- phenixbb - phenix-online.org

Phenix error in real space refinement with ligand
by Yung-Chieh Chen 06 Jun '26

06 Jun '26

Dear all, I'm trying to refine my model bound with a ligand bearing a -SF5 moiety (-pentafluorosulfanyl). I have used openbabel/Grade web server or REEL to generate/edit the cif file for the ligand. I could obtain the desired octahedral geometry for the -SF5 group. However, both cases failed in real space refinement and I got the following error message: "Number of atoms with unknown nonbonded energy type symbols: 22337...". I would be very grateful if anyone can share experience about how to tackle this issue. Thanks in advance. Best wishes, Yung-Chieh Chen

3 2

cryo em map
by iram aziz 06 Jun '26

06 Jun '26

Hello All. I got a nice 2.45 Angstrom map from cryo em data. I checked handedness, map model fitting on the chimera and opened in the coot. It looks nice. Can you please give me suggestions about the Phenix refinement steps. Thanks Iram

6 5

Handling of modified nucleotides in ribosome structures
by christian.steinmetzger＠imbim.uu.se 06 Jun '26

06 Jun '26

Dear community, I'm trying to work with a published ribosome structure (PDB 7K00, https://www.rcsb.org/structure/7k00 ) for example in phenix.combine_focused_maps or phenix.real_space_refine. Of course this structure contains a lot of modified residues and the monomer library in a fresh Phenix installation (version 1.21.2-5419) does not handle these out of the box. Since a lot of publications have used 7K00 as a starting point for their work in Phenix and since the current CCP4 monomer library plays nice with this structure I would not have expected this. Am I missing something in my Phenix setup to make it recognize such "common" modified residues in a ribosome or do I indeed need to generate parameters myself using AceDRG, eLBOW, Grade2 etc.? In the latter case, could I simply swap out the stock Phenix monomer library for the one from CCP4 as a drop-in replacement or would that be a bad idea? Thank you! Christian

5 10

26th West Coast Structural Biology Workshop - March 23-26, 2025 @ Asilomar Conference Center
by Michael Thompson 06 Jun '26

06 Jun '26

Dear Colleagues, Happy New Year!! We are writing to share information about the upcoming West Coast Structural Biology Workshop, which is scheduled for March 23-26, 2025 at its traditional location, the picturesque Asilomar Conference Center in Pacific Grove, CA. The conference website can be found at: https://wcsbw2025.macromolecules.xyz/. The WCSBW is a bi-annual meeting that showcases the latest methods, developments, and discoveries in structural biology, including X-ray Crystallography, Cryo-EM, NMR, and other methods. We strongly encourage anyone interested in method development and solutions to technical challenges in structural analysis to attend, even if you're not from the west coast. Importantly, the WCSBW aims to highlight the work of trainees, so all oral presentations (except keynotes) will be given by students and postdocs. The 26th edition of this meeting will include: * Opportunities to connect with leaders in the field, exchange practical advice, and stay at the forefront of structural biology advancements. * Exciting oral research presentations and engaging poster sessions focusing on the contributions of students and postdocs. * Inspiring keynote presentations, featuring Prof. Bil Clemons from Caltech, and Dr. Junko Yano from Lawrence Berkeley National Lab. * A 2-hour workshop hosted by the Phenix developers, detailing the use of new tools for structure determination and analysis. * A networking session with scientists from west coast biotech companies for students and postdocs who are entering the job market. * Good company and beautiful views of the pacific ocean! Some details about the conference are included below, and more information is available at our website (see link above). Please note that the registration deadline is Feb. 7, 2025. We hope to see you at Asilomar in March! -Mike Thompson (UC Merced) and Alec Follmer (UC Davis) P.S. We ask for your help in sharing this announcement with any students, postdocs, staff, colleagues, collaborators, or friends that might be interested. Thanks! Conference Details: March 23-26, 2025 at Asilomar Conference Center in Pacific Grove, CA Visit the conference website at: https://wcsbw2025.macromolecules.xyz/ Registration: https://book.passkey.com/event/50870517/owner/10793795/home Registration fee is $200, plus lodging fees (meals included). Attendees need to book their lodging accommodations at Asilomar when registering for the conference. Both single and double occupancy rooms are available. If you do not have a roommate and would like us to pair you with one to lower costs, or if you would like to register for the conference and arrange your own accommodations offsite, please contact us at wcsbw2025(a)gmail.com<mailto:[email protected]>. Abstract Submission: https://wcsbw2025.macromolecules.xyz/registration/ All oral presentations at the WCSBW, except for the keynotes, will be given by trainees. Students (undergraduate or graduate) and Postdocs are welcome to submit abstracts for oral presentations. We welcome abstracts for poster presentations from attendees at any career stage. The deadline for submitting abstracts is January 20, 2025, and attendees must be registered for the meeting in order for their abstracts to be considered. Abstracts that are submitted for oral presentations and not selected will be automatically considered as poster abstracts. --- Michael C. Thompson, Ph.D. (he/him) Assistant Professor Dept. of Chemistry and Biochemistry University of California, Merced https://thompsonlab.science<https://urldefense.com/v3/__https://thompsonlab.science__;!!LQC6Cpwp!-fv-nQ…>

2 1

Error phenix refine with ligands
by miriam.cavinato＠unimi.it 06 Jun '26

06 Jun '26

Hi everyone, I am trying to refine my model containing a ligand (a thiophene -like molecule with a 7 carbon atom cycle attached). I create restraints with ready set utility or directly with eLBOW, then I use phenix.refine and I get this error: "fatal problems in interpreting model file: number of atoms with unknown nonbonded energy type symbols: 12 Please edit the model file to resolve the problems or/and supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definition if necessary". Another problem is that as soon as I try to open REEL or open any result to check restraints, Phenix crashes... I was wondering if someone has the same issue and can help me figure it out! Thanks in advance Best regards Miriam

4 3

phenix.predict_and_build, proccess normal and no error, but not generate the PredictAndBuild_0_overall_best.pdb
by fnsoxt＠qq.com 06 Jun '26

06 Jun '26

How can i deal with it? This is the log file Starting phenix.predict_and_build on Wed Jan 1 20:55:50 2025 by xukui =============================================================================== Processing files: ------------------------------------------------------------------------------- No files found Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- full_map=/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc seq_file=/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta resolution=4.1 nproc=20 predicted_model=/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb process_predicted_model.chunk_size=10000 predict_and_build.chunk_size=10000 process_predicted_model.break_into_chunks_if_length_is=10000 predict_and_build.break_into_chunks_if_length_is=10000 Warning: Ambiguous parameter definition: resolution = 4.1 Best matches: crystal_info.resolution prediction.resolution Assuming crystal_info.resolution was intended. Warning: Ambiguous parameter definition: nproc = 20 Best matches: prediction.nproc control.nproc Assuming control.nproc was intended. Processing files from PHIL: ------------------------------------------------------------------------------- Found model, /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb Found sequence, /data2/xukui/data/jobs_pab/6b3o/6b3o.fasta Found real_map, /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { sequence_files = "/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta" default_sequence = "/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta" real_map_files = "/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc" default_real_map = "/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc" model { file = "/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb" } default_model = "/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb" } predict_and_build { break_into_chunks_if_length_is = 10000 chunk_size = 10000 } input_files { seq_file = /data2/xukui/data/jobs_pab/6b3o/6b3o.fasta map_model { full_map = /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc } predicted_model = /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb } crystal_info { resolution = 4.1 } process_predicted_model { break_into_chunks_if_length_is = 10000 chunk_size = 10000 } control { nproc = 20 } Starting job =============================================================================== ************************************************************ PHENIX predict_and_build Wed Jan 1 20:55:59 2025 ************************************************************ Working directory: /data2/xukui/data/jobs_pab/6b3o PHENIX VERSION: 1.21.1-5286 Base directory is /data2/xukui/data/jobs_pab/6b3o Creating jobname of 'PredictAndBuild_0' Working directory /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn will be created in base directory Output prefix for files will be: /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn/PredictAndBuild_0_rebuilt Running in Standard mode... Turning off all building steps except refinement Running with a cryo-EM map Mean B-iso in af2_group_0.pdb: 80.9577007535 A**2 Added predicted model /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb_A with plddt=80.96 Mean value in B-factor field for /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb (converted from plddt to plddt): 80.96 Set random_seed_iterations to 5 No templates read from templates_as_string... Total of 0 templates to be used Setting density_modify_with_model = False (default for cryo-EM) Set rmsd_for_similar_placement to 4.10 A Working directory will be based on jobname: PredictAndBuild_0 Created new temp dir: PredictAndBuild_0 ... temp-dir will be deleted at end ================================================================================ Running predict_and_build ================================================================================ Starting data: Map file: Map manager (from /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc) Unit cell: (435.2, 435.2, 435.2, 90, 90, 90) Space group: P 1 (No. 1), Unit-cell grid: (320, 320, 320), (present: (320, 320, 320)), origin shift (0, 0, 0) Working coordinate shift (-0.0, -0.0, -0.0) NCS object with 0 groups: List of sequences: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK List of models: af2_group_0.pdb Chain A extracted List of chain IDs and sequences to use A (6b3o_A): MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK B (6b3o_A): MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK C (6b3o_A): MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK ================================================================================ Running cycle 1 of predict_and_build ================================================================================ Not using any supplied msas No supplied templates will be used in prediction this cycle ================================================================================ Predicting models for 0 chains with alphafold Updating chain names in model list... Chain A: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK Total of 1 working models Total MSAs obtained: 0 Updating chain IDs Previous ID: 'A' New ID: 'A' MODEL: af2_group_0.pdb Getting processed (trimmed, B-values updated) models B-value field interpreted as pLDDT (0 - 100) Maximum rmsd of 1.50 A used Maximum B-value to be included: 59.22 A**2 Removing short segments: (chain A and resseq 537:539) Total of 492 of 605 residues kept after B-factor filtering Selection string for B-factor filtering: (chain A and resseq 15:20) or (chain A and resseq 25:136) or (chain A and resseq 145:157) or (chain A and resseq 174:200) or (chain A and resseq 207:494) or (chain A and resseq 541:586) Selecting domains as compact chains Clusters: 15 Threshold: 3.90 Clusters: 5 Threshold: 4.40 Clusters: 6 Threshold: 4.82 Clusters: 5 Threshold: 4.34 Clusters: 3 Threshold: 3.27 Clusters: 2 Threshold: 2.14 Clusters: 3 Threshold: 3.98 Clusters: 2 Threshold: 1.81 Clusters: 3 Threshold: 3.74 Clusters: 2 Threshold: 1.80 Best resolution for domains is 35.0 A giving 3 regions Selection list based on domains: (resseq 15:20) or (resseq 25:136) or (resseq 145:157) or (resseq 174:200) or (resseq 207:494) or (resseq 541:586) (492 residues) Total of 1 regions identified Obtained processed model from af2_group_0.pdb with 492 residues (of 605) =============================================================================== Finished with prediction (Job PredictAndBuild_0 cycle 1 at 2025-01-01 20:56:19) =============================================================================== =============================================================================== Getting scaffold model... (Job PredictAndBuild_0 cycle 1 at 2025-01-01 20:56:19) =============================================================================== Checking whether scaffold model is complete... ================================================================================ Getting new scaffold model in /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn/PredictAndBuild_0_scaffold_cycle_1.pdb ================================================================================ ================================================================================ Docking 1 models (to represent 3 sequences) in map to create a scaffold ================================================================================ Model to dock: af2_group_0.pdb: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK Calculating how many copies of each sequence Model: A MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK Model copies: 1 Sequence copies: 3 Remainder copies: {'MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK': 0} remainder: 0 Copies to use: 3 Setting up model for dock_and_rebuild Added model af2_group_0.pdb (A) for dock_and_rebuild Running dock_and_rebuild to dock models Total of 1 predicted models MODEL: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK ================================================================================ Running dock_and_rebuild on total of 3 chains Chain 1 (chain A from af2_group_0.pdb) Chain 2 (chain A from af2_group_0.pdb) Chain 3 (chain A from af2_group_0.pdb) ================================================================================ ================================================================================ Running on chain 1 (chain A from af2_group_0.pdb) ================================================================================ Working directory for this chain: PredictAndBuild_0/local_dock_and_rebuild_1_0 No docked model for chain A ... Running search... Running standard docking... =============================================================================== Processing input model =============================================================================== B-value field interpreted as pLDDT (0 - 100) Maximum rmsd of 1.50 A used Maximum B-value to be included: 59.22 A**2 Removing short segments: (chain A and resseq 537:539) Total of 492 of 605 residues kept after B-factor filtering Selection string for B-factor filtering: (chain A and resseq 15:20) or (chain A and resseq 25:136) or (chain A and resseq 145:157) or (chain A and resseq 174:200) or (chain A and resseq 207:494) or (chain A and resseq 541:586) Selecting domains as compact chains Clusters: 15 Threshold: 3.90 Clusters: 5 Threshold: 4.40 Clusters: 6 Threshold: 4.82 Clusters: 5 Threshold: 4.34 Clusters: 3 Threshold: 3.27 Clusters: 2 Threshold: 2.14 Clusters: 3 Threshold: 3.98 Clusters: 2 Threshold: 1.81 Clusters: 3 Threshold: 3.74 Clusters: 2 Threshold: 1.80 Best resolution for domains is 35.0 A giving 3 regions Selection list based on domains: (resseq 15:20) or (resseq 25:136) or (resseq 145:157) or (resseq 174:200) or (resseq 207:494) or (resseq 541:586) (492 residues) Total of 1 regions identified Obtained processed model with 492 residues (of 605) Wrote processed model to /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0/local_dock_and_rebuild_1_0/working_model_processed.pdb =============================================================================== Extracting unique part of map =============================================================================== Setting map-model-manager and model shift to zero during run Split model into chains: A1 Chain number: 1 id: A1 Residues: 492 ============================================================================== Searching with each chain as a seed ============================================================================== ============================================================================== Running dock-in map on domain A1 with 492 residues ============================================================================== Running dock-in-map at overall resolution of 4.1 A Density radius set to: 24.6 A Placing model in map Map has been not been offset New cell after running map_box: (435.20, 424.32, 435.20, 90.00, 90.00, 90.00) Target boxes set to 20 Choosing local part of search model to use in search... Shifting search model coordinates (0.3, 1.9, -1.9) to origin and creating search map coefficients Docking with MR... Using masked map data MODEL: full_shifted_sm_1.pdb mass: 54120 (copies: 1) Estimated solvent fraction: 0.95 Total atoms in all copies: 3781 (volume = 66567.6 A**3) Solvent fraction (as used) is about 0.94 Total good sites: 11268 Max clusters: 1 Wrote mtz data to PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/mtz_data.mtz Wrote model A1_full_shifted_sm_1.pdb to PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/A1_full_shifted_sm_1.pdb Wrote model A_from_cluster_0.pdb to PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/A_from_cluster_0.pdb

3 2

mmtbx.ringer with noise maps
by Schulz, Dr. Eike 06 Jun '26

06 Jun '26

Hi everyone, I am using mmtbx.ringer via phenix-1.21rc1-5127 to explore ED changes from END/RAPID maps. While it’s possible to provide volume scaled maps, it does seem possible to provide noise maps from END/RAPID is that correct or am I missing sth.? Related: setting gui=true enables to graphically browse through the results, it does not seem to be possible to automatically save all these plots. Is it possible to activate this? Best regards, Eike

2 1

Reminder: Phenix Postdoc Position - Berkeley, California
by Paul Adams 06 Jun '26

06 Jun '26

Dear Colleagues, The Phenix team is hiring! We are looking for talented postdoctoral candidates to join the group in Berkeley. Please see the details below, and feel free to pass on to anyone you think might be interested. To access the job posting directly: https://jobs.lbl.gov/jobs/computational-postdoctoral-fellow-6893 Cheers, Paul Berkeley Lab’s (LBNL) Molecular Biophysics and Integrated Bioimaging Division (MBIB) has an opening for a Postdoctoral Fellow to develop new computational methods for the structure determination and refinement of protein structures using the PHENIX software system. In this exciting role, you will work under the direction of the Deputy Director for this project with primary responsibilities including the development and implementation of numerical methods and new computational protocols, including the application of machine learning methods. The goals of the role include the development of automated pipelines for data analysis, structure completion and model validation. The Phenix software is used worldwide for the determination of atomic structures using X-ray and neutron crystallography and cryo-electron microscopy. The software is developed as part of an international collaboration supported by the National Institutes of Health and the Phenix Industrial Consortium. This will require the organization of results for presentation and viewing by project team members, the wider scientific community, and preparing results for publication in scientific journals. This position has an earliest start date of February 3, 2025. What You Will Do: Develop and implement computational algorithms for structure determination using crystallography and cryo-electron microscopy including: Improved methods for the optimization and completion of models Automated pipelines for data analysis, structure completion, and model validation Apply machine learning methods to problems in crystallography and cryo-electron microscopy. Develop and test new components of the PHENIX software system in collaboration with others. Document software developments. Collaborate with other researchers in the PHENIX program. Summarize research results, publish them in peer-reviewed journals, and contribute to scientific research papers and reports. Contribute to discussions on the determination of future directions. Attend group meetings or conferences/workshops, present status reports, and scientific findings as appropriate. Keep accurate and detailed research notes. What is Required: A recent Ph.D. (within the last 1-2 years) in Computational Crystallography, Computational Cryo-Electron Microscopy, Computational Biology, Bioinformatics, Computational Chemistry or a closely related field. Demonstrated experience in developing computational algorithms for solving problems. Demonstrated experience with computational methods development. Publications in macromolecular crystallography, cryo-electron microscopy or closely related fields. Good programming and mathematical skills, including familiarity with Python and other software development tools. Strong organizational skills including experience maintaining detailed and accurate records of experiment results and analyzed data. Excellent oral and written communication skills including experience organizing/presenting technical reports. Demonstrated interpersonal skills including experience conducting experiments independently and collaborating with a diverse interdisciplinary research team. Desired Qualifications: Experience with machine learning methods, programming with C++, or equivalent object-oriented programming languages. Experience with the practical aspects of crystallography and/or cryo-electron microscopy. Familiarity with macromolecular structure or computational chemistry. -- 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 ] --

2 1

Cryo_fit installation
by omar.debei＠unipr.it 06 Jun '26

06 Jun '26

Hi everyone, I was wondering if you could help me with installing cryo_fit on an Ubuntu machine. I followed the instructions here for the cryo_fit installation. Then, I tried to follow this guide to install gromacs_cryo_fit. However, I got stuck at the "Install using a provided script" step. Do I need to install GROMACS separately before proceeding? Any tips would be greatly appreciated! Many thanks, Omar

3 3

Refine partially occupied ligand in active site containing chloride ions
by Stephen.carr＠rc-harwell.ac.uk 06 Jun '26

06 Jun '26

Dear phenix bb, I am trying to refine a ligand in the active site of my protein where the ligand occupancy is ~50%. The empty active site contains two chloride ions and the residual density from these ions is very prominent when the model is refined with the ligand alone. I would like to refine the model with both the ligand and chloride ions present and have been trying to do this with altLoc flags but so far with no luck. I'm assuming that since the Cl ions more-or-less directly overlay atoms from the ligand positional refinement keeps pushing them out of the density. I'm sure there is a simple way to get around this and I would be grateful for any suggestions. Best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.carr(a)rc-harwell.ac.uk tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.

3 2