- phenixbb - phenix-online.org

What happened with Rfree between dev-2376 and now?
by Mark Saper 29 Mar '17

29 Mar '17

Hi all, I’ve been running some tests with the current dev and released versions of Phenix. If I run the same job (same input files, same parameters), the current versions consistently result in Rfree values ~1% more than Phenix version dev-2376! What changed between then and now? Thanks, Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III saper(a)umich.edu +1 (734) 764-3353

1 0

Note that R-free numbers are different than a year ago.
by Mark Saper 26 Mar '17

26 Mar '17

In July 2016, I finished a refinement with Phenix dev-2376 with these final stats start final --------------------------------------- R-work: 0.1982 0.2007 R-free: 0.2376 0.2367 RMS(angles): 0.55 0.45 RMS(bonds): 0.003 0.002 Today, I reran the exact same parameter file and input files with Phenix dev-2712: start final --------------------------------------- R-work: 0.2073 0.2037 R-free: 0.2445 0.2442 RMS(angles): 0.55 0.45 RMS(bonds): 0.003 0.002 R-free values are now higher than they used to be. This fact was also flagged when I ran Table 1 today. -Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III saper(a)umich.edu +1 (734) 764-3353

1 0

help with pdbtools
by Edward A. Berry 25 Mar '17

25 Mar '17

1. I'm trying to use pdbtools and I don't quite get the syntax. How can I specify the output file name on the command line? these don't work: phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 output file_name = shake1.pdb phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 file_name = shake1.pdb phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 --output file_name = shake1.pdb phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 --file_name = shake1.pdb phenix.pdbtools --output file_name = shake1.pdb 2chr_refine_001.pdb sites.shake=0.5 phenix.pdbtools output.file_name = shake1.pdb 2chr_refine_001.pdb sites.shake=0.5 2. for the "shake" operation, is there a random seed so that it comes out differently each time? (If I do this five times with different output file names, will they all be the different?)

3 6

DNA double helix through crystal symmetry
by wtempel 25 Mar '17

25 Mar '17

Hello, how could one restrain DNA base pairing across a crystallographic axis? Are secondary_structure.nucleic_acid restraints "symmetry-aware"? Thank you. Wolfram Tempel

3 3

Berkeley Server Downtime (3/23 - 3/24)
by Billy Poon 24 Mar '17

24 Mar '17

Dear all, On Thursday, March 23, our servers will be shut down starting at 5:00 pm Pacific for some emergency electrical work near our building. We expect that the servers will be available the next day (3/24) by 1:00 pm Pacific. There is a possibility that the outage will last longer. This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience and the short notice. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

1 1

options in phenix.merging_statistics
by Murpholino Peligro 24 Mar '17

24 Mar '17

Hello. I was wondering what is the normal situation where one should click the boxes marked as "Keep anomalous pairs separate in merging statistics" (option1) and/or "Use internal variance of the data in the calculation of the merged sigmas" (option2)? I am asking because it looks like it is detrimental to the statistics, as you can see in the file attached (CSV file with 4 columns for no options, option1, option2 and option1&2). Thanks in advance. MP

2 1

phenix ensemble ref.
by Kajander, Tommi A 23 Mar '17

23 Mar '17

Hi, is it possible to do ensemble refinement in phenix with just one domain? (and e.g. fix the other) Doens seem so? Thanks, Tommi

2 3

Re: [phenixbb] Error running phenix.rosetta_refine tests with Rosetta 3.8
by Nigel Moriarty 21 Mar '17

21 Mar '17

Oliver My Rosetta 3.7 is 2016.32. Not sure why we are different. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Tue, Mar 21, 2017 at 8:19 AM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > Hi Nigel, > > I tried with rosetta 3.7 (2016.46) and phenix dev-2719, and this time > compilation using rosetta.build_phenix_interface was successful (scons > finished building targets with no errors), but when I run rosetta.run_tests > it still crashes, though with a different error (see attached log). Any > ideas as to how to fix? > > Cheers > Oli > > > > On Mar 20, 2017, at 7:31 PM, Nigel Moriarty <nwmoriarty(a)lbl.gov> wrote: > > Oliver > > We are currently only supporting up to Rosetta 3.7 as a c++11 compiler is > required for any subsequent versions. We have compiled using a c++11 > compiler with no problems so I suggest you revert to 3.7 or check the logs > for compilation problems. > > Cheers > > Nigel > > --- > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 <(510)%20486-5709> Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 <(510)%20486-5909> Web : CCI.LBL.gov > <http://cci.lbl.gov/> > > On Mon, Mar 20, 2017 at 9:34 AM, Oliver Clarke <olibclarke(a)gmail.com> > wrote: > >> Hi, >> >> Phenix rosetta refinement worked with previous versions of rosetta and >> phenix, but with the latest Rosetta version (3.8) and latest phenix nightly >> I get a crash when running rosetta.run_tests after building the rosetta >> phenix interface, which runs a test run of phenix.rosetta_refine. It gets >> to the stage of generating initial models and then crashes - see attached >> log. Ideas for a fix welcome! >> >> Cheers >> Oli >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > > > >

1 0

Error running phenix.rosetta_refine tests with Rosetta 3.8
by Oliver Clarke 21 Mar '17

21 Mar '17

Hi, Phenix rosetta refinement worked with previous versions of rosetta and phenix, but with the latest Rosetta version (3.8) and latest phenix nightly I get a crash when running rosetta.run_tests after building the rosetta phenix interface, which runs a test run of phenix.rosetta_refine. It gets to the stage of generating initial models and then crashes - see attached log. Ideas for a fix welcome! Cheers Oli

2 1

difference map for cryo-EM (cryo-EM map minus model map)
by Pavel Afonine 16 Mar '17

16 Mar '17

For those practicing cryo-EM and tending to use Phenix nightly builds, as well as in response to a recent post (Re: [phenixbb] difference map based on the cryo-EM map): Next Phenix nightly build (dev-2612 and up) will have a command line tool to compute map-model real-space difference maps. One map is computed in real space: cryo-EM map minus model calculated map; it is locally scaled in some complex way to account for local variations and possibly poorly refined B-factors. In terms of reciprocal space it is an analog of: (F_obs, Phase_obs) - (F_calc, Phase_calc). The other map is computed using both spaces, and is analog of (F_obs-F_calc, Phase_obs); here no model phase is involved. I'm not sure which one of the two is better. Both maps are useful to locate ligands or yet not built pieces of the model (very much like in crystallography). Current limitations: - no GUI; - map must have origin at (0,0,0); - output file name can't be changed. To use: phenix.real_space_diff_map model.pdb map.ccp4 resolution=3.9 which will output two maps: map_model_difference_1.ccp4 and map_model_difference_2.ccp4 . If proving ligand is the purpose to compute this map, then obviously it should not be present in model.pdb. In future (once fully tested) this will be integrated into phenix.real_space_refine. The tool is 10 hours old and tested on just one model (5l4g, emd_4002.map), so bugs are not unexpected. Any feedback is welcome! All the best, Pavel

2 5