- phenixbb - phenix-online.org

transfering R-free flags
by Tirumala Kumar Chowdary 28 Sep '09

28 Sep '09

Hi, I am trying to refine my model against a higher resolution file. I want to transfer my R-free flags generated by phenix.refine from the lower resolution mtz to the higher resolution file. Is there a way to transfer the R-free flags in Phenix ? If not, where can I find the mtz file from my earlier refinement with R-free flags generated ? Does phenix.refine generate this file and save it for me somewhere ? Thanks Tirumal

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NCS restraints with TLS
by Joe Krahn 28 Sep '09

28 Sep '09

I am using NCS restraints with TLS. It seems that the NCS B-factor restraints are applied to the overall B-factor, rather than just the non-TLS part. Is this correct? In my structure, the disorder varies quite a bit among equivalent molecules, and I don't get good results unless the b_factor_weight is about 1e-3 or less. I am experimenting with NCS restraints in CNS, where each pair of coordinates allows an LSQ fit of B-factor scale and offset to be excluded from the B restraints. It would probably work even better with TLS, which CNS does not have. I don't know if anyone has tried this, but I think that overall molecular B-factor differences are fairly common. Joe Krahn

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NCS averaged maps?
by Francis E Reyes 26 Sep '09

26 Sep '09

With all the recent talk about kicked and filled maps, can we have phenix output an ncs averaged map for those of us who have NCS? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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extend R-free set to higher resolution
by NATHAN THOMSEN 25 Sep '09

25 Sep '09

Is there a phenix utility to extend a phenix generated R-free set to higher resolution (while still using lattice symmetry etc.)? Thanks! Nathan Thomsen UC Berkeley

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Re: [phenixbb] extend R-free set to higher resolution
by Thomas C. Terwilliger 25 Sep '09

25 Sep '09

Hi Nathan, Yes, you can use the GUI to do this (you need a recent nightly build to do it). Just click on "Reflection file editor" and you get an option to extend a free R set, maintaining the free R set you already have. All the best, Tom T >> Is there a phenix utility to extend a phenix generated R-free set to >> higher resolution (while still using lattice symmetry etc.)? Thanks! >> >> Nathan Thomsen >> UC Berkeley >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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wxu_scale is ignored with TLS
by Joe Krahn 25 Sep '09

25 Sep '09

When using TLS, the wxu_scale is changed, even if it is given in the input file. IMHO, TLS should only modify the default value, and not a user-defined wxu_scale. Thanks, Joe Krahn

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Various problems with phenix.refine
by Joe Krahn 25 Sep '09

25 Sep '09

Here are a few problems I have found using phenix.refine 1.4: If NCS restraint selection in the .def file have newline characters, the REMARK 3 formatting is messed up. It should probably replace all white-space regions with a single space. When NCS restraints contain a residue with alternate conformations, that residue gets excluded from all equivalences, even if the selections contain ALTID to avoid the redundant atoms. If the .def file has a syntax error, phenix.refine dies with an error that the file format is not recognized. Why not print syntax errors? The optimize_wxc and optimize_wxu features are useful, but it is difficult to use the result to define an improved fixed scale on subsequent rounds, without having to optimize every time. It is not obvious whether the scale written in the log represents the new wxc_scale, or if it is a multiplier versus the current wxc_scale. The log also truncates to 2 decimal places. In my case, I only get one significant digit from scale=0.05. I propose that the optimizations write something like "Optimal wxc_scale = 0.533". The input data is written as "refine_data.mtz", not using the serial number, and there seems to be no flag to disable writing it. That means I have to force overwrite to run iterations in the same directory. If each run is in its own directory, the serial number is not very useful for filenames. So, the output MTZ should have the serial number, and you might also consider an option to disable the serial number when separate directories are used. Thanks, Joe Krahn

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specifying column labels for input MTZ file
by Tirumala Kumar Chowdary 24 Sep '09

24 Sep '09

Hi, I am trying to run phenix.refine with a sharp output MTZ file (column labels H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav). Phenix.refine stopped at 'Multiple equally suitable arrays of observed xray data found. Possible choices: sharp_sad_se_eden.mtz:FP,SIGFP sharp_sad_se_eden.mtz:Fav,SIGFav Please use refinement.input.xray_data.labels' Can someone tell me on how to use this 'refinement.input.xray_data.labels' and how to specify which column labels to use. There is nothing written in the documentation about it. Thanks Tirumal

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question about rfree flag transfer
by crystallogrphy 24 Sep '09

24 Sep '09

Hi, I have built a model against a 3.7A data set by AutoBuild. The resulting model is overall_best.pdb. The data with the rfree test flags is exptl_fobs_phases_freeR_flags.mtz Later on, I got a 3.4A data, which is isomorphous with the 3.7A data. Now I want to transfer the rfree flag from the 3.7A to 3.4A data for refinement. I know one strategy if the data file is in CNS format. That is, use DATAMAN to transfer the flags and generate new test set flags in the high resolution range: 3.7-3.4A. However, when I convert the format by phenix.reflection_file_converter, it fails: phenix.reflection_file_converter exptl_fobs_phases_freeR_flags.mtz --cns=exptl_fobs_phases_freeR_flags.cv --label="PHIM" --label="FP,SIGFP" --label="FOMM" --label="FreeR_flag" --label="FC" However, the resulting data does not have any FP, SIGFP, and FreeR flags. { file: exptl_fobs_phases_freeR_flags.cv.cns } { sg=C2 a=175.385 b=102.472 c=92.057 alpha=90 beta=111.312 gamma=90 } { source of data: exptl_fobs_phases_freeR_flags.mtz:FC } NREFlections=15307 ANOMalous=FALSe DECLare NAME=DATA DOMAin=RECIprocal TYPE=REAL END INDEx 0 0 5 DATA= 0 INDEx 0 0 7 DATA= 0 INDEx 0 0 8 DATA= 0 INDEx 0 0 9 DATA= 0 INDEx 0 0 10 DATA= 0 INDEx 0 0 11 DATA= 0 INDEx 0 0 12 DATA= 0 INDEx 0 0 13 DATA= 0 I also tried mtz2various in CCP4i, the resulting hkl file does not have rfree flags at all. Does anyone know who to convert the exptl_fobs_phases_freeR_flags.mtz into cns format or simple transfer the flags by phenix?

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supported compilers for source builds
by Ben Eisenbraun 23 Sep '09

23 Sep '09

For compiling PHENIX from source, what are the supported compilers? Are the Intel or Portland compilers supported? There are notes in the list archives about using OpenMP with gcc, and hints that the Intel compiler is supported, but I didn't see any docs on building with icc/ifort. In one email Ralf mentions that you might actually lose performance compiling your own version of Solve/Resolve because gfortran optimizes poorly, which leads me to think that the distributed binaries are using ifort for at least the Solve/Resolve bits. Did I overlook some notes on how to do this? -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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