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August 2011

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Re: [phenixbb] Third issue of Computation Crystallography Newsletter - Volume 2, Number 2
by Frank von Delft 01 Aug '11

01 Aug '11

Hi, just scanned through the article on automatic weight adjustment. If I had to summarise figures 1 and 2, I'd have to conclude that the latest weight optimization only occasionally produces better results than not doing it (fig 2); and that therefore the old optimization was considerably worse than doing nothing at all. Or have I misinterpreted it? Cheers phx On 28/07/2011 19:59, Nigel Moriarty wrote: > Dear Colleagues, > > I am pleased to announce the publication of the third issue of the > Computational Crystallography Newsletter: > > http://www.phenix-online.org/newsletter/ > > A listing of the articles and short communications is given below. > Please note that the newsletter accepts articles of a general nature > of interest to all crystallographers. Please send any articles to me > at > NWMoriarty(a)lbl.gov noting that there is a Word Template on the website > to streamline production. > > Articles > -------- > > Improved target weight optimization in phenix.refine > Mite-y lysozyme crystal and structure > > > Short communications > -------------------- > > A lightweight, versatile framework for visualizing reciprocal-space data > An extremely fast spotfinder for real-time beamline applications > Hints for running phenix.mr_rosetta > > > Cheers > Nigel >

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Re: [phenixbb] problem in rosetta rebuilding
by intekhab alam 31 Jul '11

31 Jul '11

Hi, Tom sorry for the delayed response. I was abale to fix by running one model. rosetta is working fine now. thanks again Intekhab Alam On Thu, Jul 21, 2011 at 11:49 PM, Thomas C. Terwilliger < terwilliger(a)lanl.gov> wrote: > Hi Intekhab, > > I'm glad the test works at least. How about trying this: > > Run just the job that hangs, but instead of running 100 models...just run > one single model. Does that work? > > All the best, > Tom > > > >> Hi Tom > >> i tried the commnad line and it works well. we also have increased the > >> memory to 3GB (earlier it was 2GB) > >> but still the system hangs with no response overnight. > >> the specifications of my system is as: > >> Ubuntu 9.04 > >> GCC 4.2 > >> RAM 3GB > >> Rosetta 3.2 > >> Phenix 1.7.1 > >> the command line test using > >> "phenix_regression.wizards.test_command_line_rosetta_quick_tests > >> test_rosetta_rebuild" works well . > >> > >> regards > >> intekhab alam > >> On Tue, Jul 19, 2011 at 11:31 PM, Thomas C. Terwilliger < > >> terwilliger(a)lanl.gov> wrote: > >> > >>> Hi Intekhab, > >>> > >>> I'm not sure about the part about the machine shutting down...but here > >>> is > >>> a little test you can run to make sure that rosetta and phenix are > >>> working > >>> properly together in rebuilding a model: > >>> > >>> phenix_regression.wizards.test_command_line_rosetta_quick_tests > >>> test_rosetta_rebuild > >>> > >>> or a more complete set of tests: > >>> > >>> phenix_regression.wizards.test_command_line_rosetta_quick_tests > >>> > >>> All the best, > >>> Tom T > >>> > >>> > >>> > >>> >> On 07/19/2011 04:49 PM, intekhab alam wrote: > >>> >>> > >>> >>> Hi > >>> >>> i tried to run rosetta on a unix machine (ubuntu 9.04) for my data. > >>> Upto > >>> >>> MR step everything goes fine , but during the rebuilding step after > >>> 20 > >>> >>> cycles the computer shuts down. > >>> >> > >>> >> Interesting behavior for a Linux machine. > >>> >> > >>> >> Once the machine has rebooted, reading the output > >>> >> of the dmesg command and looking at events prior to the last boot > >>> >> may give you some information on why the computer hung. > >>> >> > >>> >> My guess is that you went out of memory while using mr_rosetta. > >>> >> > >>> >>> i have attached the log file for the autobuilding run of rosetta. i > >>> am > >>> >>> using phenix 1.7.1-743 version. > >>> >>> i will be grateful if some one helps me out > >>> >>> -- > >>> >>> INTEKHAB ALAM > >>> >>> LABORATORY OF STRUCTURAL BIOINFORMATICS > >>> >>> KOREA UNIVERSITY, SEOUL > >>> >>> > >>> >>> > >>> >>> > >>> >>> _______________________________________________ > >>> >>> phenixbb mailing list > >>> >>> phenixbb(a)phenix-online.org > >>> >>> http://phenix-online.org/mailman/listinfo/phenixbb > >>> >> > >>> >> _______________________________________________ > >>> >> phenixbb mailing list > >>> >> phenixbb(a)phenix-online.org > >>> >> http://phenix-online.org/mailman/listinfo/phenixbb > >>> >> > >>> > >>> _______________________________________________ > >>> phenixbb mailing list > >>> phenixbb(a)phenix-online.org > >>> http://phenix-online.org/mailman/listinfo/phenixbb > >>> > >> > >> > >> > >> -- > >> INTEKHAB ALAM > >> LABORATORY OF STRUCTURAL BIOINFORMATICS > >> KOREA UNIVERSITY, SEOUL > >> > > -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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