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

this is a run with chain problems and it never finished

http://musso.ucsc.edu/exporting_reduce/verify_fail/
http://musso.ucsc.edu/exporting_reduce/verify_fail/withchain.pdb

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

http://musso.ucsc.edu/exporting_reduce/no_chain/

http://musso.ucsc.edu/exporting_reduce/no_chain/nochain.pdb

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

http://musso.ucsc.edu/exporting_reduce/oneproc/

thanks

jpd

From: Pavel Afonine <[email protected]>
To: [email protected]
Sent: Friday, January 24, 2014 9:00 AM
Subject: Re: [phenixbb] exporting results, reduce

Hello,

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)?

Thanks,
Pavel

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

hi,
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 issue.
Using the malformed chain model took 35 hours (if it finished).
Using the no chain model took 5 hours.

thanks
jpd

From: jp d <[email protected]>
To: PHENIX user mailing list <[email protected]>
Sent: Friday, January 17, 2014 9:53 AM
Subject: [phenixbb] exporting results, reduce

hi,

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.

thanks

jpd

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