<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10pt">hi,<br>the rigid body refinement took 5 hours, not the reduce step.<br><br><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;">this is a run with chain problems and it never finished<br><span></span></div><span>http://musso.ucsc.edu/exporting_reduce/verify_fail/<br>http://musso.ucsc.edu/exporting_reduce/verify_fail/withchain.pdb<br></span><br>this is the pdb with no chain where refine took 5 hours and reduce finished normally<br><div><span>http://musso.ucsc.edu/exporting_reduce/no_chain/</span></div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color:
transparent; font-style: normal;">http://musso.ucsc.edu/exporting_reduce/no_chain/nochain.pdb<br><span></span></div><br><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;">this is a similar run with chain problems and it took 35 hours</div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;">http://musso.ucsc.edu/exporting_reduce/oneproc/<br></div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif;
background-color: transparent; font-style: normal;">thanks</div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;">jpd<br></div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica
Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: normal;"><br></div> <div class="" style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 10pt;"> <div class="" style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 12pt;"> <div dir="ltr"> <hr size="1"> <font face="Arial" size="2"> <b><span style="font-weight:bold;">From:</span></b> Pavel Afonine <pafonine@lbl.gov><br> <b><span style="font-weight: bold;">To:</span></b> phenixbb@phenix-online.org <br> <b><span style="font-weight: bold;">Sent:</span></b> Friday, January 24, 2014 9:00 AM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [phenixbb] exporting results, reduce<br> </font> </div> <div class=""><br><div id="yiv1984740490"><div>
Hello,<br clear="none">
<br clear="none">
usually Reduce takes from a fraction of a second to seconds to run
(provided I understand correctly that Jeff fixed all problems
related to "reduce runs forever"). I wonder how PDB file should look
like so Reduce runs hours. Could you please send me PDB file (off
mailing list, to my email directly)?<br clear="none">
<br clear="none">
Thanks,<br clear="none">
Pavel<br clear="none">
<br clear="none">
<div class="" id="yiv1984740490yqt79423"><div class="">On 1/24/14, 8:44 AM, jp d wrote:<br clear="none">
</div>
<blockquote type="cite">
<div class="" style="color:#000;background-color:#fff;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10pt;">
<div id="yiv1984740490">
<div>
<div class="" style="color:#000;background-color:#fff;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10pt;">hi, <br clear="none">
replying for the sake of posterity.<br clear="none">
the slow export/reduce seems to be related to a malformed
input model.<br clear="none">
the segids are ok but there are some different segids
that have the same chain.<br clear="none">
setting the chain to empty for everything resolved the
issue.<br clear="none">
Using the malformed chain model took 35 hours (if it
finished).<br clear="none">
Using the no chain model took 5 hours.<br clear="none">
<div id="yiv1984740490yui_3_13_0_ym1_9_1390433658735_9"><span>thanks<br clear="none">
jpd<br clear="none">
</span></div>
<div id="yiv1984740490yui_3_13_0_ym1_1_1390433658735_21480"><br id="yiv1984740490yui_3_13_0_ym1_9_1390433658735_11" clear="none">
</div>
<div class="" id="yiv1984740490yui_3_13_0_ym1_9_1390433658735_14" style="font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10pt;">
<div class="" id="yiv1984740490yui_3_13_0_ym1_1_1390433658735_21437" style="font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:12pt;">
<div class="" id="yiv1984740490yqt80954">
<div dir="ltr" id="yiv1984740490yui_3_13_0_ym1_1_1390433658735_21436">
<hr size="1"> <font id="yiv1984740490yui_3_13_0_ym1_1_1390433658735_21479" face="Arial" size="2"> <b><span style="font-weight:bold;">From:</span></b>
jp d <a rel="nofollow" shape="rect" class="" ymailto="mailto:yoyoq@yahoo.com" target="_blank" href="mailto:yoyoq@yahoo.com"><yoyoq@yahoo.com></a><br clear="none">
<b><span style="font-weight:bold;">To:</span></b>
PHENIX user mailing list
<a rel="nofollow" shape="rect" class="" ymailto="mailto:phenixbb@phenix-online.org" target="_blank" href="mailto:phenixbb@phenix-online.org"><phenixbb@phenix-online.org></a> <br clear="none">
<b><span style="font-weight:bold;">Sent:</span></b>
Friday, January 17, 2014 9:53 AM<br clear="none">
<b id="yiv1984740490yui_3_13_0_ym1_1_1390433658735_21597"><span id="yiv1984740490yui_3_13_0_ym1_1_1390433658735_21596" style="font-weight:bold;">Subject:</span></b>
[phenixbb] exporting results, reduce<br clear="none">
</font> </div>
<div class="" id="yiv1984740490yui_3_13_0_ym1_1_1390433658735_21442"><br clear="none">
<div id="yiv1984740490">
<div id="yiv1984740490yui_3_13_0_ym1_1_1390433658735_21441">
<div class="" id="yiv1984740490yui_3_13_0_ym1_1_1390433658735_21440" style="color:#000;background-color:#fff;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10pt;">
<div id="yiv1984740490yui_3_13_0_ym1_1_1390433658735_21478">hi,</div>
<div id="yiv1984740490yui_3_13_0_ym1_1_1390433658735_21477">we
have a large complex at low resolution
(7A) and just want <br clear="none">
</div>
<div class="" id="yiv1984740490yui_3_13_0_ym1_1_1390433658735_21439" style="color:rgb(0, 0, 0);font-size:13.3333px;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;background-color:transparent;font-style:normal;">to
see general conformational changes.
Occasionally phenix</div>
<div class="" style="color:rgb(0, 0, 0);font-size:13.3333px;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;background-color:transparent;font-style:normal;">gets
stuck at 'Exporting Results' and top shows
'reduce' running</div>
<div class="" style="color:rgb(0, 0, 0);font-size:13.3333px;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;background-color:transparent;font-style:normal;">and
using lots of RAM . so much RAM that it
starts using swap.</div>
<div class="" style="color:rgb(0, 0, 0);font-size:13.3333px;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;background-color:transparent;font-style:normal;">is
there a way to bypass or limit the reduce
step.</div>
<div class="" style="color:rgb(0, 0, 0);font-size:13.3333px;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;background-color:transparent;font-style:normal;">thanks</div>
<div class="" style="color:rgb(0, 0, 0);font-size:13.3333px;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;background-color:transparent;font-style:normal;">jpd<br clear="none">
</div>
</div>
</div>
</div>
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<pre>_______________________________________________
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