- phenixbb - phenix-online.org

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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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 11 Mar '21

11 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 08 Mar '21

08 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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