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Re: [phenixbb] Molecule and maps will not load into coot from Phenix 1.7.1-743
by Jobichen Chacko 03 Nov '11

03 Nov '11

Dear Nat, Any progress in this matter. To add, do you have any version of Phenix which is working perfectly (the communication of Phenix with pymol and coot) in ubuntu system in you lab? Jobi On Tue, Nov 1, 2011 at 5:08 PM, Jobichen Chacko <jobichenc(a)gmail.com> wrote: > Dear Nat, > Just to add when I try open the files in pymol, it doesnot open up and > show this output. > > /usr/local/phenix-1.7.1-743/build/intel-linux-2.6-x86_64/base/bin/python2.7: > No module named pymol > > Jobi > > > On Tue, Nov 1, 2011 at 10:58 AM, Jobichen Chacko <jobichenc(a)gmail.com> wrote: >> Dear Nat, >> I installed the the coot version you sent to me. Still not working. >> jobi >> >> On Tue, Nov 1, 2011 at 10:43 AM, Nathaniel Echols <nechols(a)lbl.gov> wrote: >>> On Mon, Oct 31, 2011 at 7:34 PM, Jobichen Chacko <jobichenc(a)gmail.com> wrote: >>>> Dear Nat, >>>> Thank you for your help. >>>> Please see the attached output after running coot_test.py >>>> I will also try to install the coot version you send to me. >>>> Jobi >>>> ... >>>> 'import site' failed; use -v for traceback >>> >>> Wow, that's way more broken than I was expecting. I think this means >>> a library conflict, but I've only come across this error on Mac. Can >>> you try one more thing? >>> >>> export PYTHONVERBOSE=1 >>> coot --script coot_test.py >>> >>> (If you're using csh or tcsh as your shell, the first line should be >>> "setenv PYTHONVERBOSE 1" instead.) >>> >>> -Nat >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >> >

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Ligands at special positions
by Subhani Bandara 02 Nov '11

02 Nov '11

Hi everyone, There are some ligands in my protein structure, that are very close to a special position. But they are not exactly at a special position, so when I apply symmetry in coot it generates another ligand away from the original one. How can I move them exactly on to a special position. Is there any script I can use for this? Thanks Subhani

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NMR vs Xtal structures
by Yuri 02 Nov '11

02 Nov '11

Could someone point me to a good paper on comparing of structures of the same protein determined by X-ray vs. NMR Best, -- Yuri Pompeu

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Autosol
by Kiran Kulkarni 01 Nov '11

01 Nov '11

Hi, I am getting following error message while running Autosol. *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoSol_guess_setup_for_scaling: 'nat_der_list' ******************************************************************************** *************ERROR ENDING ******************* Please help me to fix this. Details: PHENIX VERSION: 1.7.2 of 23-09-2011 PHENIX RELEASE_TAG : 869 PHENIX MTYPE : mac-intel-osx-x86_64 PHENIX MVERSION : osx-10.6.8 Space group: P41 EXPT_TYPE = SIR Native data Resolution= 3.8A Derivative data Resolution= 6.5A Program runs smoothly for derivative data alone (i.e. for SAD mode). Many thanks, -Kiran

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Molecule and maps will not load into coot from Phenix 1.7.1-743
by Jobichen Chacko 01 Nov '11

01 Nov '11

The same old problem, I tried to add the coot path using preferences. Coot version result: COOT_PREFIX is /usr/local /usr/local/bin/coot-real --version 0.6.1 (revision 2740) [with guile 1.8.7 embedded] [with python 2.6.0 embedded] The coot opens just after phenix-refine job starts and after the job finishes. But no maps and models are loaded. Thanks. Jobi

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"ATP" monomer in phenix_refine
by Zhang yu 28 Oct '11

28 Oct '11

Hi, I had a trouble of refining "ATP" in Phenix. I appreciate any help. ATP with tri-phosphate is in the 5' end of RNA chain. It is added to the RNA chain in coot as a monomer "ATP", and it could be connected to the downstream base after I changed the "_chem_comp.group" option to "RNA" in the cif file. But when I refine the model in Phenix, Phenix treated the "ATP' as a monomer and didn't connect it to the downstream base. I tried two ways to solve it 1. Add the the modified (chang the "_chem_comp.group" option to "RNA") cif file in phenix_refine, but Phenix doesn't recognize it. 2. In REEL, I found phenix has its own cif file for ATP, but the its header couldn't be edited. Any suggestions? Thanks. Yu

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Problem avoiding real space refinement
by Jerome Nwachukwu 27 Oct '11

27 Oct '11

Hi: We noticed that in some of our refinements, real space refinement was performed even though we chose not to do this. I tried to opt out of real space refinement as follows: " refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp *tls *occupancies group_anomalous ..." however, the R-free is identical whether we select real space refinement or not, and the logfile shows " Validate: |--------START--------| |--------FINAL--------| residue map_cc 2mFo-DFc mFo-DFc map_cc 2mFo-DFc mFo-DFc "LYS A 18 " 0.9359 16.78 0.00 0.9107 17.60 0.00 "ARG A 19 " 0.9513 21.82 0.00 0.9470 20.97 -6.52 <<< "ARG A 26 " 0.9440 26.72 0.00 0.9474 27.33 -2.43 "ARG A 69 " 0.9685 31.36 0.00 0.9659 32.58 0.00 "GLN A 86 " 0.9681 23.57 -5.81 0.8850 19.29 -18.27 <<< "GLU A 89 " 0.9689 26.30 -4.43 0.8977 23.67 -11.59 <<< "LYS A 93 " 0.9746 25.19 0.00 0.9682 26.47 2.90 ... " and suggesting that real space refinement was performed. Is there a way to correct this, or to ensure that real space refinement is not performed during refinement? Thank you, -Jerome Jerome C. Nwachukwu, PhD Dept. of Cancer Biology The Scripps Research Institute-Florida

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problem to add D atom on carbonyl group (enol) as alternate conformation
by Maxime Cuypers 27 Oct '11

27 Oct '11

Dear all, i have a problem that i block on for quite a while. i need to add a D atom on carbonyl group (enol) as alternate conformation to a main chain protein amide group to refine with phenix.refine. It is not something that the program phenix.reduce can perdeuterate as it is an unusual position. it actually perdeuterates all the rest of the protein successfully. Does anyone have an idea how to proceed? i tried so far to rename the residue and give .cif restraints generated with readyset for the new tautomer. phenix seemed to recognised it but it failed due to the fact it does not recognise the residue as being a residue to link to the other residues and bounds bounce off. A friend told me a cif_link was the problem. Then i tried to apply cif_modification in a parameter file with the corresponding .cif file as explained briefly on: http://www.phenix-online.org/documentation/refinement.htm#anch88 it does not solve the problem. the link between the new tautomer residue and the rest of the residues does not occur in refinement. Thanks for your help in advance. i am getting deseperate. Maxime

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exploring the conformational space of sidechains
by Francois Berenger 27 Oct '11

27 Oct '11

Hello, Is there a way to do this with Phenix? I.e., from a given model, obtain models with different but also reasonable sidechains conformations. N.b.: I don't have X-ray data so I am looking for a geometric thing, and I'm OK if the model's backbone undergoes some small movement because of the sidechains having moved. Thanks a lot, F.

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Molecule and maps will not load into coot from Phenix 1.7.1-743
by Yuri 27 Oct '11

27 Oct '11

Read the thread I waas just a part of maybe it is related -- Yuri Pompeu

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Re: [phenixbb] COOT not "connected" to PHENIX
by Yuri 25 Oct '11

25 Oct '11

I installed the version with python embedded in coot And it works!! Thanks a lot!! On Tue, 25 Oct 2011 11:41:38 -0700, Nathaniel Echols wrote: > On Tue, Oct 25, 2011 at 11:40 AM, Yuri <yuri.pompeu(a)ufl.edu> wrote: >> Now here comes the stupid question... >> How do I fix it? >> Install a different coot version or is it something in my >> architecture? > > Install a different Coot. If you're downloading from Paul Emsley's > page, you need a package with "python" in the file name. I have no > idea whether the Linux binaries distributed by CCP4 have Python or > not > (the Mac version definitely does). > > -Nat -- Yuri Pompeu

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COOT not "connected" to PHENIX
by Yuri 25 Oct '11

25 Oct '11

Hello everyone, I am running 1.7.2-869 and coot 0.6.2 By telling phenix where hte path is, I can get it to launch from any phenix job tab. However in one of my machines, even though COOT launches through phenix it is not connected to it which does not allow me to look at clashes when building in coot- a very useful feature may I add!!! In one of my RHEL5 machines it is working nicely, and I dont see any obvious differences between the working and the non-working one. Any ideas? Thank you much -- Yuri Pompeu

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phenix.phaser generate .sol file
by G Y 25 Oct '11

25 Oct '11

Dear Experts, I run phaser in phenix with GUI and script using params.eff. For both case, I can not find .sol file in the outputs. What option or command I should used in GUI and params.eff to generate the .sol file in the outputs? Thanks for your kind help! GY

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phenix.pdbtools --show-adp-statistics
by Krzysztof Bzymek 24 Oct '11

24 Oct '11

Hi, I noticed that this option is longer supported in phenix 1.7.2-869. Is there an equivalent command that would print out the statistics? Thanks, Chris

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coot from phenix
by Andreas Förster 24 Oct '11

24 Oct '11

Dear all, I'm running phenix 1.7.2-869 on RHEL 6.1 64-bit. When I click on "Open in Coot" after refinement, coot doesn't open and I get the following error in the shell from which I started phenix: /csb/soft/Linux64/share/phenix-1.7.2-869/phenix-1.7.2-869/phenix/phenix/command_line/start_coot.sh: line 33: /csb/soft/Linux/src/coot-0.6/bin/coot: No such file or directory In the script that launches coot, $PHENIX_COOT is defined as /csb/soft/Linux/src/coot-0.6/bin/coot, which doesn't exist (and is a path that we used in the old days of 32-bit). Typing phenix.find_coot_command in the shell from which phenix was started returns /csb/soft/Linux64/src/coot-0.7-rev3689/bin/coot, which is the right coot. To me it seems the phenix script to launch coot is falling back on an internally defined $PHENIX_COOT variable (that's not defined from the shell). That's shouldn't be, should it? How do I fix this short of hardwiring $PHENIX_COOT as /csb/soft/Linux64/src/coot-0.7-rev3689/bin/coot? Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

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Unusual CCP4 to Phenix data conversion result
by R.M. Garavito 24 Oct '11

24 Oct '11

In upgrading to CCP4 6.2.0 and Phenix-1.7.2-869 (from CCP4 6.1.13 and Phenix-1.7.1-743, respectively) a bug has crept into reading of the MTZ files. We tend to scale and merge XDS processed data with Scala in CCP4, then use the resulting data in CCP4 and Phenix (with great success I might add). However, I just noticed that in testing the upgraded CCP4 and Phenix on OSX 7.2 (Lion) that the MTZ file is no longer read correctly. An example is below where after the output from scaling and merging of nonanomalous data from the CCP4i GUI gives, at the end of FREERFLAG, some 47,000 reflections. Putting this into xtriage or the reflection file editor in the Phenix GUI, one finds that the data for the F and the DANO columns are used; just selecting Fs alone is impossible. The end result is a doubling of the reflection number and the switching of the anomalous flag on. Processing with earlier versions did not do this except when actually using anomalous data. Why this has happened is not clear to me, but the column order in the MTZ file changed slightly between CCP4 6.1.13 and CCP4 6.2.0. Any ideas, am I missing something, or is this a push to only refine with intensities? Regards, Michael ***************** From Scala (3.3.20) Total number unique : 46813 From FREERFLAG Number of Reflections = 47044 (including non-observed NaN reflections) MTZ column labels H K L FreeR_flag F_S13E_X2 SIGF_S13E_X2 DANO_S13E_X2 SIGDANO_S13E_X2 F_S13E_X2(+) SIGF_S13E_X2(+) F_S13E_X2(-) SIGF_S13E_X2(-) ISYM_S13E_X2 IMEAN_S13E_X2 SIGIMEAN_S13E_X2 I_S13E_X2(+) SIGI_S13E_X2(+) I_S13E_X2(-) SIGI_S13E_X2(-) ****************** In Phenix: Xtriage output choosing "Imean" Miller array info: /Users/garavito/ccp4_projects/sus1_S13/reflections_tmp.mtz:IMEAN_S13E_X2,SIGIMEAN_S13E_X2 Observation type: xray.amplitude Type of data: double, size=46772 Type of sigmas: double, size=46772 Number of Miller indices: 46772 Anomalous flag: False Xtriage output choosing "Fs" Miller array info: /Users/garavito/ccp4_projects/sus1_S13/reflections_tmp.mtz:F_S13E_X2,SIGF_S13E_X2,DANO_S13E_X2,SIGDANO_S13E_X2 Observation type: xray.amplitude Type of data: double, size=88486 Type of sigmas: double, size=88486 Number of Miller indices: 88486 Anomalous flag: True **************************************************************** R. Michael Garavito, Ph.D. Professor of Biochemistry & Molecular Biology 513 Biochemistry Bldg. Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334 Email: garavito(a)msu.edu ****************************************************************

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phenix.pdbtools
by Abhinav Kumar 21 Oct '11

21 Oct '11

Hi, I had been using the pdbtools to obtain the rmsd on various geometry parameters using the command: phenix.pdbtools my.pdb --show-geometry-statistics Now pdbtools does not recognize the option "--show-geometry-statistics" What is the option now? I am using phenix-1.7.2-869. -- Thanks, Abhinav JCSG@SSRL, SLAC Phone: (650) 926-2992 Fax: (650) 926-3292

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ligands at a special position
by Subhani Bandara 19 Oct '11

19 Oct '11

Hi, I am trying to solve a structure of a protein that is cocrystallized with a chelator complex using phenix (GUI). The complex is Tb(DPA)3 and DPA stands for dipicolinic acid. In the structure (C222) there are few Tb complexes on the two fold axis with symmetry coordinates 1/4X, 1/4Y, Z. In those, Tb and the center C (C4) and N (N1) of one DPA are sitting directly on the 2 fold axis. So I left only half of that DPA ligand structure on PDB file and changed the occupancy of N1 and C4 to 1/2 while keeping the occupancy of all other atoms of the half ligand structure at 1.00. Then I refined it while keeping above occupancies and xyz coordinated of the ligand fixed. After doing this the other half of the ligand could be built by symmetry, but it left a space between two halves(so it was not as one ligand). Can you please let me know what I can do to fix this structure. Also is there a way to keep only x and y coordinates fixed while varying z during refinement. Thanks Subhani

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Re: [phenixbb] Phenix building residues not found in input sequence file
by Thomas C. Terwilliger 18 Oct '11

18 Oct '11

Hi Allan, I assume that there is density showing protein in the region where autobuild is building these extra residues...is that right? If so...then is the remainder of the model matched very well to sequence (i.e., is more or less what you expected to see found, plus there is extra density?) It could be that there is really something in the crystal that you didn't expect. It could also be that part of the structure is not (or not correctly) assigned to sequence, so that this part of the structure really does go with part of your sequence. Does that help? It would be interesting to hear more details of this. All the best, Tom T >> Hi everyone, >> >> Apparently my Phenix (1.6.3-473) is building in extra residues in the >> C-terminal region, which is not found in my input sequence file. >> >> It's trying to build a model which is longer than I expected. Phenix >> building 87 extra amino acids. Any clue what's wrong? >> >> I made sure that these amino acids are not residues found in the >> N-terminal region or anywhere else in the protein. >> >> Allan >> >> -- >> Allan Pang >> >> PhD Student >> >> G35 Joseph Priestley Building >> Queen Mary University of London >> London >> E1 4NS >> >> Phone number: 02078828480 >>

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post-doc position at SSRL
by van den Bedem, Henry 17 Oct '11

17 Oct '11

Modeling Conformational Ensembles of Proteins and Complexes A post-doctoral position with a focus on modeling conformational ensembles of proteins and complexes is available immediately in the Structural Genomics Division of Stanford Synchrotron Radiation Lightsource at the SLAC National Accelerator Laboratory (http://ssrl.slac.stanford.edu). Macromolecules and assemblies are studied by a variety of experimental techniques, including protein crystallography and Small Angle X-ray Scattering. Nano-crystallography and single particle imaging data from the Linac Coherent Light Source (LCLS), a first-of-its-kind free electron laser, are also being targeted at these systems. Accurately modeling the conformational variability of macromolecules is essential to understanding their cellular function. This position at the forefront of computational structural biology aims to develop advanced algorithms to fit domains or proteins to experimental data from multiple sources while allowing for significant conformational changes. The goal is to automatically compute 3-D models, and to provide structural insights into functionally relevant dynamics, especially for time-resolved experiments or a series of static structures. The position offers the opportunity to closely collaborate with the Stanford Computer Science Department and work with X-ray, SAXS and LCLS nanocrystallography data. SLAC houses ample computational resources. Funding is available for up to 3 years. The starting date is as soon as possible. Candidates should have a recent PhD in computer science, applied mathematics, computational biology/crystallography or a related field with strong programming skills. Please send a CV, a short summary of your research experience and two letters of recommendation to Henry van den Bedem (vdbedem(a)slac.stanford.edu). Further details are available upon request. Relevant publications: Yao et al. Sampling-based exploration of folded state of a protein under kinematic and geometric constraints. Proteins: Structure, Function, and Bioinformatics (in press). Fraser et al. (2011) Accessing protein conformational ensembles using room-temperature X-ray crystallography. PNAS 108:16247-16252 van den Bedem et al. (2009) Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers. Acta Cryst. D65:1107-1117

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Re: [phenixbb] STOPWIZARD
by Thomas C. Terwilliger 17 Oct '11

17 Oct '11

Hi Morten, Yes, you can use STOPWIZARD to stop a phenix wizard, including mr_rosetta. However the "restarting" part is no longer enabled for most of the wizards. For mr_rosetta, you can restart. Here is how: You can re-start mr_rosetta only at the beginning of major stages (like "place_model", "rosetta_rebuild" etc)...but not in between. Normally at the end of a major stage a .pkl file is written out with text like "type this to see all the results". You can almost always give your original command, the command "start_point=xxx" and "mr_rosetta_solutions=my_pickle_file.pkl" and it should then continue on from there. I will put this in the docs... All the best, Tom T >> Dear phenixbb, >> >> The Phenix manual mentions several times that making a file named >> STOPWIZARD >> in the wizard root directory will stop the wizard in an orderly fashion >> the >> next time it checks for STOPWIZARD. There is however no mention of how to >> properly restart the wizard after having stopped it... How? I seem to >> remember something about it being >>>phenix.appropriate_wizard params_used_in_wizard.eff >> but I'd like be sure that I don't simply start over by doing that. >> >> Also can I then change the parameters before restarting the wizard? Say, >> hypothetically of course, that I've started mr.rosetta and asked for 1000 >> prerefined models and realised that it will take ridiculously long and be >> rather redundant since I specified both the .hhr file from global and >> local >> alignment and the top hit has two chains (resulting in mr.rosetta wanting >> to >> build 4000 prerefined models) but I don't want to throw away the 700 >> models >> already built. Could I do something about that? >> >> Sincerely, >> Morten Grøftehauge, PhD >> Durham University >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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STOPWIZARD
by Morten Grøftehauge 17 Oct '11

17 Oct '11

Dear phenixbb, The Phenix manual mentions several times that making a file named STOPWIZARD in the wizard root directory will stop the wizard in an orderly fashion the next time it checks for STOPWIZARD. There is however no mention of how to properly restart the wizard after having stopped it... How? I seem to remember something about it being >phenix.appropriate_wizard params_used_in_wizard.eff but I'd like be sure that I don't simply start over by doing that. Also can I then change the parameters before restarting the wizard? Say, hypothetically of course, that I've started mr.rosetta and asked for 1000 prerefined models and realised that it will take ridiculously long and be rather redundant since I specified both the .hhr file from global and local alignment and the top hit has two chains (resulting in mr.rosetta wanting to build 4000 prerefined models) but I don't want to throw away the 700 models already built. Could I do something about that? Sincerely, Morten Grøftehauge, PhD Durham University

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mr_rosetta memory usage
by Tjaard Pijning 17 Oct '11

17 Oct '11

Hi, I am currently running mr_rosetta and found that after a while the computer (running OpenSuse/linux) slows down dramatically because its memory (8 GB) is running full. I’m not sure if the program still runs or not. Is there a way to limit the amount of memory that phenix/mr_rosetta uses ? Or should I e.g. lower the amount of models being used (currently 5) ? (Before starting mr_rosetta I ran the regression test which was fine). Kind regards, Tjaard Pijning University of Groningen This is the parameter file : mr_rosetta { input_files { seq_file = gEP_mature.txt" hhr_files = "051011_3011840.hhr" alignment_files = None model_info_file = "" data = "XDS_ASCII_C2221.mtz" labin = None search_models = None copies_in_search_models = None mr_rosetta_solutions = "" ids_to_load = None map_coeffs = "" labin_map_coeffs = None map = "" display_solutions = False fragment_files = "aat000_03_05.200_v1_3" fragment_files = "aat000_09_05.200_v1_3" use_dummy_fragment_files = False sort_fragment_files = True } output_files { log = "mr_rosetta.log" params_out = "mr_rosetta_params.eff" } directories { temp_dir = "mr_rosetta/MR_ROSETTA_7/WORK_1" workdir = "mr_rosetta/MR_ROSETTA_7" output_dir = "mr_rosetta" top_output_dir = "mr_rosetta/MR_ROSETTA_7" rosetta_path = "" rosetta_binary_dir = "rosetta_source/bin" rosetta_binary_name = "mr_protocols.default" rosetta_script_dir = "rosetta_source/src/apps/public/electron_density" rosetta_pilot_script_dir = "rosetta_source/src/apps/pilot/frank/" rosetta_database_dir = "rosetta_database" } read_hhpred { number_of_models = 5 number_of_models_to_skip = 0 copies_to_extract = None only_extract_proper_symmetry = False } place_model { run_place_model = True prerefine { run_prerefine = False number_of_prerefine_models = 1000 number_of_models_in_ensemble = 1 } model_already_placed = False model_already_aligned = False number_of_output_models = 5 align_with_sculptor = True identity = None identity_for_scoring_only = 25 use_all_plausible_sg = True overlap_allowed = 300 selection_criteria_rot_value = 75 fast_search_mode = True search_down_percent = 25 mr_resolution = 3 refine_after_mr = True denmod_after_refine = True find_ncs_after_mr = True min_length_ncs = 10 fixed_ensembles { fixed_ensembleID_list = None fixed_euler_list = 0 0 0 fixed_frac_list = 0 0 0 fixed_frac_list_is_fractional = True } copies_of_search_model_to_place = None } rescore_mr { run_rescore_mr = True nstruct = 5 relax = False include_unrelaxed_in_scoring = False align = True edit_model = False stage_to_rescore = "mr_solution" } rosetta_rebuild { run_rosetta_rebuild = True stage_to_rebuild = "rescored_mr_solution" max_solutions_to_rebuild = 5 min_solutions_to_rebuild = 1 llg_percent_of_max_to_keep = 50 rosetta_models = 100 chunk_size = 1 edit_model = True superpose_model = False } rosetta_rescore { run_rosetta_rescore = True percentage_to_rescore = 20 min_solutions_to_rescore = 2 } similarity { run_similarity = False required_cc = 0.2 number_of_required_cc = 5 } refine_top_models { run_refine_top_models = True stage_to_refine = None sort_score_type = None percent_to_refine = 20 denmod_after_refine = True } average_density_top_models { run_average_density_top_models = True percent_to_average = 100 } relax_top_models { run_relax_top_models = True stage_to_relax = None number_to_relax = 2 nstruct = 5 } autobuild_top_models { run_autobuild_top_models = True number_to_autobuild = 2 quick = False phase_and_build = False macro_cycles = None morph = False edit_model = True use_map_coeffs = True } setup_repeat_mr_rosetta { run_setup_repeat_mr_rosetta = True repeats = 1 template_repeats = 0 morph_repeats = 0 number_to_repeat = 1 acceptable_r = 0.25 minimum_delta_r = None } repeat_mr_rosetta { run_repeat_mr_rosetta = True copies_in_new_search_group = 1 update_map_coeffs_with_autobuild = True } rosetta_modeling { map_resolution = 3 map_grid_spacing = 1.5 map_weight = 1 map_window = 5 include_solvation_energy = True weights_file = "" } crystal_info { resolution = 0 space_group = None chain_type = *PROTEIN DNA RNA ncs_copies = 2 } control { verbose = False debug = False raise_sorry = False dry_run = False nproc = 5 group_run_command = "sh " condor = None single_run_command = "sh " background = None ignore_errors_in_subprocess = True check_run_command = False max_wait_time = 100 wait_between_submit_time = 1 n_dir_max = 100000 number_to_print = 5 write_run_directory_to_file = None resolve_command_list = None start_point = *place_model rescore_mr rosetta_rebuild rosetta_rescore \ similarity refine_top_models average_density_top_models \ relax_top_models autobuild_top_models \ setup_repeat_mr_rosetta repeat_mr_rosetta stop_point = place_model rescore_mr rosetta_rebuild rosetta_rescore \ similarity refine_top_models average_density_top_models \ relax_top_models autobuild_top_models \ setup_repeat_mr_rosetta repeat_mr_rosetta } non_user_params { file_base = None print_citations = True highest_id = 0 is_sub_process = False dummy_autobuild = False dummy_refinement = False dummy_rosetta = False skip_clash_guard = True correct_special_position_tolerance = None comparison_mtz = "" labin_comparison_mtz = None write_local_files = False rosetta_fixed_seed = None } }

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re-building chains
by Leonid Sazanov 14 Oct '11

14 Oct '11

Hi, how exactly can one tell Autobuild to rebuild-in-place chains A and B from the input model, but build chain C de-novo? If I give it list of chains to re-build (rebuild_near_chain="A B" in GUI, dev-874 version), what happens is that either all chains are rebuild-in-place (if rebuild-in-place=True) or all chains are built de-novo (if rebuild-in-place=False). Thanks! -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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1.7.2 slow to open
by Jinsong Liu 12 Oct '11

12 Oct '11

Hi there, I wonder if there is anyone else experiencing a VERY VERY slow opening of the phenix GUI for the latest version of 1.7.2? We have RHEL 5.3 and CentOS 5.6, both machines show this. Most of the time, it will take minutes, sometime more than 10 minutes. There is no any warning or error message, after the long waiting the GUI will suddenly show up. In the older version, it usually takes seconds to load the GUI. Thanks. Jinsong -- Jinsong Liu, Ph.D. Principle Investigator & Head of Laboratory of Structural Biology Guangzhou Institute of Biomedicine and Health (GIBH) Chinese Academy of Sciences Guangzhou ( Canton ) 510630, China Phone: 86-20-32015317 (Office) E-mail: liu_jinsong(a)gibh.ac.cn

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Re: [phenixbb] mr_rosetta
by Thomas C. Terwilliger 11 Oct '11

11 Oct '11

Hi Abhinav, This format is very unforgiving. It has to have exactly 5 lines: ## TARGET SP_3n91 # hhsearch scores_from_program: 0 1.00 0 --DDDEVTMNSK.... 0 GSDNEFPDFDYQ.... -- also note I changed SP 3n91 to SP_3n91. Your PDB file name must also start with SP_3n91 in this case. You need a pdb file name with at least 5 chars before the ".pdb" and these 5 characters have to match the 5 characters after TARGET on the first line. Note that the other format read by mr_rosetta is a lot easier: > title text for sequence of target to follow VDFNGYWKMLSNENFEEYLRALDVNVALRKIANLLKPDKEIVQDGDHMIIRTLSTFRNYIMDFQVGKEFEEDLTGIDD > title text for sequence of template (supplied PDB) to follow -AFSGTWQVYAQENYEEFLRAISLPEEVIKLAKDVKPVTEIQQNGSDFTITSKTPGKTVTNSFTIGKEAEIT--TMDG All the best, Tom T >> Somebody helped me out with the format. Thanks. >> My alignment file looks like: >> ## SP 3n91 >> >> >> 0 --DDDEVTMNSK.... >> 0 GSDNEFPDFDYQ.... >> >> >> >> But phenix says >> >> ******************* ERROR ENDING *************** >> >> Sorry, the alignment file ['xx.ali'] >> does not seem to have the correct format? >> It can either start with '##' or with '> title of target seq here' >> >> ******************* ERROR ENDING *************** >> >> I do have the file starting with '##'! >> >> Thanks, >> Abhinav >> >> JCSG@SSRL, SLAC >> Phone: (650) 926-2992 >> Fax: (650) 926-3292 >> >> >> On 10/11/2011 12:23 PM, Abhinav Kumar wrote: >>> Hi, >>> >>> I am looking for file format for alignment file (*.ali) used in >>> mr_rosetta. >>> The description on the Phenix web site is not clear. >>> Can someone please describe the file format with an example? >>> -- >>> >>> Thanks, >>> Abhinav >>> >>> JCSG@SSRL, SLAC >>> Phone: (650) 926-2992 >>> Fax: (650) 926-3292 >>> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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Re: [phenixbb] mr_rosetta
by Thomas C. Terwilliger 11 Oct '11

11 Oct '11

Hi Abhinav, Here is an example. > cat WORK_1/alignment.ali ## TARGET coord # hhsearch scores_from_program: 0 1.00 0 AQLMDMRD 0 AQLMDMRD -- (the -- at the end is included in the file) You can also use one with just 4 lines (sculptor format): > title text for sequence of target to follow VDFNGYWKMLSNENFEEYLRALDVNVALRKIANLLKPDKEIVQDGDHMIIRTLSTFRNYIMDFQVGKEFEEDLTGIDD > title text for sequence of template (supplied PDB) to follow -AFSGTWQVYAQENYEEFLRAISLPEEVIKLAKDVKPVTEIQQNGSDFTITSKTPGKTVTNSFTIGKEAEIT--TMDG All the best, Tom T >> Hi, >> >> I am looking for file format for alignment file (*.ali) used in >> mr_rosetta. >> The description on the Phenix web site is not clear. >> Can someone please describe the file format with an example? >> -- >> >> Thanks, >> Abhinav >> >> JCSG@SSRL, SLAC >> Phone: (650) 926-2992 >> Fax: (650) 926-3292 >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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mr_rosetta
by Abhinav Kumar 11 Oct '11

11 Oct '11

Hi, I am looking for file format for alignment file (*.ali) used in mr_rosetta. The description on the Phenix web site is not clear. Can someone please describe the file format with an example? -- Thanks, Abhinav JCSG@SSRL, SLAC Phone: (650) 926-2992 Fax: (650) 926-3292

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Re: [phenixbb] phenix.mr_rosetta not running "prerefine"
by Thomas C. Terwilliger 11 Oct '11

11 Oct '11

Hi Laurie, The problem is that mr_rosetta needed a pdb file name with more than 4 characters before the ".pdb" for this shortcut of generating pre-refined models to work (the Rosetta routine requires a longer file name). So if you rename your PDB file this should run (it does on my machine.) I will fix mr_rosetta so that it can take your PDB file. All the best, Tom T >> On Tue, Oct 11, 2011 at 12:33 PM, Thomas C. Terwilliger < >> terwilliger(a)lanl.gov> wrote: >> >>> Hi Laurie, >>> >>> Yes, it is not doing anything. There is something that didn't work in >>> the >>> inputs. Can you send me your fasta and PDB files and I'll just run it >>> here >>> to see what is wrong? >>> >>> Thanks! >>> -Tom T >>> >>> >> OK - I am also sending: >>> >> >>> >> >>> /netscr/bettsl/rosetta_test/MR_ROSETTA_2/GROUP_OF_PLACE_MODEL_1/RUN_1/REBUILD_IN_SETS_1/RUN_1/WORK_1/rebuild.log >>> >> >>> >> On Tue, Oct 11, 2011 at 12:01 PM, Thomas C. Terwilliger < >>> >> terwilliger(a)lanl.gov> wrote: >>> >> >>> >>> Hi Laurie, >>> >>> >>> >>> Yes, something didn't work it all right. Can you send me, off-list, >>> this >>> >>> log file: >>> >>> >>> >>> >>> >>> >>> /netscr/bettsl/rosetta_test/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_1.log >>> >>> >>> >>> which I am guessing has some kind of error message in it. >>> >>> >>> >>> Thanks! >>> >>> -Tom T >>> >>> >>> >>> >> Hi - I tried the little prerefine without any data script in your >>> >>> >> documentation - I don't think it's working right. I attach the >>> >>> script >>> >>> >> file >>> >>> >> that I made (prerefine.dat) and the RUN_FILE_1.log. >>> >>> >> >>> >>> >> I can send more info offline if need be. >>> >>> >> >>> >>> >> Thanks >>> >>> >> >>> >>> >> LAurie Betts >>> >>> >> _______________________________________________ >>> >>> >> phenixbb mailing list >>> >>> >> phenixbb(a)phenix-online.org >>> >>> >> http://phenix-online.org/mailman/listinfo/phenixbb >>> >>> >> >>> >>> >>> >>> _______________________________________________ >>> >>> phenixbb mailing list >>> >>> phenixbb(a)phenix-online.org >>> >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >>> >>> >> >>> >>> >>

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refinements settings .eff
by Christian Roth 11 Oct '11

11 Oct '11

Hi Phenix gurus, I have done a refinement with an sodium ion. I had generated a phil file for the distance restraints to the surrounding water. Now i am not sure if it is really there. I removed it and removed the phil from the list in the gui. Now phenix complains about no Atom selected and stops. In the .eff file all restraints are incorporated and in I deleted therefore the geometric restraints manually from the . eff file. As a consequence an unused parameter warning appears about unused parameters or spelling errors in the input file. I guess the .eff file. My default parameter folder is empty. Does phenix load the .eff file from the previous run and would it help to remove this? I dont wanne start a new project just to be in the default configuration mode without additional information in the .eff file. I did this using the gui so I am not sure how to incorporate the --unused_ok command to which may help to convince phenix to process the job. I hope it is clear what I mean and thanks for any suggestion. Christian

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phenix.mr_rosetta not running "prerefine"
by Laurie Betts 11 Oct '11

11 Oct '11

Hi - I tried the little prerefine without any data script in your documentation - I don't think it's working right. I attach the script file that I made (prerefine.dat) and the RUN_FILE_1.log. I can send more info offline if need be. Thanks LAurie Betts

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Simulated annealing composite omit map conversion
by Yuri 11 Oct '11

11 Oct '11

The figures are good illustration of what seems to be the consensus: Finely sampled maps can represent the best mathematical approximation of the continuous electron density function. The weirdness I referred to probably has more to do with what Nathaniel alluded to previously. The fact that our eyes get so used to staring at coarse pointy density - caused by the default grid of building programs (in the case of "on the fly" map generation from coefficients). That of course can be changed if one changes the sampling rate and get their eyes used to the new look. that I suppose would become your new norm. -- Yuri Pompeu

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MR_Rosetta and dimer of heterodimer
by Morten Grøftehauge 11 Oct '11

11 Oct '11

Hi everybody, I'm trying to phase a dimer of a heterodimer of a large, ~700aa, and small, ~150aa, component. The only good search model according to HHpred covers the first 500aa of the large component. So I am wondering whether I should add the 150aa to the end of the sequence file and add them to the fragment files in order for phenix.mr_rosetta to do density modification correctly? Or does this not matter at all? According to HHpred and others the last 200aa are beta sheets, probably a a beta sandwich or two, and the 150aa component consists of helical elements but that is as close as it really gets. Cheers, Morten

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Re: [phenixbb] Simulated annealing composite omit map conversion
by Yuri 11 Oct '11

11 Oct '11

hi Nathaniel, Thats simple enough... Do I have any control over grid ( make a tighter looking mesh for publication) -- Yuri Pompeu

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Phenix not reading my sca files
by Scott Classen 10 Oct '11

10 Oct '11

Why? Error is: Unknown file format for file /home/me/phenix/autosol/s4_peak.sca Unknown file format for file /home/me/phenix/autosol/s4_infl.sca Unknown file format for file /home/me/phenix/autosol/s4_rem.sca this also does not work: phenix.reflection_file_converter s4_peak.sca --mtz . error is: file_name: s4_peak.sca file_type: None No reflection data found in input file. Please advise. Thanks, Scott Classen

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Phenix file organization
by R.M. Garavito 10 Oct '11

10 Oct '11

To the Phenix gurus, I am in the midst of reorganizing our little Mac computer cluster, and will have a mixed collection of machines with OS 10.6.8 or 10.7.1. While the reorganization is going fine for the most part, I am having a little trouble getting Phenix to work on one machine. The problem is integrating a machine (a MacPro) into the cluster with users having different UIDs from their NIS accounts on the rest of the cluster. Thus, the NIS UID leads to not only a different UID for the user, but a different account (and therefore a different "home" directory) name. Simply changing ownership of the user's directories and files globally in OS 10.6.8 leads to Phenix choking at some stage when used under the NIS UID, but without an informative error message. Things go on fine when used under the old local UID and user name. So my question is does Phenix store the absolute paths in its various project indices? Any suggestions would be helpful. Thanks, Michael **************************************************************** R. Michael Garavito, Ph.D. Professor of Biochemistry & Molecular Biology 513 Biochemistry Bldg. Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334 Email: garavito(a)msu.edu ****************************************************************

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Simulated annealing composite omit map conversion
by Yuri 10 Oct '11

10 Oct '11

"Fabricated" was probably a poorly chosen word. That implies made up data. I agree, I dont think cahnging the grid spacing would "introduce" unreal data to the maps... I just meant that it looks a little weird to have overly smooth mesh for a low res map... -- Yuri Pompeu

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Computing Robs vs Rcalc for twinned data with xtriage
by Pietro Roversi 10 Oct '11

10 Oct '11

Dear all, I am trying to run phenix.xtriage to compute Robs vs Rcalc for twinned data (from A. A. Lebedev, A. A. Vagin and G. N. Murshudov Intensity statistics in twinned crystals with examples from the PDB, Acta Crystallographica, D62, 83-95, (2006) My input: phenix.xtriage xray_data.file_name=$1.mtz xray_data.obs_labels="IMEAN, SIGIMEAN" xray_data.calc_labels="FCalc, PHICalc" xray_data.high_resolution=3.1 > phenix.xtriage.$$.log The FCalc, PHICalc columns (from CCP4-sfall) are in my mtzfile: 1 ASC -27 27 0 100.00 0.7 10.4 52.72 2.60 H H 2 NONE -90 90 0 100.00 0.7 34.2 52.72 2.60 H K 3 NONE 0 15 0 100.00 5.7 5.7 52.72 2.60 H L 4 NONE 0.0 19.0 0 100.00 9.50 9.50 52.72 2.60 I FreeR_flag 5 NONE -244.3 13664.9 0 100.00 467.59 469.74 52.72 2.60 J IMEAN 6 NONE 1.8 990.9 0 100.00 43.05 43.05 52.72 2.60 Q SIGIMEAN 7 NONE 16.2 1157.9 0 100.00 173.14 173.14 52.72 2.60 F F 8 NONE 1.7 51.3 0 100.00 12.91 12.91 52.72 2.60 Q SIGF 9 NONE 0.7 7827.1 0 100.00 257.63 257.63 52.72 2.60 F FCalc 10 NONE 0.0 360.0 0 100.00 180.24 180.24 52.72 2.60 P PHICalc and yet I get the error message: creamint:~/Projects/FactorI/Tetartohedral/P1/DataFiles> ~/Scripts/phenix_xtriage.csh AUTOMATIC_DEFAULT_free.klh_sfall1 Running phenix.xtriage No matching array: scaling.input.xray_data.calc_labels=FCalc, PHICalc Possible choices: AUTOMATIC_DEFAULT_free.klh_sfall1.mtz:IMEAN,SIGIMEAN AUTOMATIC_DEFAULT_free.klh_sfall1.mtz:F,SIGF Please use scaling.input.xray_data.calc_labels to specify an unambiguous substring of the target label. Sorry: No matching array: scaling.input.xray_data.calc_labels=FCalc, PHICalc

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Automated Mg & K ions picking
by Kristen Eisenberg 10 Oct '11

10 Oct '11

Hi Hasan, yes, we plan to extend water picking procedure so it can identify single-atom ions, but no specific tool is available to use right now. You need to inspect waters (for example, a water with "too small" refined B-factor is likely to be a metal), and density peaks (phenix.refine may not place a water into a density peak if it is too different from what is expected for water). Kristen Eisenberg Billige Flüge Marketing GmbH Emanuelstr. 3, 10317 Berlin Deutschland Telefon: +49 (33) 5310967 Email: utebachmeier at gmail.com Site: http://flug.airego.de - Billige Flüge vergleichen

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Re: [phenixbb] PHENIX atom selection language
by Kay Diederichs 09 Oct '11

09 Oct '11

Am 09.10.2011 04:20, schrieb phenixbb-request(a)phenix-online.org: > Date: Thu, 6 Oct 2011 18:19:34 -0400 > From: Jianghai Zhu<jzhu(a)idi.harvard.edu> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] PHENIX atom selection language > Message-ID:<E21B0319-CC1D-47A6-9F23-4493700B319C(a)idi.harvard.edu> > Content-Type: text/plain; charset=us-ascii > > Cool. Thanks, Pavel. It would be nice to have a list of all selection keywords and corresponding definitions somewhere. > > -- Jianghai Hi Jianghai, anybody can contribute to the CCP4 wiki, where a Phenix article already exists - check out <http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Phenix#Atom_sel…> Unfortunately the wiki is hit by spammers, and we regularly delete whole batches of these pseudo-"users" to keep the userlist clean. The spammers use @gmail.com and @hotmail.com email addresses which we now do not accept any more as new users' email - such addresses are just too easy to obtain. So if you would like to contribute make sure a) to use a email adress of your institution (e.g. university) b) and to contribute to an existing article or start a new one since we won't delete "real" users HTH, Kay

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Re: [phenixbb] Simulated annealing composite omit map conversion
by Yuri 09 Oct '11

09 Oct '11

I agree I like 0.25 (I believe thats what CNS spits out). Anything tighter looks fabricated -- Yuri Pompeu

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Simulated annealing composite omit map conversion
by Yuri 09 Oct '11

09 Oct '11

Hello Everyone, I am calculating an SA. composite omit map to show active site density. It looks like the output format is mtz coefficients. How can I get it to ccp4 or .xplor format for PyMol? Thanks -- Yuri Pompeu

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Educative Tool Idea
by Yuri 07 Oct '11

07 Oct '11

Hello Developers, This may be a silly idea after all, nonetheless: Would it be possible (worhtwhile) to have a tool that lets the user input a molecule of a certain type (probably rather small size, i.e, an amino acid or cofactor), and then input a space group. Phenix could then generate a relection file that would be displayed using either data2d or 3d viewer. Obviously there are many other factors to be considered but just an idea... -- Yuri Pompeu

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Occupancy refinement issue
by AFL 07 Oct '11

07 Oct '11

Dear All, I would like to refine the occupancy of _all_ components together for the following system: - free LYS (chain A and resname LYS) - PLP-LYS complex (chain A and resname LLP) - PLP-GLU complex (chian D and resname PPE) The LYS and LLP are defined as alternative conformations. What I've tried so far is: - just phenix.refine without any additional constraints and the result is occupancy refinement of LYS vs. LLP and separately refined PPE. - constrained_group { selection = chain A and resseq 90 # position of LYS, LLP selection = chain C and resseq 1 # PPE } Result is occupancy refinement of LYS+LLP vs. PPE and total mess in the active site (=ligands moved to new positions far away from where they should be). - constrained_group { selection = chain A and resname LYS # ALYS, BLLP doesn't work selection = chain A and resname LLP selection = chain C and resname PPE } Results in occupancy refinement of LYS vs. PPE and the LLP occupancy is set to 0.00. So, the big question is: - is what I'm trying to do doable at all? - what would be the right way to do it? I will appreciate all and any suggestions on how to proceed. Regards, Andrzej Lyskowski -- alnyds(a)gmail.com e-mail home

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PHENIX atom selection language
by Jianghai Zhu 06 Oct '11

06 Oct '11

Hi, Where can I find a complete description of PHENIX atom selection language? The examples in the PHENIX.REFINE manual are not enough. Thanks. -- Jianghai

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Fwd: Really good stats... Unreal!??
by Yuri 05 Oct '11

05 Oct '11

Hi everyone, So I am done refining a structure with around 760 residues in the model to a resolution of 2.29A. Rwork 0.18 Rfree 0.24 RMSD angle 1.1 Bond 0.008, clashscore 28. As a I last round I ran optmize_weights and got some interesting numbers. Rwork 0.17 Rfree 0.23 RMSD Angle 0.68! Bond 0.003! clashscore 10.2 I dont know how real these are. That would make this a new pdb record for tight geometry!!! Any ideas? Best, -- Yuri Pompeu -- Yuri Pompeu

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local refinement of target weights?
by Yarrow Madrona 04 Oct '11

04 Oct '11

Hello, I am wondering if there is a way to restrain geometry target weights for a ligand seperate from the rest of the molecule. I would like to impose higher restraints for the ligand than that of the protein in the same refinement run. Thanks for your help. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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combinding two CIF's and creating links in elbow
by Yarrow Madrona 04 Oct '11

04 Oct '11

Hello, 1. I have a question on creating links using elbow. I have a CIF of NO and I want to define a chemical link between NO and Fe of a HEME group. I need to input the geometry as NO is acting as a metal ligand. I really don't know where to begin. Any help would be greatly appreciated. 2. Is there a quick way of combining CIF files into one large file without a lot of copy and pasting? Thank you. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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Phenix version 1.7.2 released
by Paul Adams 30 Sep '11

30 Sep '11

The Phenix developers are pleased to announce that version 1.7.2 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical interface: ==================== - phenix.data_viewer added under Reflection Tools - New GUIs: HySS, phenix.cut_out_density, phenix.reciprocal_space_arrays General: ======== - New commands: phenix.cut_out_density, phenix.data_viewer, phenix.morph_model - Default map output format changed to CCP4 - Native support for CIF-format reflection files (e.g. from PDB) in many commands and GUI Refinement: =========== - New Xray/restraints weight optimization. Keywords optimize_wxc and optimize_wxu replaced with optimize_xyz_weight and optimize_adp_weight, respectively. - Grid searches parallelized: use 'nproc' parameter to set number of CPUs to use - this affects bulk solvent mask optimization, and XYZ and ADP weight optimization (in addition to TLS identification) - can reduce runtime by 75% or more depending on settings (see manual for details) - Modified non-bonded parameters resulting in improved geometry, especially at low resolution - Rigid-body refinement mode defaults to grouping by chain - Printout of validation statistics during coordinate refinement - Bug fix in phase-combined map calculation results in significantly improved maps - Bug fix in X-ray/ADP restraints weight calculation results in smaller B-factors deviations for bonded atoms - Experimental feature (still in testing): - Torsion-space NCS (ncs.type=torsion), automatic parameterization, similar to reference model restraints - Uses top-out potential to allow deviations between NCS related atoms New commands: ============= - phenix.cut_out_density: - carve out a region from map coefficients (MTZ file) - density may be specified as a sphere, a box, or masked around a PDB file - phenix.data_viewer: - visualization of reciprocal-space reflection data - 3D OpenGL view of all data, or 2D view of planes (pseudo-precession photograph) - phenix.morph_model: - Use after molecular replacement to improve model for rebuilding - Morphs model to match a prime-and-switch map Molecular Replacement: ====================== - Phaser (and AutoMR wizard): - significant speedup of fast rotation function Miscellaneous: ============== - phenix.reel: - better integration with main GUI, especially eLBOW - phenix.fobs_minus_fobs_map: - option to disable strict unit cell isomorphism check - phenix.ramalyze: - optional output of PNG images of Ramachandran plots; add --plot to command line arguments - phenix.fetch_pdb: - new flags: --all fetches PDB, CIF, and FASTA files simultaneously --mtz runs phenix.cif_as_mtz on downloaded CIF file For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Twinned Refinement in P 1 21 1
by Yuri 29 Sep '11

29 Sep '11

I dont see spcgrp number 20 on here? Should I be concerned? >>> Unit cell: (44.767, 130.64, 88.33, 90, 104.6, 90) Space group: P 1 (No. 1) Angular tolerance: 5.000 degrees Similar symmetries ================== Symmetry in minimum-lengths cell: C m m m (x+y,2*y,z) (No. 65) Input minimum-lengths cell: (44.767, 88.33, 130.64, 90, 90, 104.6) Symmetry-adapted cell: (44.767, 88.36, 130.64, 90, 90, 104.674) Conventional setting: C m m m (No. 65) Unit cell: (44.767, 170.956, 130.64, 90, 90, 90) Change of basis: x-1/2*z,1/2*z,-y Inverse: x+y,-z,2*y Maximal angular difference: 0.079 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (x-y,2*x,z) (No. 12) Input minimum-lengths cell: (44.767, 88.33, 130.64, 90, 90, 104.6) Symmetry-adapted cell: (44.767, 88.36, 130.64, 90, 90, 104.674) Conventional setting: C 1 2/m 1 (No. 12) Unit cell: (170.956, 44.767, 130.64, 90, 90, 90) Change of basis: 1/2*z,-x+1/2*z,-y Inverse: x-y,-z,2*x Maximal angular difference: 0.079 degrees Symmetry in minimum-lengths cell: C 1 2/m 1 (x+y,2*y,z) (No. 12) Input minimum-lengths cell: (44.767, 88.33, 130.64, 90, 90, 104.6) Symmetry-adapted cell: (44.767, 88.36, 130.64, 90, 90, 104.674) Conventional setting: C 1 2/m 1 (No. 12) Unit cell: (44.767, 170.956, 130.64, 90, 90, 90) Change of basis: x-1/2*z,1/2*z,-y Inverse: x+y,-z,2*y Maximal angular difference: 0.079 degrees Symmetry in minimum-lengths cell: P 1 1 2/m (No. 10) Input minimum-lengths cell: (44.767, 88.33, 130.64, 90, 90, 104.6) Symmetry-adapted cell: (44.767, 88.33, 130.64, 90, 90, 104.6) Conventional setting: P 1 2/m 1 (No. 10) Unit cell: (44.767, 130.64, 88.33, 90, 104.6, 90) Change of basis: x,y,z Inverse: x,y,z Maximal angular difference: 0.000 degrees Symmetry in minimum-lengths cell: P -1 (No. 2) Input minimum-lengths cell: (44.767, 88.33, 130.64, 90, 90, 104.6) Symmetry-adapted cell: (44.767, 88.33, 130.64, 90, 90, 104.6) Conventional setting: P -1 (No. 2) Unit cell: (44.767, 88.33, 130.64, 90, 90, 104.6) Change of basis: x,z,-y Inverse: x,-z,y Maximal angular difference: 0.000 degrees -- Yuri Pompeu

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