- phenixbb - phenix-online.org

model bias: phaser + prime-and-switch VS simulated annealing in phenix VS simulated annealing in cns + prime and switch
by hari jayaram 02 May '08

02 May '08

First off sorry for the cross post across bbs I have a molecular replacement solution for a single site mutant for data that goes out to 2.8 A. After molecular replacement in phaser I run the following and examine the maps for bias from the model. Option1: simluated annealing refinement in phenix using the phaser mtz Option2: take the phaser mtz and then just run prime and switch in resolve and look at the map Option3: First part: take the phaser mtz and then run simulated annealing and sigmaa in cns 1.2.2 . Second part: Run prime-and-switch using part1s model phases and modified Fs I am observing that Option 1 and Option 2 the maps are indistinguishable from each other and show very little bias from the model. In Option 3 just cns simulated annealing does not go as far at removing bias as cns simulated annealing plus prime-and-switch. Although my estimate of model bias is just a "look and see" feeling. Since I lack a thorough understanding of the relative merits of these algorithms I have the following questions 1)Does simulated annealing refinement as implemented in phenix use a prime-and-switch style approach to modify phases at any point to guide the refinement 2) Am I wrong in assuming that just simulated annealing and sigma-aa weighted maps for cns (Option 3 part 1) are not as good as cns simulated annealing + sigmaa+ prime_and_switch ( option3 part 2) Hoping to get a better idea on how well these approaches fair at removing model bias Hari Jayaram Postdoc , Brandeis University

1 0

pseudo-translational symmetry refinement
by a a 02 May '08

02 May '08

Dear all: We have a set of crystal data having psuedo-translational symmetry when examined with xtriage: ------------------------------------------------------------------------------- Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws - <I^2>/<I>^2 : 2.519 - <F>^2/<F^2> : 0.724 - <|E^2-1|> : 0.854 - <|L|>, <L^2>: 0.504, 0.337 Multivariate Z score L-test: 1.854 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data are expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not necessarily exclude it. No (pseudo)merohedral twin laws were found. Patterson analyses - Largest peak height : 67.742 (corresponding p value : 4.897e-06) The analyses of the Patterson function reveals a significant off-origin peak that is 67.74 % of the origin peak, indicating pseudo translational symmetry. The chance of finding a peak of this or larger height by random in a structure without pseudo translational symmetry is equal to the 4.8972e-06. The detected tranlational NCS is most likely also responsible for the elevated intensity ratio. See the relevant section of the logfile for more details. The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected. ------------------------------------------------------------------------------- The structure was solved by auto-sad at 2.7A. However, the r-factor can not be lowered by phenix.refine (TLS+ADP+rigid). Is there any manipuliations we can do to deal with this situation? Thanks, Zhiyong Ren, MD Anderson Cancer Center ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

6 7

mtz test set
by Mark Collins 01 May '08

01 May '08

Hi Everyone, How can I get foo.mtz in which the test set number for R-free is 0 and the working set is say 1. Thanks Mark

2 1

autosol output to electron density figure in pymol
by shivesh kumar 01 May '08

01 May '08

Dear all, I have an overall_best.pdb and overall_best_refine_map_coeffs.mtz file as an output file from Autosol.When I open this in coot I see the nice density.How can make a figure with density using pymol.Thanx in advance for the suggestions. Shivesh

4 4

Re: [phenixbb] native Patterson peak
by Peter Zwart 01 May '08

01 May '08

31 is not too bad actually. When you have such a PT peak, I would consider only an even number of copies in the ASU. When entering desperate mode, I would try all possible P2x2y2z flavors even though your systematic absences might be clear. Of course, experimental phases could be a good solution. HTH P 2008/5/1 David Garboczi <dgarboczi(a)niaid.nih.gov>: > We have datasets measured on crystals of a 19 kD protein that are > P212121, with cell constants of 66, 75, 136. > > Matthew's considerations say 3, 4, or 5 copies per au are probable. > > xtriage finds a native peak at (0.0, -0.5, 0.036) that is 31 in > height (origin=100) > > No self-rotation function peaks in xprep, that I can understand. > > Is this clearly translational symmetry that is making MR difficult? > > Hints as to how to go forward are welcome. > > thanks, > > Dave > > > -- > David N. Garboczi, PhD > Phone: 301-496-4773 > Investigator, Structural Biology Section (SBS) > Laboratory of Immunogenetics (LIG) > National Institute of Allergy and Infectious Diseases (NIAID) > National Institutes of Health (NIH) > Twinbrook 2/Room 110 > 12441 Parklawn Drive > Rockville, Maryland 20852-1742 > Fax: 301-402-0284 > Email: dgarboczi(a)niaid.nih.gov > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

1 0

Re: [phenixbb] [ccp4bb] Need Solve/Resolve advice [shameless crosspost to phenixbb]
by Peter Zwart 30 Apr '08

30 Apr '08

Hi, (sorry for the crosspost / jumping between bb's), but I don't like advertising phenix on the ccp4bb. If new to Solve (or old as well), try using phenix.autosol. The gui is relatively intuitive, the command line (at least for SAD) as simple as possible and the documentation is very thorough. Before running autosol, try running xtriage and find out if you have translational pseudo symmetry. If you have more then a single molecule in the ASU, there will be NCS, unless all molecules have *extremely* different conformations. The NCS might not be proper/closed though. HTH Peter 2008/4/30 Megan Guelker <megdg(a)rice.edu>: > CCP4bb subcribers, > > I am a new user to Solve/Resolve and am using it on a Mad dataset. Solve > outputs three sites: > > pdb coordinates fractional coordinates > -15.833 35.392 38.440 0.0486 0.4315 0.1615 > 7.834 76.449 38.475 0.5487 0.9320 0.1617 > 16.310 60.866 37.449 0.5432 0.7420 0.1574 > > I noticed that the fractional coordinates for the first two sites are > separated by 0.5 units in x and y, and they appear to be the same site from > looking at the density surrounding them. I know that Solve can output some > sites with repetition if they are results from different seeds. > > I have tried running Solve again with ADDSOLVE and these sites as input (all > three and combinations of the three) and have not been able to pull out any > additional sites. I have also tried using various resolution ranges for > Solve. The same three sites are always output. > > The FOM for the map produced by Solve is 0.45. Resolve improves the FOM to > 0.66. > > The protein has 148 aa with 4 Se sites per protein. The crystals are in > space group P3221, and there are six copies per asymetric unit. There is no > non-crystallographic symmetry. > > I am a new user to Solve, and haven't been able to find an explanation for > why the output sites are so similar and separated by 0.5 units. Does anyone > have any experience with this type of result? I would appreciate any input > and suggestions on how to locate additional sites. > > Thank you for your consideration, > Megan Guelker > > -- > Megan Guelker > Graduate Student > Rice University > Department of Biochemistry & Cell Biology > 6100 Main St. - MS 140 > Houston, TX 77005 > 713-348-2492 (lab) > megdg(a)rice.edu > -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

1 0

Refining low resolution structure
by Humberto Pereira 29 Apr '08

29 Apr '08

Dear all I was trying to refining a low resolution structure with Phenix. The crystal belongs to the SG P6122 with one monomer per ASU. The monomer contains approximately 270 residues. There isn't any NCS operators. The crystal diffracts up to 4.0 Angstrons, with good statistics, however I have only 4204 unique reflections. I solved the structure by MR by Phaser and the solution was quite reasonably. Initially I performed a phenix refining cicle with SA + rigid body, however the Rs values is very divergent (43 and 59%), so I decided to use the key xray_data.r_free_flags.ignore_r_free_flags=true in order to save my precious reflections with and without SA, and I also use the group_adp., in those cases the R is about 39-40%. I want a help to decide the best refinement strategies for low resolution refinement with phenix. BTW I'm trying to produce some different constructions of the gene, expecting improve the resolution. Thanks Humberto

2 1

optimize_wxc won't run
by Nian Huang 29 Apr '08

29 Apr '08

Dear All, I am a novel phenix user. There is a problem whenever I use option optimize_wxc in phenix. The error message looks like following, ----------xray term weight optimization (wxc)---------- Traceback (most recent call last): File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/command_line.py", line 82, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/driver.py", line 1143, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 449, in refinement_machine log = log) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 256, in __init__ self.wxc_optimization() File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 511, in wxc_optimization wxc = self.holder.wxc AttributeError: weight instance has no attribute 'holder' I don't know what's the problem. Could it be my installation? Nian Huang, Ph.D. Dept. of Biochemsitry UT Southwestern Medical Center

4 3

"gnomebreakpad": libgnomebreakpad.so: error
by shivesh kumar 23 Apr '08

23 Apr '08

Dear all, We are using Fefora core 8. To start phenix, we give the command phenix in the terminal, after 30-40 minutes it shows the following error message *Gtk-Message: Failed to load module "gnomebreakpad": libgnomebreakpad.so: cannot open shared object file: No such file or directory and after 1hr of this message the GUI comes.There is no problem in running phenix afterwards and also with any other programs like CCP4, CNS etc... I have put this query earlier also and I got reply as follows yum install bug-buddy It didn't work for us.If anyone can suggest the solution, it would be very helpful for us.Thanx in advance. shivesh *

2 1

twinning analysis
by Andreas Förster 23 Apr '08

23 Apr '08

Hey all, I've been digging around with a nasty dataset for a while, twinning, pseudosymmetry, etc. Phenix.xtriage has helped me make some guesses as to what's going on, but phenix.twin_map_utils fails. I used an mtz file obtained from XDS via f2mtz and cad as xray data, like so: phenix.twin_map_utils xray_data.file=blah.mtz model=blah.pdb unit_cell=86.623,86.623,121.357,90,90,120 space_group=P65 Here's the error: Traceback (most recent call last): File "/usr/local/2008_02_08_1610/cci_apps_sources/mmtbx/mmtbx/command_line/twin_map_utils.py", line 7, in <module> twin_map_utils.run(args=sys.argv[1:]) File "/usr/local/2008_02_08_1610/cci_apps_sources/mmtbx/mmtbx/twinning/twin_map_utils.py", line 256, in run tmp_params = utils.r_free_flags_params.extract() AttributeError: 'module' object has no attribute 'r_free_flags_params' I see the error on a recent macbook pro with current cci_apps. How can I get around it? Thanks Andreas ps. I apologize if that question posted to the board earlier. I wrote from a wrong account.

2 1