse: collapse;
border: medium none;" border="1" cellpadding="0" cellspacing="0">
<tbody>
<tr style="">
<td style="width: 239.4pt; border: 1pt solid windowtext;
padding: 0in 5.4pt;" valign="top" width="319">
<p class="MsoNormalCxSpMiddle" style="margin-bottom:
0.0001pt; text-align: justify;"><u><span
style="font-size: 12pt; font-family:
"Arial","sans-serif";">no
hydrogens</span></u></p>
</td>
<td style="width: 239.4pt; border-width: 1pt 1pt 1pt medium;
border-style: solid solid solid none; border-color:
windowtext windowtext windowtext -moz-use-text-color;
padding: 0in 5.4pt;" valign="top" width="319">
<p class="MsoNormalCxSpMiddle" style="margin-bottom:
0.0001pt; text-align: justify;"><u><span
style="font-size: 12pt; font-family:
"Arial","sans-serif";">with
hydrogens</span></u><span style="font-size: 12pt;
font-family:
"Arial","sans-serif";"></span></p>
</td>
</tr>
<tr style="">
<td style="width: 239.4pt; border-width: medium 1pt 1pt;
border-style: none solid solid; border-color:
-moz-use-text-color windowtext windowtext; padding: 0in
5.4pt;" valign="top" width="319">
<p class="MsoPlainTextCxSpFirst" style="text-align:
justify;"><span style="font-size: 12pt; font-family:
"Arial","sans-serif";"># Date
2011-07-29 Time 19:09:58 EDT -0400 (1311980998.46 s)</span></p>
<p class="MsoPlainTextCxSpMiddle" style="text-align:
justify;"><span style="font-size: 12pt; font-family:
"Arial","sans-serif";">wall clock
time: 2646.75 s</span></p>
<p class="MsoPlainTextCxSpMiddle" style="text-align:
justify;"><span style="font-size: 12pt; font-family:
"Arial","sans-serif";">�</span></p>
<p class="MsoPlainTextCxSpMiddle" style="text-align:
justify;"><span style="font-size: 12pt; font-family:
"Arial","sans-serif";">Start
R-work = 0.2891, R-free = 0.3267</span></p>
<p class="MsoPlainTextCxSpLast" style="text-align:
justify;"><span style="font-size: 12pt; font-family:
"Arial","sans-serif";">Final
R-work = 0.2868, R-free = <span style="background:
none repeat scroll 0% 0% yellow;">0.3304</span></span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;
text-align: justify;"><span style="font-size: 12pt;
font-family:
"Arial","sans-serif";">�</span></p>
</td>
<td style="width: 239.4pt; border-width: medium 1pt 1pt
medium; border-style: none solid solid none; border-color:
-moz-use-text-color windowtext windowtext
-moz-use-text-color; padding: 0in 5.4pt;" valign="top"
width="319">
<p class="MsoPlainTextCxSpFirst" style="text-align:
justify;"><span style="font-size: 12pt; font-family:
"Arial","sans-serif";"># Date
2011-07-29 Time 20:14:20 EDT -0400 (1311984860.16 s)</span></p>
<p class="MsoPlainTextCxSpMiddle" style="text-align:
justify;"><span style="font-size: 12pt; font-family:
"Arial","sans-serif";">wall clock
time: 6517.60 s</span></p>
<p class="MsoPlainTextCxSpMiddle" style="text-align:
justify;"><span style="font-size: 12pt; font-family:
"Arial","sans-serif";">�</span></p>
<p class="MsoPlainTextCxSpMiddle" style="text-align:
justify;"><span style="font-size: 12pt; font-family:
"Arial","sans-serif";">Start
R-work = 0.2910, R-free = 0.3273</span></p>
<p class="MsoPlainTextCxSpLast" style="text-align:
justify;"><span style="font-size: 12pt; font-family:
"Arial","sans-serif";">Final
R-work = 0.2720, R-free = <span style="background:
none repeat scroll 0% 0% yellow;">0.3353</span></span></p>
<p class="MsoNormalCxSpFirst" style="margin-bottom:
0.0001pt; text-align: justify;"><span style="font-size:
12pt; font-family:
"Arial","sans-serif";">�</span></p>
</td>
</tr>
<tr style="">
<td style="width: 239.4pt; border-width: medium 1pt 1pt;
border-style: none solid solid; border-color:
-moz-use-text-color windowtext windowtext; padding: 0in
5.4pt;" valign="top" width="319">
<p class="MsoPlainText" style="text-align: justify;"><span
style="font-size: 12pt; font-family:
"Arial","sans-serif";">clashscore
<span style="background: none repeat scroll 0% 0%
yellow;">31.77</span></span></p>
</td>
<td style="width: 239.4pt; border-width: medium 1pt 1pt
medium; border-style: none solid solid none; border-color:
-moz-use-text-color windowtext windowtext
-moz-use-text-color; padding: 0in 5.4pt;" valign="top"
width="319">
<p class="MsoNormalCxSpFirst" style="margin-bottom:
0.0001pt; text-align: justify;"><span style="font-size:
12pt; font-family:
"Arial","sans-serif";">clashscore
<span style="background: none repeat scroll 0% 0%
yellow;">96.12</span></span></p>
</td>
</tr>
<tr style="">
<td style="width: 239.4pt; border-width: medium 1pt 1pt;
border-style: none solid solid; border-color:
-moz-use-text-color windowtext windowtext; padding: 0in
5.4pt;" valign="top" width="319">
<p class="MsoPlainText" style="text-align: justify;"><span
style="font-size: 12pt; font-family:
"Arial","sans-serif";">cbeta <span
style="background: none repeat scroll 0% 0% yellow;">0</span></span></p>
</td>
<td style="width: 239.4pt; border-width: medium 1pt 1pt
medium; border-style: none solid solid none; border-color:
-moz-use-text-color windowtext windowtext
-moz-use-text-color; padding: 0in 5.4pt;" valign="top"
width="319">
<p class="MsoNormalCxSpFirst" style="margin-bottom:
0.0001pt; text-align: justify;"><span style="font-size:
12pt; font-family:
"Arial","sans-serif";">cbeta <span
style="background: none repeat scroll 0% 0% yellow;">151</span></span></p>
</td>
</tr>
<tr style="">
<td style="width: 239.4pt; border-width: medium 1pt 1pt;
border-style: none solid solid; border-color:
-moz-use-text-color windowtext windowtext; padding: 0in
5.4pt; background-color: rgb(255, 255, 255);" valign="top"
width="319">
<p class="MsoPlainText" style="text-align: justify;"><span
style="font-family: "Courier New";
background-image: none; background-repeat: repeat;
background-attachment: scroll; background-position: 0%
0%; -moz-background-clip: border;
-moz-background-origin: padding; -moz-background-size:
auto auto;">rama 12.62</span><span style="font-family:
"Courier New";">% outliers</span><span
style="font-size: 12pt; font-family:
"Arial","sans-serif";"></span></p>
</td>
<td style="width: 239.4pt; border-width: medium 1pt 1pt
medium; border-style: none solid solid none; border-color:
-moz-use-text-color windowtext windowtext
-moz-use-text-color; padding: 0in 5.4pt;" valign="top"
width="319">
<p class="MsoNormalCxSpFirst" style="margin-bottom:
0.0001pt; text-align: justify;"><span style="font-size:
10.5pt; font-family: "Courier New";
background: none repeat scroll 0% 0% rgb(255, 255,
255);">rama 19.67</span><span style="font-size:
10.5pt; font-family: "Courier New";
background-color: rgb(255, 255, 255);">% outliers</span><span
style="font-size: 12pt; font-family:
"Arial","sans-serif";"></span></p>
</td>
</tr>
</tbody>
</table>
<p class="MsoNormalCxSpMiddle" style="text-align: justify;"><span
style="font-size: 12pt; font-family:
"Arial","sans-serif";">�</span></p>
<p class="MsoNormalCxSpMiddle" style="text-align: justify;"><span
style="font-size: 12pt; font-family:
"Arial","sans-serif";">Interestingly in
previous release
version the same refinement runs produced:</span></p>
<p class="MsoNormalCxSpMiddle" style="text-align: justify;"><span
style="font-size: 12pt; font-family:
"Arial","sans-serif";">without H
clashscore = 77.580195/cbeta
=8</span></p>
<span style="font-size: 12pt; font-family:
"Arial","sans-serif";">with H clashscore =
119.729960/cbeta=330</span><br>
<br>
<br>
<pre wrap="">
<fieldset class="mimeAttachmentHeader"></fieldset>
_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<br>
</body>
</html>