- phenixbb - phenix-online.org

ADP-BEF-link.cif
by Heidi Schubert 10 Jun '24

10 Jun '24

Hi AAA ATPase modelers Could anyone send me the .cif file to define the link between ADP and a BeFx ion? I’m hoping this has not only the revised angle/bond info between O3B and Be but also the new angle between the Be and Fs different from the planar simple ion. AND, for my hexamer I assume the apply_link.def file then just reads with repetitive 5-line groups: refinement.pdb_interpretation.apply_cif_link { data_link = ADP-BEF residue_selection_1 = chain A and resname ADP and resseq 901 residue_selection_2 = chain A and resname BEF and resseq 902 } Where I change out the chain name but keep calling them residues_selection1 and 2? Many thanks Heidi Heidi Schubert Research Professor Department of Biochemistry University of Utah Rm 116 BPRB 20 S 2030 E Salt Lake City, UT 84112 heidi(a)biochem.utah.edu<mailto:[email protected]> 801-585-9776

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high and low resolution in Phenix 1.21.1-5286-000
by Dominik Oberthuer 30 May '24

30 May '24

Hi, because of an update to Sonoma, I also had to update to Phenix 1.21.1-5286-000. When I'm running phenix.refine from the GUI, use an MTZ with resolution e.g. from 1.65 - 51A, use "High resolution" and "Low resolution" to refine against a specific range of data, phenix.refine does not cut off the data beyond the limits set there, but instead takes all of the data. For sure, I cut the MTZ before, but many times it is about trying out which data to include and not include and this is not really how it should be... Is this known? Is there any way to solve this issue? Thanks! Dominik -- Dr. Dominik Oberthür CFEL - Center for Free-Electron Laser Science - DESY Coherent Imaging Division Notkestrasse 85 22607 Hamburg Germany phone: +49 (0)40 8998 6394 dominik.oberthuer(a)cfel.de

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NIGMS Mature Synchrotron Program Evaluation
by Paul Adams 20 May '24

20 May '24

Dear Colleagues, Apologies for the US-centric posting, but I think this is of interest to many of the bulletin board subscribers who make use of synchrotron facilities in the US. NIH is seeking feedback on the Mature Synchrotron Program: https://grants.nih.gov/grants/guide/notice-files/NOT-GM-24-019.html This program supports synchrotron-based user resources where the technologies are at an advanced level, including Macromolecular Crystallography, Small-Angle and Wide-Angle X-ray Scattering, fiber diffraction, and other synchrotron-based techniques that generate important data, with an emphasis on structural biology. Responses to the RFI will be accepted through 6/17/2024. All comments will be anonymous and should be submitted electronically via a web form at: https://www.research.net/r/P30_RFI As the Director of one of the resources it has been suggested that I help make the community aware of the RFI, so there is the opportunity to provide feedback in a timely manner. Feel free to pass this on to any of your colleagues who may be interested. Cheers, Paul -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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"<" symbol in reflection mmcif status column
by Kreitler, Dale 17 May '24

17 May '24

Looking at some output reflection cif files from phenix.refine I'm wondering what does "<" mean in the status column and why would F_calc_with_sovlent structure factors also be missing for these reflections? In some cases I can see it coincides with unobserved reflections, but this doesn't seem consistent. Any insight or links to documentation that describe these values would be much appreciated. Thank you, Dale loop_ _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au _refln.pdbx_FWT _refln.pdbx_PHWT _refln.pdbx_DELFWT _refln.pdbx_DELPHWT _refln.pdbx_r_free_flag _refln.status _refln.pdbx_F_calc_with_solvent _refln.pdbx_phase_calc_with_solvent ... 30 0 48 65.2227 18.9183 72.4766 0 5.77152 -2.25565e-14 3 o 77.6435 1.95165e-15 30 0 49 206.068 7.45891 200.645 120 ? ? 19 < ? ? 30 0 50 33.324 17.5773 1.10423 -120 0.328059 -120 10 o 0.916822 -120 30 0 51 23.7705 14.8724 10.7438 180 2.40893 1.88332e-14 6 o 16.3173 180 ... 32 7 2 ? ? 11.4163 118.276 ? ? 5 < ? ? 32 7 3 ? ? 52.373 -121.74 ? ? 10 < ? ? 32 7 4 ? ? 33.1269 -26.1149 ? ? 3 < ? ? 32 7 5 ? ? 106.054 -86.2146 ? ? 19 < ? ? ============================= Dale Kreitler AMX Beamline Scientist National Synchrotron Light Source II Building 745, Rm. 5L143 Upton, NY 11973 631-344-7318

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ADP refinement in phenix.real _space_refine
by Luca Pellegrini 16 May '24

16 May '24

While refining a protein-DNA complex in a cryoEM map (~2.5-7A), I have noticed the following behaviour of ADP refinement: - If NCS is on for the protein chains, no ADP refinement of the DNA takes place. - If NCS is off, ADP refinement behaves oddly: one strand of dsDNA is refined with atomic ADPs, the other strand with group ADPs (one per nucleotide). The group ADPs take up unphysical values (lower ADPs in poor map regions), whereas the atomic ADPs look sensible. - To get the ADP refinement of DNA to behave normally, I need to both leave NCS out and set nproc=1 explicitly (haven’t tried other values). I wonder if any of this has been seen before or am I not doing this correctly? Phenix-dev-5330 iMac, Catalina 10.15.7, 8-core Intel i9 Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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ligand links
by Heidi Schubert 14 May '24

14 May '24

Hi, Do you think you can link one ligand to two other molecules. (one NON-POLYMER and one peptide). I guess my other option is to create a new ligand. I assumed you pre-deleted the atoms that are supposed to be deleted in the link? I did delete them and it complained and I put them back in and it’s complaining. Pretty similar errors, but I’m wondering if it’s just the second link that’s causing problems. I’ve got files PNS.cif ACE.cif PNS-SER.cif ACE-PNS.cif apply_link_ACE-PNS.def apply_link_PNS-SER.def Heidi [A screenshot of a computer error Description automatically generated]

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Error upon Phenix installation - Manjaro WSL2
by Nicolas Caramello 03 May '24

03 May '24

Dear PhenixBBers, I call upon your wisdom because I recently tried to install Phenix 1.20 on a windows subsystem for linux distribution of Manjaro (Archlinux based) and have failed with the following error : ========================================================================== Phenix Installation version: 1.20.1-4487 machine type: intel-linux-2.6-x86_64 OS version: 5.15.146.1-microsoft-standard-WSL2 destination: /home/my_machine/phenix-1.20.1-4487 # of processors: 20 ========================================================================= Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 268, in <module> installer(sys.argv[1:]).install() File "/home/my_machine/phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 200, in install self.install_from_binary() File "/home/my_machine/phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 349, in install_from_binary self.reconfigure(log=log) File "/home/my_machine/phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 431, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/home/my_machine/phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py", line 55, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/home/my_machine/phenix-1.20.1-4487/conda_base/bin/python /home/my_machine/phenix-1.20.1-4487/modules/cctbx_project/libtbx/configure.py --current_working_directory /home/my_machine/phenix-1.20.1-4487/build --command_version_suffix 1.20.1-4487 phenix phaser phasertng solve_resolve labelit dials xia2 iota prime amber_adaptbx --use_conda' failed with exit code 127 Trying to install Phenix 1.21 has produced the same error. I have not managed to solve this, regardless of whether I was running the installation command with sudo privileges or as root. For context, I successfully installed Phenix 1.20 on the same machine and same distribution 6 months ago, but had to reinstall everything since and it does not work anymore now. Have you heard of such an error? Do you have a hint on how to fix it? Best regards, Nicolas Caramello PhD student Structural Biology Group - ESRF /Institut für Nanostruktur/- /und/ Festkörperphysik- Universität Hamburg

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ccp4 thread: "what happened to Molprobity"
by Pavel Afonine 01 May '24

01 May '24

Hi All, I hope someone from Molprobity end reads CCP4 mailing list where people report issues with Molprobity (server and from within Phenix). Just in case this needs someone's attention. Pavel

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on the criteria for outliers, phenix.molprobity and wwPDB validation
by Jorge Iulek 29 Apr '24

29 Apr '24

Hi all, I had already noticed that outliers spotted by phenix with its validation tool, with the nice feature to carry one straight to the "suspicious" residue in a coot session for visual inspection, differs a bit from what comes spotted from wwPDB validation, generally the latter spotting some few more residues. To one current structure, which at low resolution, I notice there is a bit larger difference between the number of spotted residues. I see from wwPDB validation, molprobity is also used to spot outliers for many of the analyses. I see the current molprobity version used is 4.02b-467, but I could not yet devise the molprobity version used by phenix. Of course, there would also be the "library" used in each case to spot the outliers. Maybe someone ever listed what is considered in each case, and their differences, or a link to that is welcome for me. What would be the best criteria for spotting is of course a good discussion. But a superficial question I would make is if there is a way to make phenix.molprobity output to resemble the one from wwPDB validation, at least the ones accounted by molprobity? Jorge

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Phenix resolve_cryo_em with local resolution
by Reza Khayat 29 Apr '24

29 Apr '24

Hi, Is it possible to run resolve_cryo_em and have it consider the local resolution of the two half maps in the final map? I have a 3.7Angstrom map were certain domains, too small for local refinement with single particle analysis, are smeared out in the resolve_cryo_em map. Their densities are stronger when I low pass filter the original maps. The adjust_local_resolution_coloring = True option seems to be what I need; however, including this option in the command line results in: Please run this program with the --show-defaults option to see what parameters are available. PHIL parameters in files should be fully specified (e.g. "output.overwrite" instead of just "overwrite") The command line I use is: phenix.resolve_cryo_em map_file_name=Class001_full_box_40.ccp4 half_map_file_name_1=Class001_half1_box_40.ccp4 half_map_file_name_2=Class001_half2_box_40.ccp4 resolution=4.0 dm_resolution=3.5 cycles=1 box_before_analysis=False density_modify_unsharpened_maps=True nproc=16 force_nproc=True model_1=Class001.pdb seq_file=Class001.fasta ncs_copies=1 output_directory="Class001_local" adjust_local_resolution_coloring=True > Class001_local.log Any help would be appreciated. Thanks. Best wishes, Reza Reza Khayat, PhD City College of New York Associate Professor Department of Chemistry and Biochemistry Co-Director NIH G-RISE program

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