Search results for "look through"

Re: [phenixbb] merging in hires data in AutoBuild

by Terwilliger, Thomas C

Hi Desiree, I'm sorry, yes, that is a bug in Phenix version 1.7.3-928. It has since been fixed, so if you are able to download any recent version of Phenix it should work correctly. Please let me know if that does not do it! All the best, Tom T ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Desiree Ho-Chi Fong, Ms [desiree.fong(a)mail.mcgill.ca] Sent: Monday, March 26, 2012 2:39 PM To: phenixbb(a)phenix-online.org Subject: [phenixbb] merging in hires data in AutoBuild Hello all, I am using PHENIX 1.7.3-928 and I am trying to merge a high resolution native data set with a MAD data set in AutoBuild. I have run AutoBuild through the GUI as well as on the command line. Here is the command I used: phenix.autobuild data=AutoSol_run_1_/exptl_fobs_phases_freeR_flags_1.mtz hires_file=hires.mtz model=AutoSol_run_1_/overall_best.pdb rebuld_in_place=True The data file, exptl_fobs_phases_freeR_flags.mtz from AutoBuild only includes data to the resolution of the MAD data set. The higher resolution native data was not incorporated into this mtz file. Looking at the log file, the hires data was merged with expel_fobs_phases_freeR_flags_1.mtz from AutoSol (with AutoBuild after) and followed by anisotropy correction. This was then used for density modification. However, the high resolution data was never included in the mtz file for refinement in AutoBuild. My understanding is that if hires data is specified in AutoBuild, the phases would be extended and included in map calculation as well as subsequent refinement. The output exptl_fobs_phases_freeR_flags.mtz from AutoBuild would also include the hires data for subsequent refinement. Is this correct? Thank you for your help. Desiree _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

13 years, 10 months

Re: [phenixbb] TRIED resolve ...NEED A BIGGER VERSION... message

by Tom Terwilliger

Hi Ben, Yes, that is just FYI. There are a few sizes of resolve and this means the smallest wasn't big enough. I'll change the message so that it is more informative... All the best, Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss On Jan 5, 2009, at 8:09 AM, Ben Eisenbraun wrote: > > Howdy Phenixians, > > One of my users is running phenix.autobuild, and while it seems to run > okay, the output contains this warning: > > TRIED resolve ...NEED A BIGGER VERSION... > > Looking through phenix/phenix/autosol/run_resolve.py, it seems like > this > is an informational message, but I'm not sure, so I figured I'd ask. > > Is this actually an error? > > This is phenix-1.3-final on OS X 10.5. > > Thanks. > > -ben > > -- > Ben Eisenbraun > Structural Biology Grid Harvard Medical > School > http://sbgrid.org http://hms.harvard.edu > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb

17 years, 1 month

Re: [phenixbb] Running Autobuild after Autosol

by Thomas C. Terwilliger

Hi Katya, AutoBuild will look through all the autosol runs and choose the solution with the highest final score, and use that one. You can see this near the beginning of the AutoBuild run: Appending solution 4060.75360229 1 75.3602294036 exptl_fobs_phases_freeR_flags_1.mtz solve_1.mtz Appending solution 59.3469818876 2 59.3469818876 None solve_2.mtz Best solution 4060.75360229 1 75.3602294036 exptl_fobs_phases_freeR_flags_1.mtz solve_1.mtz AutoSol_run_2_ In this case it took run 2 with the solution solve_1.mtz with score of 4060.7 over the solution solve_2.mtz with score of 59. If you want to choose a different AutoSol solution, then you will need to explicitly tell AutoBuild all the files that you want to use. All the best, Tom T >> Hi, >> >> how do I specify running Autobuild after Autosol, in the command line >> mode? I see the "phenix.autobuild after_autosol" option in the manual, >> but how will Autobuild know which Autosol run to use? >> >> Katya >> >> >> >> -- >> Ekaterina Heldwein, Ph.D. >> Assistant Professor >> Department of Molecular Biology and Microbiology >> Tufts University 136 Harrison Ave >> Boston, MA 02111 >> >> phone: 617-636-0858 >> fax: 617-636-0337 >> e-mail: katya.heldwein(a)tufts.edu >> >> >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

16 years, 5 months

Re: [phenixbb] How to manually define NCS group for phenix.autobuild?

by Tom Terwilliger

Hi Jason, You should be able to do simple edits to an autobuild.ncs_spec file, for example changing the residues where ncs applies, and it should be read by autobuild. You can check if an ncs_spec file is ok by running it through phenix.find_ncs: phenix.find_ncs my_ncs_spec.ncs_spec should reformat it and write out files for resolve and phenix.refine. If that doesn't help, can you send me before and after ncs_spec files and I'll have a look. All the best, Tom T On Jul 15, 2010, at 7:33 AM, J J wrote: > Hello everyone, > > It is easy to manually define NCS group in phenix.refine, but how to > manually define it in phenix.autobuild? phenix.simple_ncs_from_pdb > will generate an .ncs_spec file which can be used in autobuild, but > what if I want to define ncs group myself, say removing some > residues from the automatically detected one. I can manually remove > them from the .ncs_spec file, but the operations defined in > the .ncs_spec is no longer valid? Thanks in advance > > Jason > > U Pitt > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

15 years, 6 months

Re: [phenixbb] Autobuild

by Terwilliger, Thomas C

Hi Heather, Oh I see. Yes, it is probably better to refine before building, either directly as you did or by setting refine_before_rebuild=True. Autobuild really has just three ways of filling in those loops. One is running fit-loops (which it does in the middle of a cycle). Another is build_outside_model which it also does in the middle of a cycle. The third is just getting a better starting model so that chain extension fills in more residues. You can have autobuild just do build_outside model by turning off all the other building options but my guess is it is not worth it (if you really want to do this you can see how this is done by looking at a parameters file for a sub-process run of autobuild when only build_outside_model is run). My guess is that the unbuilt part of the structure might not be really clear in the maps. If this is the case, then it is pretty hard to build that part of the model. Usually the best thing to do is get the best possible model (run autobuild, then phenix.refine, fix everything that is indicated by the Molprobity analysis and that you can see in the map), then use that in either refinement to get a 2Fo-DFc sigmaA-weighted map or phenix.autobuild maps_only=True to get a density-modified map. Then examine that map to see if there is anything that clearly should be built. You note that "once I ran fit_loops, I would get an error if I tried to put the new pdb file through refinement.". If you could send me all the inputs and commands necessary to repeat that (or perhaps just the output PDB file) off-line then I can try and fix that problem. All the best, Tom T ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Heather L Condurso [condurso(a)bc.edu] Sent: Friday, September 06, 2013 5:14 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Autobuild Tom, First, I had refine input model before rebuilding turned off. I thought this meant whether it would refine before doing anything else which I didn't really think was necessary but maybe I was wrong. I found an autobuild.eff file and it looks like all that was different in my refinement was that I hadn't selected simulated annealing in autobuild and had in refine. I can run it again with these adjusted parameters to see if I get a better result. As for the maps, the refine maps are definitely better than the autobuild maps but not by all that much. These missing regions are pretty long so fit_loops hasn't been too helpful. I also had the problem that once I ran fit_loops, I would get an error if I tried to put the new pdb file through refinement. Something about missing fields but it had only added a residue here and there across many monomers so I gave up. I guess what would be helpful to me is how best to use my computing time to try to get autobuild to get me the best possible model it can. I can input my refined structure but what parameters will make autobuild focus on extending the model to build in the missing regions instead of continually trying to rebuild a model that is already at a CC=0.90 around the built atoms? Thanks, Heather On Fri, Sep 6, 2013 at 6:32 PM, Terwilliger, Thomas C <terwilliger(a)lanl.gov<mailto:[email protected]>> wrote: Hi Heather, Hmm... a little hard to tell what the problem is. So first: autobuild should have refined this model as one of the first things it did. Did it get about the same R that you got when refining it directly with phenix.refine? If no, then have a look at the refinement .eff files (the autobuild one is in AutoBuild_run_1_/TEMP0 unless that was cleaned up) and see what is different. Next....what happens if you just run phenix.refine to get a map, also take the map from this autobuild run, and look at them along with your model. Is one a lot better than the other? If you take your best working map and run phenix.fit_loops with this model...how does that do? All the best, Tom T ________________________________ From: phenixbb-bounces(a)phenix-online.org<mailto:[email protected]> [phenixbb-bounces(a)phenix-online.org<mailto:[email protected]>] on behalf of Heather L Condurso [condurso(a)bc.edu<mailto:[email protected]>] Sent: Friday, September 06, 2013 3:54 PM To: PHENIX user mailing list Subject: [phenixbb] Autobuild I'm a bit confused about what is going on with my autobuild run. I solved a structure from anomalous data to 2.7A but many loops are missing. I ran phaser with the current model and native data that extends to 2.4A and got a solution and started autobuild from there. I used mostly the default settings and rebuild_in_place=False. After a pretty short time I realized the run was over and at the bottom of the log I see this: Cycle 3 R/Rfree=0.28/0.35 Built=488 Placed=467 AutoBuild_build_cycle AutoBuild Run 162 Fri Sep 6 14:33:39 2013 Deciding if we should continue... Recent R change per cycle: 0.0 Ending these build cycles as the recent change in R per cycle has been 0.0 and the required value of change is -0.005 and the R is somewhat acceptable at 0.276670644792 All done with build cycles in this region AutoBuild_set_up_build AutoBuild Run 162 Fri Sep 6 14:33:40 2013 All omit/non-omit regions completed finished AutoBuild Run 162 Fri Sep 6 14:33:40 2013 Finishing AutoBuild Run 162 Facts written to AutoBuild_run_162_/AutoBuild_Facts.dat AutoBuild Run 162 Summary of model-building for run 162 Fri Sep 6 14:33:40 2013 Files are in the directory: /Users/heather/Desktop/M/AutoBuild_run_162_/ Starting mtz file: /Users/heather/Desktop/M/ImportRawData_run_4_/A-3_xx_PHX.mtz Sequence file: /Users/heather/Desktop/M/m.pir Best solution on cycle: 2 R/Rfree=0.26/0.33 Summary of output files for Solution 1 from rebuild cycle 2 --- Model (PDB file) --- pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb --- Model (CIF file) --- cif_pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.cif --- Refinement log file --- log_refine: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_refine --- Model-building log file --- log: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log --- Model-map correlation log file --- log_eval: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_eval --- 2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT FOFCWT PHFOFCWT --- refine_map_coeffs: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_map_coeffs.mtz --- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- refine_data: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz --- Density-modified map coefficients FWT PHWT --- denmod_map_coeffs: /Users/heather/Desktop//AutoBuild_run_162_/overall_best_denmod_map_coeffs.mtz You might consider making one very good model now with: phenix.autobuild \ data=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz \ model=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb \ rebuild_in_place=True \ seq_file=/Users/heather/Desktop/M/m.pir My full sequence is 325 amino acids so only about 75% is build in. I am hoping autobuild can help find at least some of these missing residues. Why would the change in R be zero? What is meant by "You might consider making one very good model now with:"? I tried running autobuild with these new files and rebuild_in_place=true and get the same type of message. Is this the best that autobuild can do? I also ran the phaser solution through refinement and can significantly lower the Rs from 0.26/0.33 to 0.22/0.30. I appreciate any advice on how best to proceed. I am using 1.8.2-1472 if that matters. Thanks, Heather _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb

12 years, 5 months

Re: [phenixbb] anomalous difference map

by Randy J. Read

Since you have a molecular replacement model, the other option you should try is to ask Phaser to look for the anomalous scatterers with log-likelihood-gradient maps in the SAD likelihood target. In our experience, this gives significantly better signal-to-noise on average than simple model-phased anomalous difference Fouriers. By default, Phaser will put in anomalous scatterers where there are peaks above 6 times the rms of the log-likelihood-gradient map, and it does this iteratively, i.e. putting the anomalous scatterers into the model makes the model and makes the log-likelihood-gradient map more sensitive, so it carries on doing rounds of this until there are no more peaks to interpret as anomalous scatterers. At the end, you'll have a flat log-likelihood-gradient map but you'll also have a list of sites that were all 6sigma in at least one of the maps. As a bonus, you'll also have phases and a map that combine the information from your molecular replacement model and the anomalous scattering. You can do this either through AutoSol (if you did the molecular replacement with AutoMR you will have been given the option to press a button to run AutoSol, which is convenient) or directly through Phaser-EP. In each case you have to give a PDB file identified as a partial molecular replacement solution. Let me know if you have any difficulty finding the right options. Best wishes, Randy Read On Mar 26 2011, Jason wrote: >On Sat, Mar 26, 2011 at 11:29 AM, Nathaniel Echols <nechols(a)lbl.gov> wrote: > >> On Fri, Mar 25, 2011 at 9:20 PM, Jason <phenix.upitt(a)gmail.com> wrote: >> > 1) Synchrotron Fluorescence scan indicates the heavy atom definitely >> > presents in my protein (my control is a second protein with the same >> ligand >> > showed no absorbance spectrum) >> >> Keep in mind that a positive fluorescence scan does not necessarily >> mean that the element of interest is bound and well-ordered in the >> crystal - it is easy to get an excellent scan without seeing anything >> in the maps later. >> > >Indeed, but hopefully it's not the case. > > >> > When I load the mtz file to phenix.maps GUI, the mtz label pulldown >> > menu indicates 4 possible choices for the column to use:(1) IMEAN, >> > SIGIMEAN (2) I(+), sigI(+), I(-), sigI(-) merged (3) F(+), sigF(+), >> > F(-), >> sigF(-) >> > merged (4) F, sigF, Dano SigDano. I have tried the choices of (2) (3) >> > and (4). However, there is barely any anomalous signal at 4sigma, >> > which makes >> me >> > wondering if something is not right. The first thing coming to my >> > mind is the mtz labels: I(+), sigI(+), I(-), sigI(-) merged. What does >> > merged mean? Could this be the reason? Other issues that could causing >> > the >> trouble? >> >> The "merged" means that the input data were only partially merged - >> this usually happens when processing in HKL2000 using the "no merge >> original index" setting, where the reflections are not merged to the >> asymmetric unit (anomalous or not). I've never used XDS, but I guess >> it must do something similar. Phenix doesn't really deal with data >> like that; it always merges equivalents (while leaving Friedel pairs >> alone by default). This usually doesn't have any impact on the >> anomalous signal. If XSCALE has an option to merge the data more >> completely, this should make the "merged" tag go away. >> > >I went through the xds menu again and found that the "merged" seems ok in >terms of anomalous signal. > > >> It sounds like your element of interest isn't very well ordered; do >> you see the rest of the ligand in the normal maps? > > >I was hoping to identify the ligand binding position by resolving the >anomalous map first. Shouldn't this be the procedure to locate ligand? > > If you really want >> to be sure that it's not a data-handling issue, you could try >> reprocessing in other programs and confirming the result. > > > I know CCP4 can also generate anomalous difference map. But I myself have > never done it (I googled online and found it not that straight forward). > Can anybody go through it for me please, or there are other handy > programs that can make anomalous difference map? > > >> I don't >> know if radiation damage could be at fault, but it's always a >> possibility. >> >> -Nat >> > >====================== >Jason >Structural Biology Department >University of Pittsburgh >====================== >

14 years, 10 months

Re: [phenixbb] Completeness issue by phenix - revisited

by Mischa Machius

Could it be that you reserved 10% of your data for Rfree and are looking at the completeness for the work set? Do you have an I/sigma(I) cutoff that is high? If not, it might help to post the some of the Phenix output, e.g., the table with the completeness data along with the resolution limits, etc. Best - MM On Feb 3, 2010, at 10:42 PM, J. Fleming wrote: > Hi, > > I'm having a problem using phenix.refine with my x-ray data. My completeness is always 89% when it should be 99%. My data was originally processed with CCP4i. I found an old post (see below) with a potential fix that doesn't work for me. I've tried changing the 'Anomalous flag: True' to 'Anomalous flag: False' but my completeness is still 89%. I've clicked through a variety of other setting in the GUI that I thought would help but no luck. Does anyone have any ideas? > > Thanks in advance, > Jon > > > ----- Original Message ----- > From: "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov> > > To: phenixbb at phenix-online.org > Sent: Monday, December 15, 2008 12:59:12 PM GMT -05:00 US/Canada Eastern > Subject: Re: [phenixbb] Completeness issue by phenix > > > Hi YoungJin, > > I suspect phenix.refine decided your mtz file contains anomalous data > when you actually have non-anomalous data. Could you look in the > phenix.refine output for something like this: > > ================================== X-ray data ================================= > > > F-obs: > 1yjp.mtz:FOBS_X,SIGFOBS_X > > R-free flags: > 1yjp.mtz:R-free-flags > > Miller array info: 1yjp.mtz:FOBS_X,SIGFOBS_X > Observation type: xray.amplitude > Type of data: double, size=495 > Type of sigmas: double, size=495 > > Number of Miller indices: 495 > Anomalous flag: False > ^^^^^ > in particular here > > If you see "Anomalous flag: True" try adding this to the phenix.refine > command line: > > > xray_data.force_anomalous_flag_to_be_equal_to=False > > Let me know if this doesn't help. > If it does help, I'd be interested to know how the .mtz file was > generated. > > Ralf > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

16 years

Re: [phenixbb] Discrepancy between Phenix GUI and command line for MR

by Randy John Read

Hi Xavier, We haven’t noticed that, or at least any effect is small enough not to stand out. There shouldn’t be a lot of overhead in communicating with the GUI (i.e. updating the terse log output and the graphs) but if there is we should look into it and see if we can do something about it. Could you tell me how much longer (say, in percentage terms) a job takes when you run it through the GUI compared to running the same job outside the GUI on the same computer? Also, it’s possible the architecture matters so could you say which type of computer and operating system you’re using? If it’s a Mac, is it one with an Intel processor or an ARM (M1 or M2) processor? (By the way, we finally managed to track down and fix an issue that cause Phaser to run really slowly on an M1 or M2 Mac when using the version compiled for Intel, once I got my hands on a new Mac.) Best wishes, Randy > On 4 Jul 2023, at 10:44, Xavier Brazzolotto <xbrazzolotto(a)gmail.com> wrote: > > Dear Phenix users > > I’ve noticed that molecular replacement was clearly slower while running from the GUI compared to using the command line (phenix.phaser). > > Did you also observe such behavior? > > Best > Xavier > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

2 years, 7 months

Re: [phenixbb] XDS data

by Nathaniel Echols

On Tue, Jan 14, 2014 at 4:42 AM, Tim Gruene <tg(a)shelx.uni-ac.gwdg.de> wrote: > I would like to run Phaser-EP through the phenix GUI. When I first > uploaded the XDS_ASCII.HKL file, there was an error message about "No > valid observed reflections found in this file". Can you send me the first three lines of the file? My guess is that it looks like this: !FORMAT=XDS_ASCII MERGE=FALSE FRIEDEL'S_LAW=TRUE which would be interpreted by our XDS reader as being non-anomalous, even though since it's unmerged there is probably nothing stopping us from using the anomalous data anyway. (I need to double-check this, because I don't understand why it would claim "FRIEDEL'S_LAW=TRUE" if I+ and I- are actually kept separate.) If you instead produce a file that starts like this: !FORMAT=XDS_ASCII MERGE=TRUE FRIEDEL'S_LAW=FALSE then it will be accepted by the Phaser-EP GUI. Subsequently I > uploaded an unmerged hklf4 file. The GUI tells me I need to let phenix > know about it being hklf4 by appending '=hklf4'. However, when I do > so, there is an error message the file did not exist and the Data file > line goes red. Where should I correctly append '=hklf4'? > This may simply be a bug. Which version are you using? I had attempted to make the GUI handle SHELX files more sensibly (to the extent that's even possible), but I can't remember how successful I was, and it may have been after version 1.8.4 was released. In general, SHELX format is the least compatible of the supported inputs; it's just missing too much information. -Nat

12 years

[phenixbb] Completeness issue by phenix - revisited

by J. Fleming

Hi, I'm having a problem using phenix.refine with my x-ray data. My completeness is always 89% when it should be 99%. My data was originally processed with CCP4i. I found an old post (see below) with a potential fix that doesn't work for me. I've tried changing the 'Anomalous flag: True' to 'Anomalous flag: False' but my completeness is still 89%. I've clicked through a variety of other setting in the GUI that I thought would help but no luck. Does anyone have any ideas? Thanks in advance, Jon ----- Original Message ----- From: "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov <http://www.phenix-online.org/mailman/listinfo/phenixbb>> To: phenixbb at phenix-online.org <http://www.phenix-online.org/mailman/listinfo/phenixbb> Sent: Monday, December 15, 2008 12:59:12 PM GMT -05:00 US/Canada Eastern Subject: Re: [phenixbb] Completeness issue by phenix Hi YoungJin, I suspect phenix.refine decided your mtz file contains anomalous data when you actually have non-anomalous data. Could you look in the phenix.refine output for something like this: ================================== X-ray data ================================= F-obs: 1yjp.mtz:FOBS_X,SIGFOBS_X R-free flags: 1yjp.mtz:R-free-flags Miller array info: 1yjp.mtz:FOBS_X,SIGFOBS_X Observation type: xray.amplitude Type of data: double, size=495 Type of sigmas: double, size=495 Number of Miller indices: 495 Anomalous flag: False ^^^^^ in particular here If you see "Anomalous flag: True" try adding this to the phenix.refine command line: xray_data.force_anomalous_flag_to_be_equal_to=False Let me know if this doesn't help. If it does help, I'd be interested to know how the .mtz file was generated. Ralf

16 years

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