- phenixbb - phenix-online.org

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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rotamers in real space refine
by Leonid Sazanov 17 Mar '21

17 Mar '21

Hi, We still have a problem of some Trp and Tyr residues going out of very clear density in high-resolution (~2.5 A) EM maps upon real space refine in phenix, even the latest version. Is there may be a more extensive rotamer library (including those pseudo-"outliers") available somewhere to be used in Phenix? Many thanks, Leonid -- Prof. Leonid Sazanov FRS IST Austria Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: sazanov(a)ist.ac.at

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Migrating all phenix projects to a new location without breaking all of the file paths.
by Leonard,Paul G 15 Mar '21

15 Mar '21

Hi, Does anyone have instructions I can follow for how to move all of my phenix directories to a new location without messing up all of the file paths in each project. Our IT department wants to relocate files on our server which will change all of the top directory locations to something new so before that happens I think there is a way I can have a file that will allow me to recreate all of the phenix projects in the GUI with the new file paths but I can't recall how to do it. Thanks in advance for your assistance. Best wishes, Paul Institute Senior Research Scientist MD Anderson Cancer Center 1881 East Road Houston TX 77054 USA Tel: 732 397 8539 email: pleonard1(a)mdanderson.org The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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Is the Phenix website down?
by Joel Tyndall 14 Mar '21

14 Mar '21

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Re: [phenixbb] Question about Phenix refinement
by Dorothee Liebschner 12 Mar '21

12 Mar '21

Hi, This tutorial explains how to set parameters: https://www.youtube.com/watch?v=qB8W_6yuw5k&t=2s Best wishes, Dorothee On Fri, Mar 12, 2021 at 7:39 AM Zhang, Wen <wz15(a)iu.edu> wrote: > Hi, > > This is Wen from Indiana University. I have a question about the > refinement using Phenix. I got a Phenix Error, saying “Polymer crosses > special position element xxxxxxxxx. Use > allow_polymer_cross_special_position=True to keep going.” I also find this > keyword online, but am still not sure how I can change this key word. > Should I input the command somewhere? What should I do exactly? > > > > Thanks > > Wen > -- Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Adding hydrogens back on lipids
by Noor Agip 12 Mar '21

12 Mar '21

Hi, Is there a way to add hydrogens back on lipids using Readyset? I tried this with no success. Best wishes, Noor

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Refining ligands in a structure
by Joel Tyndall 12 Mar '21

12 Mar '21

Hi folks, It has been a while since we have done much with phenix. We are refining a structure with a known ligand, voriconazole (exists on the pdb). We get an error regarding a lack of .cif file/restraints. Do we normally need to specify a cif file given this is a known ligand and can be retrieved in Coot? I assume that phenix would call on a known library of ligands/monomers that are known. Is this the correct library? phenix-installer-1.17.1-3660-intel-windows-x86_64\modules\chem_data\chemical_components\ Many thanks 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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Postdoctoral position in drug discovery at Vanderbilt University (Nashville, TN)
by Harp, Joel M 09 Mar '21

09 Mar '21

Postdoctoral position in drug discovery An opening is available in the drug discovery laboratory of Dr. Stephen Fesik for a post-doc in the field of protein x-ray crystallography. Responsibilities will include protein expression and purification, and all aspects of x-ray crystallography including preparation of protein-inhibitor complexes, crystallization, home/synchrotron data collection, and structure determination. Additional experiences in molecular biology including construct design, cloning, site-directed mutagenesis, and experience with recombinant protein expression in eukaryotic cells are highly preferred. The ideal candidate should be self-motivated and be able to communicate efficiently in a highly collaborative environment. Please send cv to jason.phan(a)Vanderbilt.Edu<mailto:[email protected]>

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Spatial query acceleration structure in cctbx?
by Russell M. Taylor II 08 Mar '21

08 Mar '21

As part of integrating the MolProbity tools more tightly with the CCTBX, I'm modifying the Probe code that will be shared by it and Reduce to use native CCTBX structures. One of the structures is a spatial map to accelerate the search for nearby atoms in a model. Before building my own (3D grid with near neighbors listed, ability to insert and remove atoms as they move), I wanted to check and see what was already available in the CCTBX. I looked at the page listing the CCTBX core objects and functions and did not see one, and searching for "spatial" and "accel" in the source tree did not turn up anything promising. Is there one already in there? If not, is this something that others would find to be a useful tool and, if so, where should it live? Otherwise, I'll make it part of Probe. Thanks, Russ Taylor --- Russell M. Taylor II, Ph.D. russ(a)reliasolve.com taylor(a)redbudlabs.com rtaylor(a)aqueti.com russ(a)outloveracism.org www.cs.unc.edu/~taylorr

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PAIREF Webinar (23rd March 2021, 15:00 CET)
by Petr Kolenko 08 Mar '21

08 Mar '21

Dear colleagues, We are pleased to announce the webinar on paired refinement to be held on March 23, 2021, from 3 PM (CET) to 4 PM (CET). This protocol provides an accurate estimation of the high-resolution cutoff (https://journals.iucr.org/m/issues/2020/04/00/mf5044/). The "PAIREF webinar" will be a free virtual event for up to 300 participants. The meeting will be recorded. Please register and receive your Zoom link here: https://kipl-indico.fjfi.cvut.cz/e/pairef We will cover: 1. Introduction to paired refinement. 2. Installation of PAIREF for CCP4 and/or PHENIX users. 3. Short tutorial (files will be provided). 4. Discussion. Feel free to contact us with your data. Best regards, Petr Kolenko, Martin Maly, Kay Diederichs and Jan Dohnalek

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error for "rosetta.run_tests"
by Smith Lee 06 Mar '21

06 Mar '21

Dear All, For rosetta installation for use in phenix, in the .bashrc I have: export PATH="/home/usrname/rosetta_src_2020.08.61146_bundle":$PATHexport PATH="/home/username/phenix11914122installdir/phenix-1.19.1-4122/build/bin":$PATH and I have the .bashrc file sourced. However when I run "rosetta.run_tests", I got the following error: --...... End of input processing Sorry: The RosettaScripts executable could not be located. Please set the environmental variable PHENIX_ROSETTA_PATH or add the appropriate directory to your PATH environment variable. ---- I am looking forward to getting your advice on how to solve the error issue. Smith

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phenix.molprobity geo
by Paul Emsley 04 Mar '21

04 Mar '21

Hello, I'd like to compare the restraints generated by Coot to the validation provided by molprobity. When I run phenix.molprobity on my model, it gives me (amongst other things) this: ----------------------- Histogram of nonbonded interaction distances: 1.87 - 2.42: 526 2.42 - 2.96: 3217 2.96 - 3.51: 3639 3.51 - 4.05: 5026 4.05 - 4.60: 6847 Nonbonded interactions: 19255 Sorted by model distance: nonbonded pdb=" O LEU A 21 " pdb=" H GLY A 26 " model vdw 1.874 1.850 nonbonded pdb=" H ILE A 71 " pdb=" O TYR A 80 " model vdw 1.920 1.850 nonbonded pdb=" H GLY A 34 " pdb=" O GLU A 54 " model vdw 1.925 1.850 nonbonded pdb=" O ILE A 71 " pdb=" H TYR A 80 " model vdw 1.937 1.850 nonbonded pdb=" HE ARG A 40 " pdb=" HG1 THR A 76 " model vdw sym.op. 1.955 2.100 -x+3/2,-y,z+1/2 ... (remaining 19250 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. -------------------------- I don't understand this lilst. Should I be concerned by those interactions? Which of these atom pairs are contributing to the clashscore? Perhaps the details are in the .geo file? How do I get a .geo file? I googled, I didn't find the answer. How could I have found the answer without asking here? Thanks, Paul.

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Re: [phenixbb] executing Phenix in a python script on a Windows OS
by Muriel Gelin 02 Mar '21

02 Mar '21

Here is what I have: In a prompt: C:\Users\MG>C:\Users\MG\Phenix\phenix-installer-1.19.1-4122-intel-windows-x86_64\phenix_env.bat C:\Users\MG>phenix.refine Usage: phenix.refine [options] [reflection_file] [pdb_file] [parameter_file] -------------------------------------------------------------------------------- In python: source = subprocess.Popen(str(r"C:\Users\MG\Phenix\phenix-installer-1.19.1-4122-intel-windows-x86_64\phenix_env.bat"), stdin=subprocess.PIPE, stdout=subprocess.PIPE, shell=True) >>> phenix.refine Traceback (most recent call last): File "<stdin>", line 1, in <module> NameError: name 'phenix' is not defined >>> py phenix.refine File "<stdin>", line 1 py phenix.refine ^ -------------------------------------------------------------------------------- If somebody see what is the problem. I'm afraid I am stuck ... Thank you all. Muriel Le 02/03/2021 à 11:03, gelin a écrit : > Dear Bernhard, > > Thank you for your answer. > > Executing phenix_env.bat in Windows command prompt works well, since I > can then execute phenix.refine in the prompt. > > So I tried to add in my python script something like that: > source = subprocess.Popen(my_path\phenix_env.bat, > stdin=subprocess.PIPE, stdout=subprocess.PIPE, > stderr=subprocess.PIPE) > Unfortunately, it doesn't work. I suppose the prompt environment is > not modified. > > Do you know how to do that in my python script so that I can then > execute something like: > xtriage = subprocess.Popen(["phenix.xtriage", my_mtz, > "parameters.reporting.log=" + "xtriage.log")], > stdin=subprocess.PIPE, > stdout=subprocess.PIPE, stderr=subprocess.PIPE) > > Thank you for you help. > > Muriel > > Le 2021-03-01 18:36, Bernhard Rupp a écrit : >> Here is what I did: >> >> Install phenix >> >> make a batch command in your path (eg phx.bat) that executes the >> environment setup, eg. >> C:\Phenix\phenix-installer-1.19-4092-intel-windows-x86_64\phenix_env.bat >> >> Open terminal, execute that batch (modify as you like), and there you go >> >> c:\data\Dropbox\Refinements\5okl>phenix.refine >> Usage: phenix.refine [options] [reflection_file] [pdb_file] >> [parameter_file] >> .... >> >> Best, BR >> >> -----Original Message----- >> From: phenixbb-bounces(a)phenix-online.org >> <phenixbb-bounces(a)phenix-online.org> On Behalf Of Muriel Gelin >> Sent: Monday, March 1, 2021 09:08 >> To: phenixbb(a)phenix-online.org >> Subject: [phenixbb] executing Phenix in a python script on a Windows OS >> >> Dear Phenix community, >> >> I wrote a python script to automate the processing of our data with >> Phenix. I'm not a developer by profession, but a crystallographer, and >> write scripts usually under Linux. My colleagues working under Windows >> asked me to share my script. >> >> I managed to run a simple python script under windows, no problem. But >> for a script that executes Phenix, it's not so easy (for me). >> >> Under Linux, I manage to source phenix_env.csh, but under Windows what >> is the command to setup Phenix in order to simply use phenix.refine >> or phenix.xtriage in my script? >> >> All I can find is this page >> https://www.mrc-lmb.cam.ac.uk/public/xtal/doc/phenix/install-setup-run.html >> >> >> but I don't think it answers my question. >> >> Thank you in advance for your help! >> >> Muriel >> >> -- >> Dr Muriel Gelin >> >> Research Engineer >> Centre de biochimie Structurale de Montpellier Team "ABCIS: Avanced >> Biology, Chemistry, Informatics Studio" >> >> CNRS UMR 5048 - UM - INSERM U 1054 >> 29 rue de Navacelles >> 34090 MONTPELLIER Cedex - FRANCE >> http://www.cbs.cnrs.fr >> >> Tel: (33) 04 67 41 77 12 >> >> >> -- >> This message has been scanned for viruses and dangerous content by >> MailScanner, and is believed to be clean. >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org > -- Dr Muriel Gelin Research Engineer Centre de biochimie Structurale de Montpellier Team "ABCIS: Avanced Biology, Chemistry, Informatics Studio" CNRS UMR 5048 - UM - INSERM U 1054 29 rue de Navacelles 34090 MONTPELLIER Cedex - FRANCE http://www.cbs.cnrs.fr Tel: (33) 04 67 41 77 12 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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on rosetta installation for phenix
by Smith Lee 02 Mar '21

02 Mar '21

Dear All, I have tried to install Rosetta for phenix use based on the guide in https://www.phenix-online.org/documentation/reference/rosetta_install.html. After the "tar xzf..." command, I added the directory for the installed rosetta (something like "export PHENIX_ROSETTA_PATH=/your-path-to-rosetta-here/") to my .bashrc (and in fact I also have added into /bash_profile) and sourced it. For the final step to build the interface for rosetta_refine, as for my gcc version is 8.3.1, I have deleted the original site.settings in the directory ${PHENIX_ROSETTA_PATH}/main/source/tools/build/, and exactly copied the content in https://www.phenix-online.org/documentation/extras/site.settings and save it as site.settings in the directory ${PHENIX_ROSETTA_PATH}/main/source/tools/build/. Command "nproc" displays 12, then I run "rosetta.build_phenix_interface nproc=12". In the running step for the above command, I remember it asked me "whether to install "sed" (I do not what is "sed" for), I answer "y" and "enter", it seems like the computer stopped. I opened another terminal, and all commands like "ls","cd" failed to work. I restarted the computer, but I cannot log into my centos username account anymore. I restarted the computer by initiating the centos secure start system, and deleted the export directory for the rosetta from the .bashrc and .bash_profile. In this way I restarted the computer and I can log into my centos user name account as usual. But as you know, my rosetta still did not work. Thus, will you please advice what is wrong for my installation fof the rosetta (for phenix use) and how to make it workable? I am looking forward to getting your reply. Best wishes, Smith

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Computational Crystallography Newsletter – Jan. 2021
by Nigel Moriarty 01 Mar '21

01 Mar '21

Folks The latest issue of the CCN is available on the website. Please consider contributing to future issues. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. January 2021 <http://phenix-online.org/newsletter/CCN_2021_01.pdf> Articles - HKLviewer, a new 3D reflection data viewer for CCTBX <http://phenix-online.org/newsletter/CCN_2021_01.pdf#page=15> - Running CCTBX and PyMOL in the same Jupyter Notebook <http://phenix-online.org/newsletter/CCN_2021_01.pdf#page=26> Short Communications - PDB50: Celebrating 50 Years of the Protein Data Bank in 2021 <http://phenix-online.org/newsletter/CCN_2021_01.pdf#page=5> - Lessons from using the Cambridge Structure Database: II – Element specification X/Z <http://phenix-online.org/newsletter/CCN_2021_01.pdf#page=6> - The Importance of Being Positive: Charged ligands that bind nucleic acids <http://phenix-online.org/newsletter/CCN_2021_01.pdf#page=9> Fitting tips #20 - In-plane or out-of-plane H atom placement on the edges of aromatic rings <http://phenix-online.org/newsletter/CCN_2021_01.pdf#page=2> 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

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executing Phenix in a python script on a Windows OS
by Muriel Gelin 01 Mar '21

01 Mar '21

Dear Phenix community, I wrote a python script to automate the processing of our data with Phenix. I'm not a developer by profession, but a crystallographer, and write scripts usually under Linux. My colleagues working under Windows asked me to share my script. I managed to run a simple python script under windows, no problem. But for a script that executes Phenix, it's not so easy (for me). Under Linux, I manage to source phenix_env.csh, but under Windows what is the command to setup Phenix in order to simply use phenix.refine or phenix.xtriage in my script? All I can find is this page https://www.mrc-lmb.cam.ac.uk/public/xtal/doc/phenix/install-setup-run.html but I don't think it answers my question. Thank you in advance for your help! Muriel -- Dr Muriel Gelin Research Engineer Centre de biochimie Structurale de Montpellier Team "ABCIS: Avanced Biology, Chemistry, Informatics Studio" CNRS UMR 5048 - UM - INSERM U 1054 29 rue de Navacelles 34090 MONTPELLIER Cedex - FRANCE http://www.cbs.cnrs.fr Tel: (33) 04 67 41 77 12 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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on rosetta installation for phenix use
by Smith Lee 28 Feb '21

28 Feb '21

Dear All, I have tried to install Rosetta for phenix use based on the guide in https://www.phenix-online.org/documentation/reference/rosetta_install.html. After the "tar xzf..." command, I added the directory for the installed rosetta (something like "export PHENIX_ROSETTA_PATH=/your-path-to-rosetta-here/") to my .bashrc (and in fact I also have added into /bash_profile) and sourced it. For the final step to build the interface for rosetta_refine, as for my gcc version is 8.3.1, I have deleted the original site.settings in the directory ${PHENIX_ROSETTA_PATH}/main/source/tools/build/, and exactly copied the content in https://www.phenix-online.org/documentation/extras/site.settings and save it as site.settings in the directory ${PHENIX_ROSETTA_PATH}/main/source/tools/build/. Command "nproc" displays 12, then I run "rosetta.build_phenix_interface nproc=12". In the running step for the above command, I remember it asked me "whether to install "sed" (I do not what is "sed" for), I answer "y" and "enter", it seems like the computer stopped. I opened another terminal, and all commands like "ls","cd" failed to work. I restarted the computer, but I cannot log into my centos username account anymore. I restarted the computer by initiating the centos secure start system, and deleted the export directory for the rosetta from the .bashrc and .bash_profile. In this way I restarted the computer and I can log into my centos user name account as usual. But as you know, my rosetta still did not work. Thus, will you please advice what is wrong for my installation fof the rosetta (for phenix use) and how to make it workable? I am looking forward to getting your reply. Best wishes, Smith

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Collection of articles from ISDSB2019 now published in IUCr Journals
by John R Helliwell 26 Feb '21

26 Feb '21

Dear Colleagues, A collection of articles from the International Symposium on Diffraction Structural Biology 2019 held in Osaka is now online in IUCr Journals at https://journals.iucr.org/special_issues/2021/ISDSB2019 Several of these articles are open access. Best wishes, Atsushi Nakagawa, John Helliwell and Yuriko Yamagata

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NCS/pseudo-symmetry
by Muhammad Bashir Khan 25 Feb '21

25 Feb '21

Dear All; *I collected data set which can be easily processed in a space grouop P21 (P1211)* *at approx 3.7A. I procedeed with MR using phaser in phenix which give a solution with two copies. * ** There were 8 solutions ** Pdb and/or Mtz files have been written with results for 1 of these solutions ** Solution #1 written to PDB file: Khan_phaser.1.pdb ** Solution #1 written to MTZ file: Khan_phaser.1.mtz Solution #1 annotation (history): SOLU SET RFZ=3.4 TFZ=4.2 PAK=0 LLG=15 TFZ==5.5 RFZ=2.8 TFZ=27.6 PAK=5 LLG=1173 TFZ==36.5 LLG=1210 TFZ==36.8 PAK=6 LLG=1210 TFZ==36.8 SOLU SPAC P 1 2 1 SOLU 6DIM ENSE ense_1 EULER 7.6 86.4 3.3 FRAC 0.20 0.00 0.18 BFAC -1.90 #TFZ==5.5 SOLU 6DIM ENSE ense_1 EULER 7.6 86.4 3.2 FRAC 0.05 0.00 0.51 BFAC 1.60 #TFZ==36.8 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0444 #RMSD 1.29 #VRMS 1.64 Solution #2 annotation (history): SOLU SET RFZ=3.0 TFZ=5.5 PAK=0 LLG=10 RFZ=2.7 TFZ=25.6 PAK=0 LLG=1165 TFZ==34.8 LLG=1198 TFZ==34.0 PAK=4 LLG=1198 TFZ==34.0 SOLU SPAC P 1 2 1 SOLU 6DIM ENSE ense_1 EULER 10.7 83.5 177.9 FRAC 0.24 -0.00 0.14 BFAC -3.15 SOLU 6DIM ENSE ense_1 EULER 169.3 96.4 357.9 FRAC 0.91 -0.00 0.52 BFAC 1.82 #TFZ==34.0 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0705 #RMSD 1.29 #VRMS 1.65 Solution #3 annotation (history): SOLU SET RFZ=3.4 TFZ=4.1 PAK=1 LLG=-1 RFZ=2.8 TFZ=34.6 PAK=1 LLG=1146 TFZ==39.7 LLG=1185 TFZ==39.2 PAK=3 LLG=1186 TFZ==39.2 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 8.2 86.4 2.0 FRAC 0.01 -0.00 0.01 BFAC -1.69 SOLU 6DIM ENSE ense_1 EULER 8.3 86.4 2.0 FRAC -0.14 -0.00 0.34 BFAC 1.72 #TFZ==39.2 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0406 #RMSD 1.29 #VRMS 1.64 Solution #4 annotation (history): SOLU SET RFZ=3.5 TFZ=5.0 PAK=6 LLG=13 RFZ=2.9 TFZ=30.5 PAK=6 LLG=1156 TFZ==34.4 LLG=1183 TFZ==33.6 PAK=7 LLG=1183 TFZ==33.6 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 359.5 82.0 2.7 FRAC -0.18 -0.00 0.47 BFAC -2.89 SOLU 6DIM ENSE ense_1 EULER 359.5 82.1 2.8 FRAC -0.02 -0.00 0.14 BFAC 2.57 #TFZ==33.6 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0529 #RMSD 1.29 #VRMS 1.64 Solution #5 annotation (history): SOLU SET RFZ=3.5 TFZ=5.0 PAK=6 LLG=13 RFZ=3.0 TFZ=29.0 PAK=6 LLG=1115 TFZ==34.1 LLG=1178 TFZ==33.6 PAK=7 LLG=1178 TFZ==33.6 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 359.9 80.8 0.7 FRAC -0.18 -0.00 0.47 BFAC -1.57 SOLU 6DIM ENSE ense_1 EULER 180.1 99.2 180.7 FRAC 0.34 0.50 0.20 BFAC 2.47 #TFZ==33.6 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0405 #RMSD 1.29 #VRMS 1.64 Solution #6 annotation (history): SOLU SET RFZ=3.5 TFZ=4.6 PAK=1 LLG=-0 RFZ=2.8 TFZ=36.2 PAK=1 LLG=1136 TFZ==35.0 LLG=1169 TFZ==34.6 PAK=1 LLG=1169 TFZ==34.6 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 359.2 83.0 1.5 FRAC 0.06 0.01 0.03 BFAC -2.58 SOLU 6DIM ENSE ense_1 EULER 359.2 82.9 1.4 FRAC -0.09 0.01 0.36 BFAC 2.08 #TFZ==34.6 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0869 #RMSD 1.29 #VRMS 1.66 Solution #7 annotation (history): SOLU SET RFZ=3.5 TFZ=4.6 PAK=1 LLG=-0 RFZ=2.8 TFZ=35.3 PAK=1 LLG=1122 TFZ==35.4 LLG=1149 TFZ==34.5 PAK=1 LLG=1148 TFZ==34.5 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 359.2 82.5 2.4 FRAC 0.06 0.01 0.03 BFAC -1.93 SOLU 6DIM ENSE ense_1 EULER 180.8 97.5 182.4 FRAC 0.78 -0.49 0.31 BFAC 2.44 #TFZ==34.5 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0809 #RMSD 1.29 #VRMS 1.65 Solution #8 annotation (history): SOLU SET RFZ=3.4 TFZ=4.1 PAK=1 LLG=-1 RFZ=2.8 TFZ=33.9 PAK=1 LLG=1083 TFZ==38.5 LLG=1146 TFZ==38.5 PAK=4 LLG=1146 TFZ==38.5 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 8.1 86.1 2.6 FRAC 0.01 -0.00 0.00 BFAC -1.77 SOLU 6DIM ENSE ense_1 EULER 8.1 86.2 2.6 FRAC 0.17 -0.00 -0.33 BFAC 1.66 #TFZ==38.5 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0762 #RMSD 1.29 #VRMS 1.65 CPU Time: 0 days 6 hrs 35 mins 53.63 secs ( 23753.63 secs) Finished: Tue Feb 16 23:27:36 2021 *Got the following warnings:* WARNINGS -------- ------------------------------------------------------------------------------------------ Warning: Intensity moments suggest possibility of twinning. Tests based on possible twin laws will be more definitive. ------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------ Warning: The composition you have entered gives a solvent content of 87%, which is extremely unlikely. You should increase the composition. After running xtraige for the .mtz, I get this warning about NCS Frac. coord. : 0.157 -0.000 -0.333 Distance to origin : 119.294 Height relative to origin : 33.056 % p_value(height) : 8.504e-04. Translational pseudo-symmetry is very likely present in these data. Be aware that this will change the intensity statistics and may impact subsequent analyses, and in practice may lead to higher R-factors in refinement. Upon an attempt at initial refinement with different stratageis, the R-fators are stuck at Start R-work = 0.5066, R-free = 0.5233 Final R-work = 0.4831, R-free = 0.4965 The question is that there is something that is not being recognized for example merohedral twinning or that the NCS/pseudosymmetry is not being addressed correctly. Any suggestions would be highly appreciated. Regards; 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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Postdoc position, Plant Hormone Transporting Membrane Proteins (Denmark)
by Bjørn Panyella Pedersen 25 Feb '21

25 Feb '21

Dear colleagues, We have an open postdoc position. 3 days left before deadline. Come joint us. Great working environment, World-class science. Good work/life balance. /Bjørn ----------------------------------- Postdoctoral position in Structure of Plant Hormone Transporting Membrane Proteins at Aarhus University, Denmark. online posting: https://tinyurl.com/MBGpostdoc We are looking for a highly skilled and motivated postdoc with an interest in working on plant hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins and an interest for plant biology. Starting date is negotiable. Funding is available through an ERC grant for at least 2 years of employment. An extension is possible for up to a total maximum of 4 years of employment as a postdoc. The position: The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of plant hormone-transporting membrane proteins as defined by the ERC project MUM-GROW (pedersenlab.dk). Exact project will be shaped out in dialogue with top runners. The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems, and the methods uses are primarily crystallography and cryo-EM. 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. - 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 https://international.au.dk/life/ for details. Aarhus University offers relocation service to international researchers. You can read more about it at https://international.au.dk/life/researcherscomingtoau/. Deadline: All applications must be made online (https://tinyurl.com/MBGpostdoc) and received by March 1st 2021.

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EMBO workshop on Molecular Neurobiology
by Janssen, B.J.C. (Bert) 24 Feb '21

24 Feb '21

Dear all, a gentle reminder of the upcomingEMBO workshop on "Molecular Neurobiology", a virtual meeting taking place on 21-25 May 2021. The deadline for registration, 28 February, is approaching fast. Only four days left. The virtual meeting brings together world leading scientists, group leaders and young researchers with a keen interest in the latest science occurring at the interfaces of structural biology, biophysics, molecular & cellular imaging and neuroscience. Given its cross-disciplinary nature, the meeting presents a broad overview of molecular neurobiology, ample opportunities for discussions and a sneak peek into the latest developments. See http://meetings.embo.org/event/20-molneuro for more information and application guidelines. Best wishes, Bert Bert Janssen Bijvoet Center for biomolecular research Utrecht University Padualaan 8, 3584 CH, Utrecht

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reminder - postdoc position at Astex
by Gabor Bunkoczi 23 Feb '21

23 Feb '21

Dear All, Just a quick reminder that Astex has an opening for a skilled post-doctoral researcher with an interest in software development. The aim of the project is to develop new methods for automated ligand fitting guided by experimental electron density/electrostatic potential maps, and will focus on locating, sharpening and classifying unmodelled regions of density, determining the identity of the binder using density shape and other physical properties derived from the surroundings, and subsequently fitting the molecule taking potential interactions with the environment into account. For more information about the position, please see the full advert: https://astx.com/wp-content/uploads/2021/01/SI-Post-Doc-2019-Mol-Sci-new-ad… Interested candidates should liaise with the HR department. For informal enquiries, please feel free to contact me directly. Best wishes, Gabor Bunkoczi Astex Therapeutics Ltd 436 Cambridge Science Park Cambridge CB4 0QA, UK This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately.

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Virtual Annual CCP4/APS Crystallographic School (2021) in the US
by Xu, Qingping 22 Feb '21

22 Feb '21

Dear Colleagues, We are pleased to announce the virtual annual CCP4/APS crystallographic school "From data collection to structure refinement and beyond" will be held on June 14-25, 2021 at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2021/index.php. Dates: June 14 through 25, 2021 (with a weekend break on June 19 and 20th) Location: Virtual/Remote The school comprises two parts: remote data collection workshop and virtual crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA at APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections - lectures, tutorials, and hands-on (interactive troubleshooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, contact info and other details can be found at the School website. Applicants: Graduate students, postdoctoral researchers and early-career faculty, along with commercial/industrial researchers are encouraged to apply. Only about 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 1st, 2021. To apply, visit https://www.ccp4.ac.uk/schools/APS-2021/application.php. Fees: There is no fee for attending the virtual school for the chosen applicants. We hope to see you at the school. Charles, Garib and Qingping

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Re: [phenixbb] Autosol help: FOM is great but map is trash
by Kay Diederichs 19 Feb '21

19 Feb '21

Hi Alex, I'm not a Phenix developer, but I have seen many cases like this, where reflections can be indexed with different cells, and one unit cell axis differs by a factor of 2. This just means that every second reflection (namely the odd one) along the reciprocal space direction corresponding to that axis is weak. It is not a priori clear which of the two choices is the best for structure solution and refinement. This depends on whether the weak reflections actually carry structural information (e.g. about tNCS with a translation close to 0.5), or whether they are a result of a crystal defect. It may sometimes happen that the crystal form is not suitable at all, since both choices don't refine well! Concerning P212121, P21212, P2122, etc: these are all primitive orthorhombic, and data processing alone cannot tell you which one is correct - they give identical data processing statistics. Typically, absent reflections along h00 0k0 00l should tell about screw axes, but in case of tNCS and two different cell choices the correct choice may not be obvious. Molecular replacement and subsequent refinement of all possibilities should help. Furthermore, contrary to what you write, it _is_ possible for all the orthorhombic space groups to account for reflections in both cell choices, so don't jump to conclusions too early. Just explicitly specify the (big or small) cell parameters in the data processing program of your choice! It may also help to try a different data processing package. Hope this helps, Kay Am 19.02.2021 um 04:28 schrieb phenixbb-request(a)phenix-online.org: > Message: 4 > Date: Thu, 18 Feb 2021 18:15:15 -0500 > From: Alex Johnson<algejohnson(a)gmail.com> > To:[email protected] > Subject: [phenixbb] Autosol help: FOM is great but map is trash > Message-ID:<6BE0A20E-F46B-482A-A675-22B685A2AFBE(a)gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Phenix team, > > I am attempting to phase a protein structure from SeMet-labeled crystals and have encountered some issues in using Autosol that appear unusual, as they have not been encountered by any members of my group. The short summary is that while I achieved great statistics from beam line collection and Autosol produces solutions with FOM (>0.4) from multiple crystals processed to ~2.4-3.0 A, the output maps are of poor quality and Autobuild can never build with Rfree <0.5. There is only one methionine for the ~30 kDa protein, but the crystals appear to have good anomalous signal with anomalous multiplicity >15 overall and delanon in the inner shell >0.5. There appears to be translational NCS and the dataset can be processed with good statistics in several space groups (P212121, P21212, P2122, etc) but this doesn?t solve the phase problem. The axis drops by half in processing in the P212121 versus P21212 space groups: from one crystal they are 48.37 101.56 110.39 90 90 90 (in P212121) and 101 > .62 48.35 55.19 90 90 90 (in P21212). > > If anyone in the community has encountered similar problems please let me know! I am all ears to any possible solutions and am also installing additional methionine for labeling but unsure whether this will overcome the other issues. > > Thanks, > > Alex Johnson > Postdoc, Kranzusch lab, Dana-Farber Cancer Institute > algejohnson(a)gmail.com <mailto:[email protected]> > > > > > >

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