[phenixbb] exporting results, reduce

jp d yoyoq at yahoo.com
Fri Jan 24 09:17:13 PST 2014

the rigid body refinement took 5 hours, not the reduce step.

this is a run with chain problems and it never finished

this is the pdb with no chain where refine took 5 hours and reduce finished normally


this is a similar run with chain problems and it took 35 hours


 From: Pavel Afonine <pafonine at lbl.gov>
To: phenixbb at phenix-online.org 
Sent: Friday, January 24, 2014 9:00 AM
Subject: Re: [phenixbb] exporting results, reduce


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)?


On 1/24/14, 8:44 AM, jp d wrote:

>replying for the sake of posterity.
>the slow export/reduce seems to be related to a malformed
              input model.
>the segids are ok but there are  some different segids
              that have the same chain.
>setting the chain to empty for everything resolved the
>Using the malformed chain model took 35 hours (if it
>Using the no chain model took 5 hours.
> From: jp d <yoyoq at yahoo.com>
>To: PHENIX user mailing list <phenixbb at phenix-online.org> 
>Sent: Friday, January 17, 2014 9:53 AM
>Subject: [phenixbb] exporting results, reduce
>we have a large complex at low resolution (7A) and just want 
>to see general conformational changes. Occasionally phenix
>gets stuck at 'Exporting Results' and top shows 'reduce' running
>and using lots of RAM . so much RAM that it starts using swap.
>is there  a way to bypass or limit the reduce step.
>phenixbb mailing list
>phenixbb at phenix-online.org
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