Re: [phenixbb] exporting results, reduce

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 To: PHENIX user mailing list 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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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 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, phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb