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Error from f_model_all_scales.py
by John Bruning 20 Dec '16

20 Dec '16

Hi (Pavel), I have a dataset (P31) which I am processing with the pairwise combinations of reindexing operators (4 incl. no reindexing therefore h,k,l) and twin laws (4 incl. no twinning as h,k,l). While some of these combinations are fine during refinement (Vers 1.11.1), for some combinations I get the following error, which ultimately kills the refinement. Thanks in advance and apologies if I am missing something stupid. Incidentally, a different dataset seems to tolerate all combinations. *approx_equal eps: 1e-05* *approx_equal multiplier: 10000000000.0* *0.512707954357 approx_equal ERROR* *0.514972857238 approx_equal ERROR* Traceback (most recent call last): File "/Applications/phenix-1.11.1-2575/build/../modules/phenix/ phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/command_line.py", line 154, in run call_back_handler=call_back_handler) File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/driver.py", line 1529, in run call_back_handler = call_back_handler).result File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/strategies.py", line 121, in __init__ log = log) File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/fmodels.py", line 159, in run fmodel.update_solvent_and_scale(initialise=True) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/twinning/twin_f_model.py", line 797, in update_solvent_and_scale params=params, log=log, apply_back_trace=apply_back_trace) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1457, in update_all_scales params = params, log = log, refine_hd_scattering=refine_hd_scattering) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/bulk_solvent/f_model_all_scales.py", line 38, in __init__ refine_hd_scattering = refine_hd_scattering, log = log) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/bulk_solvent/f_model_all_scales.py", line 61, in compute refine_hd_scattering = refine_hd_scattering) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/bulk_solvent/f_model_all_scales.py", line 329, in update_solvent_and_scale_twin * assert approx_equal(self.r_all(), o_kbu_sol.r(), 1.e-5)* *AssertionError*

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phenix rosetta interface
by CPMAS Chen 16 Dec '16

16 Dec '16

Hi, All, When I compile phenix-1.11-2567 and rosetta-bin-mac_2016.37.58930_bundle interface, I got the following error message. Any suggestion to fix this? Thanks! src/core/scoring/cryst/PhenixInterface.cc:253:11: error: no matching member function for call to 'dump_pdb' pose_asu.dump_pdb( pdbout , "1" ); ~~~~~~~~~^~~~~~~~ src/core/pose/Pose.hh:1525:2: note: candidate function not viable: no known conversion from 'char [256]' to 'std::ostream &' (aka 'basic_ostream<char> &') for 1st argument dump_pdb( ^ src/core/pose/Pose.hh:1518:2: note: candidate function not viable: requires single argument 'file_name', but 2 arguments were provided dump_pdb(std::string const & file_name) const; ^ src/core/pose/Pose.hh:1521:2: note: candidate function not viable: requires single argument 'out', but 2 arguments were provided dump_pdb(std::ostream & out) const; ^ src/core/scoring/cryst/PhenixInterface.cc:916:11: error: no matching member function for call to 'dump_pdb' pose_asu.dump_pdb( buffer , "1" ); ~~~~~~~~~^~~~~~~~ src/core/pose/Pose.hh:1525:2: note: candidate function not viable: no known conversion from 'char [256]' to 'std::ostream &' (aka 'basic_ostream<char> &') for 1st argument dump_pdb( ^ src/core/pose/Pose.hh:1518:2: note: candidate function not viable: requires single argument 'file_name', but 2 arguments were provided dump_pdb(std::string const & file_name) const; ^ src/core/pose/Pose.hh:1521:2: note: candidate function not viable: requires single argument 'out', but 2 arguments were provided dump_pdb(std::ostream & out) const; ^ 2 errors generated. scons: *** [build/src/release/macos/16.1/64/x86/clang/8.0/python/core/scoring/cryst/PhenixInterface.os] Error 1 scons: building terminated because of errors. Thanks! -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Asymmetric unit content
by Sharan Karade 12 Dec '16

12 Dec '16

Dear all, I have solved the structure in C121 space group, having five molecules in asymmetric unit, my supervisor have doubt about the fifth molecule becoz of poor density fit, if i delete the fifth molecule, there is a space for the molecule and crystal is not continuous, i calculated difference map from Phenix by deleting fifth molecule and got the Map showing presence of molecule. My supervisor want me to get SetMet data, but crystals are diffracting poor (7A). Is there any way to convince my guide. advance thanks for valuable suggestions. -- Sharan C/O Dr. J V Pratap Senior Research Fellow, CSIR-Central Drug Research Institute, Lucknow

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Recent improvements in Phaser for systematically weak data
by Randy Read 09 Dec '16

09 Dec '16

Dear all, Between the last official release of Phenix (version 1.11.1-2575, released on 26 October) and a recent CCP4 update (7.0.023 released on 23 November), we fixed a problem in which the fast rotation function was not properly accounting for the effect of measurement errors in intensities. Under many circumstances (i.e. with well-measured data to the resolution needed to solve the structure by MR), the change is not noticeable. However, if you have systematically weak data (particularly from high levels of anisotropy or potentially from the effects of translational non-crystallographic symmetry), the fix can mean the difference between failing to solve the structure, because the correct orientation has not been generated, or solving it with a default run of Phaser. We recommend that anyone trying to solve a structure with substantial anisotropy (anisotropic deltaB of 50 A^2 or greater) and/or translational NCS should update to a newer version of either package. If you're using CCP4, you should get the latest update, because there was a problem with the version of coot distributed with the 7.0.023 update. If you're using Phenix, you should get a recent nightly build, i.e. dev-2608 or something even newer. Please note that you want to provide data to Phaser in the form of intensities rather than amplitudes to get the best results for such data! So far, I've found 3 of our test cases where this makes a real difference, but I would be interested in hearing from anyone who finds that this makes a difference for other cases. Best wishes, Randy Read ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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iNEXT access: NMR Extended Support and more!
by Anastassis Perrakis 06 Dec '16

06 Dec '16

Dear all, I should perhaps offer sincere apologies for posting the crystallography boards with NMR news ;-). However, I will not do that, as I sincerely hope you will see that in an era of integration of structural methods, such opportunities can offer the chance for excellent and exciting scientific endeavours. iNEXT (http://www.inext-eu.org <http://www.inext-eu.org/>) is committed to bring structural methods closer to non-experts, by funding access to world class infrastructures for Structural Biology. Major tools for achieving that goal are the so-called Extended Support modalities. We are happy to announce the start for acess to the iNEXT Enhanced Support modality for NMR (NMR assignment, structure, dynamics). In this mode, the NMR groups in Florence, Frankfurt and Utrecht are involved in guiding and training NMR novices. This iNEXT access modality also targets "new users with backgrounds other than Structural Biology”, so please feel free to forward that also to your biochemistry friends. Facility personnel will be involved to guide assignments, titrations, structure calculations, relaxation analyses, etc. I also want to bring your attention to a few more iNEXT news: - The Structural Audit, now allows multiple samples in a related project to be submitted in a single application for stability assessment and crystallisation screening; a basic analysis by SAXS, EM, or NMR is also supported (single click in application!) if an appropriate sample is available. - The Enhanced Support modality "From macromolecular sample to X-ray data collection” is now better integrated with Structural Audit; applications can be combined, so in case of a successful Audit, you could rapidly proceed to further X-ray experiments (crystal optimisation, SAXS and/or crystallography) - The Enhanced Support modality "Advanced light imaging” to support structural studies with in cells measurement of protein interaction kinetics, have also been made recently available. - The Enhanced Support modality "Cryo-EM sample optimisation” for hands-on assistance in optimizing a sample for single particle EM is a great chance to move your sample towards cryo-EM! - The Enhanced Support modality "Macromolecular interactions” is your chance for access to a Biophysics facility with various instruments and hands-on support for performing and analysing experiments to quantify a variety of interactions. - All the High-End modalities (X-rays, NMR, cryo-EM) are always open for access! So, please, submit your proposal now! <https://www.structuralbiology.eu/update/submit-proposal?t=inext> … and keep in mind that a limited amount of the funding (~10%) can go towards projects that are not in an EU-country or associated country. On behalf of the iNEXT Management, Best wishes, Tassos Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

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phenix.real_space_refine crashes for very large pdb files
by #AHMED TOFAYEL# 02 Dec '16

02 Dec '16

Dear developers and users, My phenix.real_space_refine run crashes with the error mentioned below when I have used following command to run it on a complete ribosome (containing coordinates for small subunit and large subunit in a single pdb file): phenix.real_space_refine model.pdb map.mrc resolution=4.5 reference_coordinate_restraints.enabled=true reference_coordinate_restraints.selection="chain A and resseq 2:700" reference_coordinate_restraints.sigma=0.05 secondary_structure.enabled=True res.eff > out.out >From the out.out file I can see that, it ran for 5 macro_cycles and started group b-factor refinement which reads (last few lines): |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.153923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.144348 restraints weight = 1067.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147257 restraints weight = 482.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.149066 restraints weight = 262.900| |-----------------------------------------------------------------------------| The run crashes at this point.... However, phenix.real_space_refine runs fine when I am refining a protein chain or a complex (for eg: just the large or the small subunit of a ribosome). Does it have to do with my pdb file being so big after merging of both subunits where I have also crossed 99999 atoms and atom serial numbers start from A0000? A related question: What is the latest consensus of using chain IDs and atom serial numbers to use in phenix.real_space_refine for handling large files like ribosome pdbs ? I have found some information on: http://cci.lbl.gov/hybrid_36/ The error in terminal reads: Traceback (most recent call last): File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 782, in <module> o = run(sys.argv[1:]) File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 518, in __init__ self.caller(func = self.run_macro_cycles, prefix="Macro-cycles") File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 547, in caller status = func(prefix=prefix, **kwargs) File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 540, in run_macro_cycles log = self.log) File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 66, in __init__ self.caller(self.refine_adp, "ADP refinement") File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 71, in caller status = func(prefix=prefix) File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 317, in refine_adp adp_refinery.refine() File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/refinement/real_space/adp.py", line 78, in refine b_isos_refined = self.refine_box_with_selected(selection=sel) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/refinement/real_space/adp.py", line 56, in refine_box_with_selected fmodel.update_all_scales(update_f_part1=False, apply_back_trace=True) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1452, in update_all_scales self.apply_scale_k1_to_f_obs() File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1500, in apply_scale_k1_to_f_obs r_start = self.r_work() File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 2004, in r_work selection = selection) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1972, in _r_factor f_model = self.f_model_scaled_with_k1_w().data() File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1730, in f_model_scaled_with_k1_w data = self.scale_k1_w()*self.f_model_work().data()) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 2048, in scale_k1_w selection=selection) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 182, in _scale_helper raise RuntimeError("Zero denominator in scale calculation.") RuntimeError: Zero denominator in scale calculation. Best regards, Tofayel

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difference map based on the cryo-EM map
by Smith Lee 01 Dec '16

01 Dec '16

Dear All, Supposed by phenix.real_space_refine I got a PDB of protein-ligand, will you please let me know how to get the subtraction map (difference map?) which only show the density of the ligand, so that I can see whether the ligand was well resolved in the map, or whether the built ligand fits well with the ligand density? Smith

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Incrementing high resolution cutoff in phenix.mtz2map or phenix.cut_out_density
by Andrew Morin 30 Nov '16

30 Nov '16

Hello, I am trying to find a convenient way to generate maps using phenix.mtz2map at increasingly greater values of d_min. For example: I have a .mtz file of a structure solved at 2.4A. I run phenix.mtz2map with d_min=none and obtain a map using all of the resolution data. I would like to also create 10 more maps with d_min = 3.4, 4.4, 5.4, 6.4,...12.4A. An mtz of 1.7A would increment at 2.7, 3.7...11.7A, etc. Might anyone know of a handy way to automate this over a large number of mtz files? ALTERNATIVELY - I am performing a phenix.cut_out_density step prior to this. So if it might be easier to automate a incrementing high resolution cutoff in phenix.cut_out_density, that would also work. Thanks for your help. -Andrew

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Refine only selective chains in a complex using phenix.real_space_refine
by #AHMED TOFAYEL# 30 Nov '16

30 Nov '16

Dear all, Is it possible using phenix.real_space_refine to locally refine a protein or RNA chain (against a cryo-EM map) which is part of a big complex. During the run, I would like to keep most of my complex constant in space except neighboring one or two protein/RNA molecules which I would like to see getting adjusted to remove clashes. I am using the program through command-line. Best regards, Tofayel NTU Singapore

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Can't Run Rosetta_refine
by NISHANT SINGH 29 Nov '16

29 Nov '16

Hi Everyone, I am trying to run Phenix's rosetta refine. I seem to have downloaded and compiled the rosetta package fine, as I got the following statement after compiling was done: scons: done building targets. but I am failing at running: rosetta.build_phenix_interface. It says that command not found. I am attaching my env page with this email. bmbs-imac:rosetta_bin_mac_2016.32.58837_bundle Kumar$ env ROSETTA3_DB=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH//main/database TERM_PROGRAM=Apple_Terminal SHELL=/bin/bash TERM=xterm-256color TMPDIR=/var/folders/cb/5v492std3d31jr42j7h3jm9h0000gp/T/ Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.KEC4L2Cjos/Render TERM_PROGRAM_VERSION=387 OLDPWD=/Applications TERM_SESSION_ID=A82EA51D-0920-4F3B-BE03-92AE0C40A44B USER=Kumar SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.tMihawGOC7/Listeners __CF_USER_TEXT_ENCODING=0x1F6:0x0:0x0 ROSETTA_BIN=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH//main/source/bin PATH=/Library/Frameworks/Python.framework/Versions/3.5/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/Users/Kumar/miniconda2/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin PWD=/Applications/rosetta_bin_mac_2016.32.58837_bundle LANG=en_US.UTF-8 XPC_FLAGS=0x0 XPC_SERVICE_NAME=0 SHLVL=1 HOME=/Users/Kumar LOGNAME=Kumar DISPLAY=/private/tmp/com.apple.launchd.BhETYwyInl/org.macosforge.xquartz:0 PHENIX_ROSETTA_PATH=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH/ _=/usr/bin/env bmbs-imac:rosetta_bin_mac_2016.32.58837_bundle Kumar$ env ROSETTA3_DB=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH//main/database TERM_PROGRAM=Apple_Terminal SHELL=/bin/bash TERM=xterm-256color TMPDIR=/var/folders/cb/5v492std3d31jr42j7h3jm9h0000gp/T/ Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.KEC4L2Cjos/Render TERM_PROGRAM_VERSION=387 OLDPWD=/Applications TERM_SESSION_ID=A82EA51D-0920-4F3B-BE03-92AE0C40A44B USER=Kumar SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.tMihawGOC7/Listeners __CF_USER_TEXT_ENCODING=0x1F6:0x0:0x0 ROSETTA_BIN=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH//main/source/bin PATH=/Library/Frameworks/Python.framework/Versions/3.5/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/Users/Kumar/miniconda2/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin PWD=/Applications/rosetta_bin_mac_2016.32.58837_bundle LANG=en_US.UTF-8 XPC_FLAGS=0x0 XPC_SERVICE_NAME=0 SHLVL=1 HOME=/Users/Kumar LOGNAME=Kumar DISPLAY=/private/tmp/com.apple.launchd.BhETYwyInl/org.macosforge.xquartz:0 PHENIX_ROSETTA_PATH=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH/ _=/usr/bin/env bmbs-imac:rosetta_bin_mac_2016.32.58837_bundle Kumar$

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