- phenixbb - phenix-online.org

how to extend R-free set
by Robert Immormino 21 Jun '10

21 Jun '10

Hi, Hopefully I'm just missing something obvious.... I'm trying to copy the Rfree set from an old set of data, to a new mutant structure....and extend to higher resolution. I've tried: phenix.reflection_file_converter old.mtz --label="R-free-flags" new.sca --label="i_obs,sigma" --mtz new.mtz and several other combination, but I am still failing to get phenix to read multiple data files and output the desired mtz. I can get just the Rfree flags or the I and SigI, but not both. I also tried with phenix.refine phenix.refine --dry-run old.pdb old.mtz new.sca ligands.cif refinement.input.xray_data.labels="i_obs,sigma" refinement.input.xray_data.r_free_flags.label="R-free-flags" This seems closer, but I get the error: Sorry: R-free flags not compatible with F-obs array: missing flag for 492 F-obs selected for refinement: Thanks, -bob

7 11

find_all_ligands vs. ligand_identification
by Mark A Saper 21 Jun '10

21 Jun '10

Could someone explain the difference between the GUI "ligand_identification" routine and the documented command line "find_all_ligands". The latter appears to have more flexible input parameters. I'm not sure the GUI for ligand_identification is working correctly. Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

2 1

LAST CHANCE TO REGISTER FOR DIFFRACTION METHODS GRC
by A Leslie 21 Jun '10

21 Jun '10

The biannual Gordon Conference on Diffraction Methods in Structural Biology will be held at Bates College in Lewiston, Maine from 18-23rd July. The program covers all aspects of macromolecular structure solution from crystallization to structure solution and refinement and includes sessions on complementary techniques and the potential of free electron lasers. Many of the leading methods developers will be present and the format of the meeting, with free afternoons, provides ample opportunities for informal discussions. The registration deadline is *** THIS COMING SUNDAY, 27th June *** = ======================================================================== Limited funds are still available to support new student and postdoctoral applications, contact andrew(a)mrc-lmb.cam.ac.uk for details. = ======================================================================== Further details, including a full program and details on the application procedure can be obtained from: http://www.grc.org/programs.aspx?year=2010&program=diffrac We hope to see you there ! Andrew Leslie (Chair) & Ana Gonzalez (Vice Chair) Outline Program Diffraction Methods in Structural Biology, 18-23rd July 2010, Bates College, Lewiston, Maine Sunday pm: Macromolecular Structures, Pushing the boundaries Discussion leader: Michael Rossmann 1. ABC Transporters: Doug Rees 2. The Spliceosome : Kyoshi Nagai Monday am: Crystallisation and the diffraction experiment Discussion leader: Bob Sweet 1. Nanolitre crystallisation: Seth Harris 2. Twinning and disorder: Todd Yeates 3. Simulating the diffraction experiment: James Holton 4. Microcrystallography: Gwyndaf Evans Monday pm: Radiation damage and data collection strategies Discussion leader: Vivian Stojanoff 1. Radiation damage, experimental: Martin Weik 2. Microbeams: Yanhui Zou 3. Testing data collection strategies with the Pilatus: Marcus Mueller Tues am: Synchrotron developments and automated data processing Discussion leader: Thomas Schneider 1. Synchrotrons, latest developments: Sean Mc Sweeney 2. Synchrotrons, latest developments: Janet Smith 3. Data processing with Xia2/CHEF: Graeme Winter 4. Data processing with AUTOPROC: Clemens Vonrhein Tues pm: Complementary techniques Discussion leader: Ana Gonzales 1. Electron tomography: Sriram Subramaniam 2. SAXS: Hiro Tsuruta 3. Spectroscopy: Carrie Wilmot Weds am: Structure solution and refinement Discussion leader: Paul Adams 1. SAD Phasing: Randy Read 2. Molecular replacement with BALBES: Garib Murshudov 3. PHENIX: Tom Terwilliger 4. TLS: Ethan Merritt Weds pm: Challenging problems/Membrane Proteins Discussion leader: Michael Wiener 1. Using cubic lipidic phase: Martin Caffrey 2. Membrane Proteins: Stephen White 3. Heterogeneity, low solubility and low resolution: structural pursuit on the ternary Myddosome complex in Toll-like receptor signaling: Hao Wu Thurs am: Selected Posters and Map improvement and Model building Discussion leader: Tassos Perrakis 1. COOT: Paul Emsley 2. Modelling nucleic acids: Johan Hattne Thursday pm: Future Methods, FELs, Diffraction imaging Discussion leader: Ed Lattman 1. Opportunities fof membrane protein analysis with FELs: Petra Fromme 2. Single particle imaging with pulsed hard Xray lasers: Anton Barty 3. Femtosecond nanocrystallography of membrane proteins using LCSL: John Spence

1 0

"Open in Coot" not working on 1.6.1-357
by Ben Eisenbraun 19 Jun '10

19 Jun '10

Howdy PHENIXians, I can't seem to get the "Open in Coot" option to work in PHENIX. I tested version 1.6.1-357 on 32 and 64-bit linux as well as the OS X Intel version, and while Coot will open, it won't display the working data. 'phenix.find_coot_command' works fine from the command line. On the linux machines, when Coot opens, it doesn't have the "Connected to PHENIX" button. On the OS X Intel machine, it does have the button, but it still won't display the working data. Any ideas? -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

6 25

is derivative data useful for looking for the missingpart of the model?
by Jacob Keller 16 Jun '10

16 Jun '10

> Hi Fengyun, > > How have you determined whether you in fact have the full-length protein > in your crystals? It sounds like, from your statistics, that everything is > already modelled--it seems hard to believe that 80% of the whole protein > would give such good R values. Do others agree? > > You could run some of your crystals on a gel next to a sample which is > known to be full-length, and you could get the answer. > > Jacob > > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > Dallos Laboratory > F. Searle 1-240 > 2240 Campus Drive > Evanston IL 60208 > lab: 847.491.2438 > cel: 773.608.9185 > email: j-keller2(a)northwestern.edu > ******************************************* > > ----- Original Message ----- > From: <fn1(a)rice.edu> > To: <phenixbb(a)phenix-online.org> > Sent: Tuesday, June 15, 2010 5:59 PM > Subject: [phenixbb] is derivative data useful for looking for the > missingpart of the model? > > >> Hi everyone, >> >> I got a partial model, consisting of 80% of the whole molecule, from the >> molecular replacement. The native data reflects to 2.3 A, and now the >> R/Rfree= 0.22/0.28. My problem is that the missing part of the model is >> important for us, but there is not any density for this region now. >> >> Meantime, we have several heavy atom derivative data. My question is >> that if refine the model against the derivative data, will the heavy >> atom appear in the difference map if existing? Any suggestions on how to >> use the derivative data to locate the missing part of model? >> >> Thanks in advance! >> Regards, >> Fengyun >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >

2 1

phaser spacegroup within phenix
by John M. Berrisford 16 Jun '10

16 Jun '10

Hello I've just spotted a discrepancy between phenix run from ccp4i and from the phenix GUI regarding spacegroup selection run phaser runs. Within the CCP4 GUI you can specify the space group for a phaser molecular replacement run to be the space group of the mtz or a sub-space group (i.e P222 or P212121 etc...). For some reason this isn't as obvious within the phenix GUI. I have an mtz processed in P21 and when I load it into the phenix phaser GUI it tells me its P21 (P 1 21 1) and gives me no other options. However, when I run the molecular replacement job it decides that the space group could be either P2 or P21 and runs both - which in my case runs in P2 and gives a partial solution, not the full solution I would expect in P21. A bit annoying as I know my space group is actually P21. After a few minutes of head scratching, the only way I found to fix it to run in P21 is to enter the "other settings" menu and select "none" within "alternative space groups". I guess this is what your suppose to do, but its not obvious. Can the phenix GUI be changed so that its as obvious as the ccp4 GUI as to what is actually going to run when you press "run". Thanks John I'm running phenix 1.6.1 on OS X. -- John Berrisford Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44 1223 252882

3 2

Re: [phenixbb] phaser spacegroup within phenix
by John M. Berrisford 16 Jun '10

16 Jun '10

Hi Nat I don't think its a bug, just phaser getting a little bit confused. Phaser ran in both P2 and P21 using the phenix default, not P21 - the space group of the mtz. This default is probably the right thing to do if you don't know the space group of your crystal, but then you wouldn't have scaled the mtz in P21. In my case the reason phaser failed to find a solution is that the P2 solution had a higher initial LLG than the P21 solution while finding the first copy of 4 in my A.U.. So phaser picked P2 to continue the molecular replacement and subsequently stopped due to clashes during packing. John On Tue, Jun 15, 2010 at 8:45 AM, John M. Berrisford <jmb(a)mrc-mbu.cam.ac.uk>wrote: > > I have an mtz processed in P21 and when I load it into the phenix phaser > > GUI it tells me its P21 (P 1 21 1) and gives me no other options. However, > > when I run the molecular replacement job it decides that the space group > > could be either P2 or P21 and runs both - which in my case runs in P2 and > > gives a partial solution, not the full solution I would expect in P21. A bit > > annoying as I know my space group is actually P21. > > After a few minutes of head scratching, the only way I found to fix it to > > run in P21 is to enter the "other settings" menu and select "none" within > > "alternative space groups". I guess this is what your suppose to do, but its > > not obvious. > Point taken - I'll move this to the main window (and label it more clearly - sorry). The result you're describing sounds like it might be a bug, though; shouldn't Phaser try P21 as well and get the full solution, instead of settling for P2? This is what I would expect for the default behavior. -Nat -- John Berrisford Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44 1223 252882

3 2

Re: [phenixbb] is derivative data useful for looking for the missing part of the model?
by Thomas C. Terwilliger 15 Jun '10

15 Jun '10

Hi Francis, Yes, you can do that. It requires one extra step to do the combination. You need to make a script like the one below (see https://solve.lanl.gov/Resolve/html_resolve_manual/resolve_sample_scripts.h…): All the best, Tom T Merging phase sets with different origins You can merge phase sets with different origins with this script. It uses an FFT convolution to find the best allowed offset between the maps calculated with the two phase sets. Merging the files REQUIRES HL coefficients (see above for generating them if you do not have them). Note: the FP and SIGFP in the output file will come from the hklin file NOT the hklmerge file: phenix.resolve <<EOD hklin random_1_hl.mtz ! File with target map (fixed) labin FP=FP PHIB=PHIM FOM=FOMM HLA=HLAM HLB=HLBM HLC=HLCM HLD=HLDM hklmerge random_2_hl.mtz ! File to be offset labmerge FP=FP PHIB=PHIM FOM=FOMM HLA=HLAM HLB=HLBM HLC=HLCM HLD=HLDM hkl_offset_file resolve_off.mtz ! The hklmerge file, offset all by itself hkl_merge_file resolve_merge.mtz ! The hklmerge file offset, then merged with hklin EOD >> Thanks so much!It looks promising. >> If I have two or more derivative data and want to combine all these >> information. Can I just do MRSAD individually for each dataset, and >> combine them? >> >> >> ÒýÓÃ Nathaniel Echols <nechols(a)lbl.gov>£º >> >>> On Tue, Jun 15, 2010 at 4:03 PM, Francis E Reyes >>> <Francis.Reyes(a)colorado.edu >>>> wrote: >>> >>>> Using the model to find the heavy atom sites and then calculating >>>> phases on >>>> those sites (without model) might help. ( I believe phenix will output >>>> a >>>> phase combined map (model + experimental phases)). >>>> >>> >>> Correct, this is the default behavior if you provide a model directly to >>> AutoSol (or Phaser). There is however a semi-automatic way to use the >>> model >>> phases to find sites without biasing the experimental map; see the >>> documentation here: >>> >>> https://www.phenix-online.org/version_docs/1.6.2-432/autosol.htm#anch126 >>> >>> (The AutoBuild step is optional - you could just look at the >>> density-modified map after AutoSol is done.) >>> >>> -Nat >>> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

1 0

is derivative data useful for looking for the missing part of the model?
by fn1＠rice.edu 15 Jun '10

15 Jun '10

Hi everyone, I got a partial model, consisting of 80% of the whole molecule, from the molecular replacement. The native data reflects to 2.3 A, and now the R/Rfree= 0.22/0.28. My problem is that the missing part of the model is important for us, but there is not any density for this region now. Meantime, we have several heavy atom derivative data. My question is that if refine the model against the derivative data, will the heavy atom appear in the difference map if existing? Any suggestions on how to use the derivative data to locate the missing part of model? Thanks in advance! Regards, Fengyun

3 4

Re: [phenixbb] input sharp phases into phenix.autosol
by Thomas C. Terwilliger 15 Jun '10

15 Jun '10

Hi Michael, If I understand correctly, you want to take a file that has experimental phases, density modify it, and autobuild a model. Plus you want to take the inverse hand of the phases and do the same thing. For the first part you have two easy options: phenix.autobuild my_exptl_phases.mtz my_seq.dat ha_file=my_ha_file phenix.build_model my_exptl_phases.mtz my_seq.dat ha_file=my_ha_file These do more or less the same thing, but build_model is a lot faster (but not quite as good), and requires version 1.6.2-242 or higher. For phases from sharp, you will want to specify the columns of data to be used for FP SIGFP PHIB FOM HLA HLB HLC HLD for each method above. (The way to specify these are different in the two methods. For autobuild you just list the column labels to be used for the above items with labels="myFP mySIGFP myPHIB myFOM myHLA myHLB myHLC myHLD", and for build_model you specify a regular labin line: labin="FP=myFP SIGFP=mySIGFP...etc" For the second part, flipping the hand of a file with experimental phases...I am not sure if we have a tool for that. Perhaps someone else can comment. All best, Tom T >> Hi, >> >> I hope what I want to do is not considered a crime :-) Is there a way to >> input phases e.i. from sharp into phenix.autosol (preferably the command >> line version) to run resolve with both hands and autobuild for a SAD or >> SIRAS case? >> >> Thanks! >> Michael >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

4 3