[phenixbb] exporting results, reduce

Pavel Afonine pafonine at lbl.gov
Fri Jan 24 09:00:04 PST 2014


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 <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
>
> 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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