- phenixbb - phenix-online.org

Fwd: Thank you for registering - Phenix Workshops - April 7 & 14
by Nigel Moriarty 05 Apr '21

05 Apr '21

Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 ---------- Forwarded message --------- From: Ashley Dawn <ashleydawn(a)lbl.gov> Date: Mon, Apr 5, 2021 at 9:56 AM Subject: Thank you for registering - Phenix Workshops - April 7 & 14 To: Ashley Dawn <ashleydawn(a)lbl.gov> Cc: Nigel Moriarty <nwmoriarty(a)lbl.gov>, Christopher Schlicksup < cjschlicksup(a)lbl.gov>, phenixdev <developers(a)phenix-online.org> Good morning, Thank you for registering for the Phenix Workshops that begin this Wednesday. *AGENDA: * *7 APR *(click to add to google calendar) <https://calendar.google.com/event?action=TEMPLATE&tmeid=MHRzaGc4ZDR0MDVpcjd…> - 3.45pm - Start of Zoom session (for people to debug any issues) - 4.00pm - Paul Adams - Phenix Overview - 4.30pm - Tom Terwilliger - Map Improvement - 5.45pm - Tom Terwilliger - Model Building - 7.00pm - Question/Answer session *14 APR * (click to add to google calendar) <https://calendar.google.com/event?action=TEMPLATE&tmeid=NXBhcmkxcTYzdmp1ZGN…> - 3.45pm - Start of Zoom session (for people to debug any issues) - 4.00pm - Pavel Afonine - Real Space Refine - 5.15pm - Nigel Moriarty - Ligands and Restraints - 6.00pm - Jane Richardson - Validation - 7.00pm - Question/Answer session Cheers, The Phenix Developer Team Ashley Dawn (she/her/hers) [image: A button for name playback in email signature] <https://www.name-coach.com/ashley-dawn> Senior Administrator Molecular Biophysics & Integrated Bioimaging Lawrence Berkeley Laboratory 1-510-486-5455

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Please register - Phenix Workshops - April 7 & 14
by Paul Adams 05 Apr '21

05 Apr '21

Dear Colleagues, The Phenix developers will be holding an online *Phenix User Workshop on the 7th and 14th of April at 4-9pm PDT.* These times will work best for researchers in Asia and Australasia. The format of the workshop will be demos of the use of Phenix programs combined with slides to explain the theory. We expect an interactive meeting where attendees can ask questions for the Phenix team to answer. The workshop will cover aspects of macromolecular crystallography in Phenix, with the final emphasis based on the applicants’ research interests. To apply please fill out this form <https://forms.gle/X18KrWR6GvRUKYJ49>. We will make every effort to accommodate all applicants, but may need to defer some requests to a future workshop if demand is high. We are hoping this workshop will be a success, in which case we plan to host more in the future. *AGENDA:* *7 APR * - 3.45pm - Start of Zoom session (for people to debug any issues) - 4.00pm - Paul Adams - Phenix Overview - 4.30pm - Tom Terwilliger - Map Improvement - 5.45pm - Tom Terwilliger - Model Building - 7.00pm - Question/Answer session *14 APR * - 3.45pm - Start of Zoom session (for people to debug any issues) - 4.00pm - Pavel Afonine - Real Space Refine - 5.15pm - Nigel Moriarty - Ligands and Restraints - 6.00pm - Jane Richardson - Validation - 7.00pm - Question/Answer session Cheers, The Phenix Developer Team -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL ( http://biosciences.lbl.gov/divisions/mbib) 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) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area ( http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley ( http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley ( http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ AshleyDawn(a)lbl.gov <LBenvenue(a)lbl.gov> ] [ 1-510-486-5455 ]

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phenix.ligand_identification search_center
by Tanner, John J. 31 Mar '21

31 Mar '21

Phenix BB: I would like to use phenix.ligand_identification to analyze an electron density feature in the active site of an enzyme; however, I do not see how to specify search_center in the gui. Thus, the program places the ligands into a strong density feature on the surface of the protein. When I run it from the command line with search_center specified, it seems to ignore the search center coordinates and again places the ligands into the density feature on the surface. My command script: [tannerjj@europa ligandID]$ cat ligandID.com phenix.ligand_identification \ mtz_in = "/titan/tanner/MmP5CDH/THLP/MmALDH4A1_THLP8-1_003.mtz" \ mtz_type = diffmap \ input_labels = "FOFCWT PHFOFCWT" \ ligand_list = "DPR PRO HYP HZP UYA UY7" \ model = "/titan/tanner/MmP5CDH/THLP/MmALDH4A1_THLP8-1_003.pdb" \ ncpu = 4 \ output_dir = "/titan/tanner/MmP5CDH/THLP/ligandID/temp" \ number_of_ligands = 6 \ job_title = "THLP8-1_003 D,L-Pro and 4 OH-Pro stereoisomers" \ search_center = "-12.597 11.990 21.741" [tannerjj@europa ligandID]$ Thanks, Jack -- John J. Tanner Professor of Biochemistry and Chemistry Associate Chair of Biochemistry Department of Biochemistry University of Missouri 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Email: tannerjj(a)missouri.edu<mailto:[email protected]> https://cafnrfaculty.missouri.edu/tannerlab/ Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A

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phenix.local_aniso_sharpen
by Luca Pellegrini 31 Mar '21

31 Mar '21

Hi, Is there a way to estimate the resolution of the map obtained from phenix.local_aniso_sharpen? I find that it produces nice maps, but there’s no output information that I can see. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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cif. file for AFITT
by Muhammad Bashir Khan 26 Mar '21

26 Mar '21

Hello all Could somebody explain how I can generate a cif. file of ligand for AFITT. I am using afitt in phenix refinement using the ligand cif. file generated by the elbow. But it complains. I have two different types of ligands in the structure. Thanks Bashir -- ------------------------------------------------------ Muhammad Bashir Khan, Ph.D. Research Associate Department of Biochemistry Medical Science Bldg. Lab 3-27 University of Alberta Edmonton AB, T6G 2H7 Phone: 780-492-4577- e-mail: mbk(a)ualberta.ca <cbrooks1(a)ualberta.ca>

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Unusual ligand conformation
by Joel Tyndall 26 Mar '21

26 Mar '21

Hi all, We have been finalising a structure with a ligand complexed to heme. I have been checking the close to final structure and I noticed that the ligand looks distorted away from what one would expect. We use Phenix.refine We initially used the grade server for our restraints files. I also just used elbow to generate a new one. Looking at both, the restraints look reasonable (similar in both) however the initial output pdb from elbow is distorted further. The angles /lengths looked reasonable and are similar to small molecule structures (CCDC). The planarity of a bi-phenyl moiety is very distorted. [cid:[email protected]] Are we missing something? Do we need to tell phenix.refine to not over refine the model? Should elbow give a distorted model? Apologies if this is all online but my uni cant seem to access phenix.org! Thanks in advance Joel Joel Tyndall | BSc(Hons) PhD Associate Professor in Medicinal Chemistry School of Pharmacy | He Rau Kawakawa University of Otago | Te Whare Wānanga o Otāgo PO Box 56 9054 Dunedin | Ōtepoti New Zealand | Aotearoa Ph: 64 3 479 7293 Skype: jtyndall Website | pharmacy.otago.ac.nz

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map to model FSC calculation
by C.J. 23 Mar '21

23 Mar '21

Hi All, I'm new to phenix and a bit confused to map to model FSC calculation. Which program should I use, phenix.mtriage or phenix.map_model_cc? If both work, what is the difference between them? Thank you! Jianhao

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Re: [phenixbb] FSC curves
by Pavel Afonine 19 Mar '21

19 Mar '21

Hi Juliana, > After running phenix real space refine with different refinement > strategies. My map-model FSC curve has some interesting features: > > 1. It does not starts at 1 as it does the map FSC curve, is that ok? > What could be causing this? > which one is it? Is it FSC(half_map1, half_map2) or FSC(experimental_map, model_map) ? > 1. It has a dip around 5-6Å, this deep can be a bit up or down > depending the refinement strategy I use, therefore the FSC model > at 0.5 can cut the resolution at 3.9 or 6 Å. What this deep mean? > Am I doing something wrong in the refinement? > How different these models are? > 1. The mask and unmask curves completely overlap, is that ok? > This suggests to me the map is probably already masked or somehow 'normalized'.. > 1. Also, my refinement shows a high clash score (15-20), if I change > the nonbonded_weight parameter from 100 (default) to higher values > the clash score decreases but the FSC curves gets lower them the > FSC curve crosses the 0.5 cutoff at 6A. > When it comes to clashscore, generally the lower the better but zero is not the goal. Looking at one of screenshots I see you have 2.42% of atoms with occupancy less than 1. Do you really see partially occupied atoms in 4A resolution map? Unlikely! So.. please check those out! I can run more diagnostics for you if you share maps and models (off-list of course!). Pavel

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on "Tutorial: Solving a structure with cryo-EM data using docking"
by Smith Lee 19 Mar '21

19 Mar '21

Dear All, For "Tutorial: Solving a structure with cryo-EM data using docking", it is easy to download the emd_20026_half_map_1_box.ccp4 and emd_20026_half_map_2_box.ccp4 from the emd-20026 depositation, but will you please let me know step by step how to get the tutorial used seq.dat, 20026_auto_sharpen_A.ccp4 (any other name for this file? Cannot find the exact name file in emd_20026 depositation), apoferritin_chainA_rsr.pdb (it mentioned "model refined against sharpened map", which sharpened map, and what was the refinement method ued?), run_denmod_dock.csh? I am looking forward to getting your reply. Best wishes, Smith

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Ligand refinment problum
by Muhammad Bashir Khan 18 Mar '21

18 Mar '21

Hello all; I have a crystal structure with four molecules per unit of the cell. It contains two different ligands. Four are similar while the fifth one is different. Placed all the five ligands manually by coot. Now I want to refine. Before refinement, I run the ReadySet to generate the cif. file. It shows an error. Then I supply the cif. file of both the ligand coming from the elbow, It still shows the following error. screenshot attached. Any help would be appreciated. Sincerely; Bashir -- ------------------------------------------------------ Muhammad Bashir Khan, Ph.D. Research Associate Department of Biochemistry Medical Science Bldg. Lab 3-27 University of Alberta Edmonton AB, T6G 2H7 Phone: 780-492-4577- e-mail: mbk(a)ualberta.ca <cbrooks1(a)ualberta.ca>

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