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Hello,<br>
<br>
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>
<br>
Thanks,<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 1/24/14, 8:44 AM, jp d wrote:<br>
</div>
<blockquote
cite="mid:1390581841.72650.YahooMailNeo@web161701.mail.bf1.yahoo.com"
type="cite">
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<div
style="color:#000;background-color:#fff;font-family:HelveticaNeue,
Helvetica Neue, Helvetica, Arial, Lucida Grande,
sans-serif;font-size:10pt;">hi, <br>
replying for the sake of posterity.<br>
the slow export/reduce seems to be related to a malformed
input model.<br>
the segids are ok but there are some different segids
that have the same chain.<br>
setting the chain to empty for everything resolved the
issue.<br>
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="yiv7398296616yui_3_13_0_ym1_9_1390433658735_9"><span>thanks<br>
jpd<br clear="none">
</span></div>
<div
id="yiv7398296616yui_3_13_0_ym1_1_1390433658735_21480"><br
id="yiv7398296616yui_3_13_0_ym1_9_1390433658735_11"
clear="none">
</div>
<div
class="yiv7398296616yui_3_13_0_ym1_9_1390433658735_13"
id="yiv7398296616yui_3_13_0_ym1_9_1390433658735_14"
style="font-family:HelveticaNeue, Helvetica Neue,
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<div
class="yiv7398296616yui_3_13_0_ym1_1_1390433658735_21401"
id="yiv7398296616yui_3_13_0_ym1_1_1390433658735_21437"
style="font-family:HelveticaNeue, Helvetica Neue,
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<div class="yiv7398296616yqt1922881029"
id="yiv7398296616yqt80954">
<div dir="ltr"
id="yiv7398296616yui_3_13_0_ym1_1_1390433658735_21436">
<hr size="1"> <font
id="yiv7398296616yui_3_13_0_ym1_1_1390433658735_21479"
face="Arial" size="2"> <b><span
style="font-weight:bold;">From:</span></b>
jp d <a class="moz-txt-link-rfc2396E" 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 class="moz-txt-link-rfc2396E" 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="yiv7398296616yui_3_13_0_ym1_1_1390433658735_21597"><span
id="yiv7398296616yui_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="yiv7398296616y_msg_container"
id="yiv7398296616yui_3_13_0_ym1_1_1390433658735_21442"><br
clear="none">
<div id="yiv7398296616">
<div
id="yiv7398296616yui_3_13_0_ym1_1_1390433658735_21441">
<div
class="yiv7398296616yui_3_13_0_ym1_1_1390433658735_21407"
id="yiv7398296616yui_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="yiv7398296616yui_3_13_0_ym1_1_1390433658735_21478">hi,</div>
<div
id="yiv7398296616yui_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="yiv7398296616yui_3_13_0_ym1_1_1390433658735_21408"
id="yiv7398296616yui_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="yiv7398296616yui_3_13_0_ym1_1_1390433658735_21409"
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="yiv7398296616yui_3_13_0_ym1_1_1390433658735_21410"
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="yiv7398296616yui_3_13_0_ym1_1_1390433658735_21411"
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="yiv7398296616yui_3_13_0_ym1_1_1390433658735_21412"
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="yiv7398296616yui_3_13_0_ym1_1_1390433658735_21413"
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>
<br clear="none">
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