- phenixbb - phenix-online.org

Phenix Postdoc Position - Berkeley, California
by Paul Adams 24 Jan '25

24 Jan '25

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

Error in Windows installation: Phenix 1.21.2-54
by Jobichen Chacko 18 Jan '25

18 Jan '25

ImportError : __import__("gltbx_glu_ext"): DLL load failed while importing gltbx_glu_ext: A dynamic link library (DLL) initialization routine failed. sys.path: C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\libsvm C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\phenix\wxGUI2\command_line C:\ProgramData\phenix-1.21.2-5419\python39.zip C:\ProgramData\phenix-1.21.2-5419\DLLs C:\ProgramData\phenix-1.21.2-5419\lib C:\ProgramData\phenix-1.21.2-5419 C:\ProgramData\phenix-1.21.2-5419\lib\site-packages C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\mmtbx\suitename Traceback (most recent call last): File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\boost_adaptbx\boost\python.py", line 22, in import_ext try: mod = __import__(name) ImportError: DLL load failed while importing gltbx_glu_ext: A dynamic link library (DLL) initialization routine failed. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\MainWindow.py", line 745, in <lambda> menu.add_command("Run now", lambda evt: self.run()) File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\Programs\Refine\Main.py", line 426, in run self.start_process(config_file, output_dir, process_type) File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\Templates.py", line 701, in start_process run_notebook = self.create_run_notebook() File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\Programs\Refine\Main.py", line 532, in create_run_notebook from wxGUI2.Programs.Refine import Output File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\Programs\Refine\Output.py", line 5, in <module> from wxGUI2 import GLViewer, AdvancedWidgets, Buttons File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\GLViewer.py", line 10, in <module> from crys3d.wx_combined_viewer import viewer_phil File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\crys3d\wx_combined_viewer.py", line 4, in <module> from crys3d.wx_selection_editor import selection_editor_mixin File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\crys3d\wx_selection_editor.py", line 6, in <module> from crys3d.wx_model_viewer import model_scene, model_viewer_mixin File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\crys3d\wx_model_viewer.py", line 10, in <module> from gltbx.wx_viewer import wxGLWindow File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\gltbx\wx_viewer.py", line 8, in <module> from gltbx.glu import * File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\gltbx\glu.py", line 3, in <module> ext = bp.import_ext("gltbx_glu_ext") File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\boost_adaptbx\boost\python.py", line 31, in import_ext raise ImportError( Dear All, I am getting this error when trying to run Phenix-refine. Any idea how to fix this? Thank you. Jobi ImportError: __import__("gltbx_glu_ext"): DLL load failed while importing gltbx_glu_ext: A dynamic link library (DLL) initialization routine failed. sys.path: C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\libsvm C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\phenix\wxGUI2\command_line C:\ProgramData\phenix-1.21.2-5419\python39.zip C:\ProgramData\phenix-1.21.2-5419\DLLs C:\ProgramData\phenix-1.21.2-5419\lib C:\ProgramData\phenix-1.21.2-5419 C:\ProgramData\phenix-1.21.2-5419\lib\site-packages C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\mmtbx\suitename

2 3

Error opening REEL and ligand refinement in Coot
by Marian Oliva 17 Jan '25

17 Jan '25

Dear all, I posted this problem a couple of days ago through phenix help mail address but I got no answer (not sure if it was delivered properly). Maybe here I am luckier. I have recently upgrade my machine to Ubuntu MATE 1.26 and re-install all crystallography software I often use, including Phenix version dev-5493. I am working in a structure of a protein bound to a new ligand. I built the ligand with chemDraw, get the SMILE, get a universal SMILE string in cactus.nci.nih.gov <http://cactus.nci.nih.gov/>, and used eLbow for ligand restraints generation and optimization (using default parameters). First problem. When I try to open the ligand in REEL. Phenix crash with the following message in the terminal libGL error: MESA-LOADER: failed to open nouveau: /usr/lib/dri/nouveau_dri.so <http://nouveau_dri.so/>: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri) libGL error: failed to load driver: nouveau libGL error: MESA-LOADER: failed to open nouveau: /usr/lib/dri/nouveau_dri.so <http://nouveau_dri.so/>: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri) libGL error: failed to load driver: nouveau libGL error: MESA-LOADER: failed to open swrast: /usr/lib/dri/swrast_dri.so <http://swrast_dri.so/>: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri) libGL error: failed to load driver: swrast The program 'main.py' received an X Window System error. This probably reflects a bug in the program. The error was 'BadValue'. (Details: serial 39668 error_code 2 request_code 152 minor_code 24) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.) Second, when I open the structure in Coot (0.9.8.95) from Phenix and try to perform real space refine zone to the ligand, the attached window pops-up. Is this because I did something wrong during the installation? Is there a bug I am not aware of? Any help will be really appreciate. Many thanks in advance, Marian

1 0

Re: phenix.predict_and_build, proccess normal and no error, but not generate the PredictAndBuild_0_overall_best.pdb
by Tom Terwilliger 09 Jan '25

09 Jan '25

On Thu, Jan 9, 2025 at 11:13 AM Oleg Sobolev <osobolev(a)lbl.gov> wrote: > Hi Tom, > > I fished out the following from my Spam folder, but it is on PhenixBB. Can > you please take a look? > > Best regards, > Oleg Sobolev. > > ---------- Forwarded message --------- > From: <fnsoxt(a)qq.com> > Date: Sun, Jan 5, 2025 at 8:03 PM > Subject: [phenixbb] phenix.predict_and_build, proccess normal and no > error, but not generate the PredictAndBuild_0_overall_best.pdb > To: <phenixbb(a)phenix-online.org> > > > 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 > _______________________________________________ > phenixbb mailing list -- phenixbb(a)phenix-online.org > To unsubscribe send an email to phenixbb-leave(a)phenix-online.org > Unsubscribe: phenixbb-leave@%(host_name)s > -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

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PostDoc and Associate Researcher positions in structural biology field at ISMMS in NYC
by Wang, Wei 13 Dec '24

13 Dec '24

Dear all, I'd like to draw your attention to the availability of postdoctoral and associate researcher positions in my newly started lab at Icahn School of Medicine at Mount Sinai in New York City. Our lab focuses on elucidating protein dynamics and functions under disease-related conditions, with a strong collaborative tie to the Mount Sinai Center for Transformative Disease Modeling. I hereby sincerely invite colleagues to join my lab for the mutual research interest. For more details on the available positions and the application process, please visit the following links: Postdoctoral candidate please visit: https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-postd… Associate Researcher candidate please visit: https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-assoc… Please don't hesitate to reach out if you have any questions. I would be glad to talk with you. Wei Wang, PhD Assistant Professor Department of Genetics and Genomic Sciences Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai e: wei.wang(a)mssm.edu<mailto:[email protected]>

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open position for a 2(+2) year postdoc working on plant hormone transport at Aarhus University, Denmark.
by Bjørn Panyella Pedersen 25 Nov '24

25 Nov '24

Dear colleagues, Please pass this along anyone who might be interested. Thanks! /Bjørn Postdoctoral position in biophysical and structural characterization of auxin transport, Aarhus University, Denmark online posting: https://international.au.dk/about/profile/vacant-positions/job/postdoctoral… We are looking for a highly skilled and motivated postdoc with an interest in working on auxin hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins. The position will be open from spring 2025, but starting date is negotiable. Funding is available for at least 2 years of employment, with an extension possible for up to a total of 4 years. The position: The position seeks to strengthen ongoing activities in the our group related to the function and mechanism of hormone-transporting membrane proteins in plants (pedersenlab.dk). Examples of our research can be found in: Schulz & Ung et al. "Transport of herbicides by PIN-FORMED auxin transporters" bioRxiv (2024) Andersen et al. Basis of Glucose and Fructose Selectivity in Sugar Transport Proteins" bioRxiv (2024) Bavnhøj et al. “Structure and sucrose binding mechanism of the plant SUC1 sucrose transporter.” Nature Plants 7 (2023) Ung et al. “Structures and mechanism of the plant PIN-FORMED auxin transporter” Nature 609 (2022). The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems and proton driven transport, and the methods uses are primarily structural biology (cryo-EM, crystallography) and biochemistry. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - an exciting interdisciplinary environment with many national, international and industrial collaborators. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See “life in Denmark” at Aarhus and surroundings for further details on the city and the university (https://international.au.dk/life/locations/aarhusandsurroundings). Deadline: All applications must be made online and received by 20. Dec. 2024. See details here: https://international.au.dk/about/profile/vacant-positions/job/postdoctoral…

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Tool to calculate Q-scores?
by Guillaume Gaullier 29 Oct '24

29 Oct '24

Hello phenixbb, It would be convenient to have a tool to calculate Q-scores [1], with suggested command-line name phenix.qscore or phenix.model_map_qscore. It would work just like phenix.model_map_cc but report Q-scores instead (average per chain by default, but if requested also per-residue backbone / side chain / whole residue averages, or per ligand). And phenix.validation_cryoem could report these scores as well, in addition to the CCs that it already reports. There is already a tool to do this in ChimeraX [2], which is very helpful for interactive work. But for automated calculation of these scores from many models and maps, it would be more convenient to have a phenix tool for it. If it already exists, sorry I overlooked it (but I looked up both the latest documentation and phenix command completion and couldn't find anything like it), and I'll be happy if somebody can point me to it! Cheers, Guillaume [1]: https://doi.org/10.1038/s41592-020-0731-1 [2]: https://github.com/tristanic/chimerax-qscore När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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MASSIF-1 10 year celebration symposium
by Matthew BOWLER 25 Oct '24

25 Oct '24

Dear CCP4 community, I would like to draw your attention to a one day symposium we are holding here in Grenoble to celebrate 10 years of fully automatic data collection at the ESRF/EMBL beamline MASSIF-1 - from starting with basic characterisation and data collection we now measure crystal volumes, dynamically adapt beam diameters, automatically collect and merge kappa sweeps, helical and multi-crystal data sets and even automatically mount crystals from trays using the EMBL CrystalDirect robot. With a great line-up of speakers we will highlight some of the research enabled by MASSIF-1, how it has inspired other beamlines around the world, as well as some history of the project. You can find more details in the attached flyer and register in the link below. We look forward to seeing you in Grenoble! Matthew Bowler and Didier Nurizzo. https://www.esrf.fr/home/events/conferences/2024/massif-1-symposium.html -- Matthew Bowler Project Leader MASSIF1@ESRF European Molecular Biology Laboratory 71 avenue des Martyrs CS 90181 F-38042 Grenoble France =================================================== Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.20.71.99 http://www.embl.fr/ http://www.esrf.eu/MASSIF1 https://twitter.com/id30_massif1 https://www.embl.org/people/person/mbowler/ ===================================================

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Bursaries available for CCP4 Study Weekend 2025 - Using software, AI and other methods to advance macromolecular models
by Karen McIntyre - STFC UKRI 25 Oct '24

25 Oct '24

Standard Student Bursaries As in year’s past, CCP4 has made funding available for students, to help with the costs of attending Study Weekend, in the form of a bursary. All students are eligible for a standard bursary which covers the registration fee plus one night’s accommodation in halls. Bursaries will be given out to all students registering during the early bird registration period – 26th September to 11th November 2024. Students obtaining a standard bursary will only need to pay for any additional night’s accommodation. Students wishing to stay in the hotel rather than Rutland halls, will have 1 nights accommodation subsidised at the halls rate and will therefore pay a reduced rate for this night. Additional nights accommodation will need to be paid at the standard cost. Please also note that should you obtain a bursary and cancel after the latest cancellation date of 6 December 2024 you WILL be liable to pay.  This is because we have had a number of students obtaining bursaries and then cancelling last minute.  Places can be transferred to other people at no charge.  Travel bursaries Limited funds will also be made available to help pay travel costs for students and young post-docs from non-UK laboratories. Please send a separate letter, signed by your supervisor and stating the expected cost of travel in pounds sterling, to justify applications for travel support. Supervisors are asked to nominate only one candidate from their Laboratory. Delegates are expected to travel by the most economic means possible. Candidates from less favoured regions will be given preference. Applications should be e-mailed to ccp4sw(a)stfc.ac.uk<mailto:[email protected]> : Lauren Giles CCP4 Study Weekend Travel Bursary Applications for travel bursaries need to be in by Thursday 31st October 2024. Regards Karen McIntyre CCP4 Project Administrator CCP4 ED&I Champion UKRI-STFC Rutherford Appleton Laboratory Harwell Campus Didcot OX11 0QX Phone: +44 (0) 1235 44 5790 [cid:[email protected]] STFC is part of UK Research and Innovation, a public body funded by the UK government. For more information visit www.ukri.org<http://www.ukri.org/> [A grey circle with red text Description automatically generated] Affiliatated Member of the Institute for Continuous Improvement in the Public Sector ***Please note I only work part-time – hours are Monday to Thursday 08:30 to 13:30 and Friday 10:30 to 15:30**********

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NIH would like your input
by Paul Adams 14 Oct '24

14 Oct '24

Dear Colleagues, For those of you in the US, you might want to know that NIH issued a Request for Information about their National Resources and Biomedical Technology Optimization and Dissemination programs: https://www.research.net/r/NRRs_and_Biomedical_Technology_Optimization_and_… Unfortunately, it closes tomorrow, but it is a short form. They are interested in experiences with existing resources, but are most interested in hearing ideas for expanding the programs to new technologies. Currently funded resources can be found here: https://www.nigms.nih.gov/Research/mechanisms/Pages/NIGMS-National-and-Regi… Information about the Biomedical Technology Optimization and Dissemination program can be found here: https://www.nigms.nih.gov/grants/Pages/btod.aspx NIH would appreciate your thoughts about additional technologies that would benefit the community by support through these programs. 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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