June 2019 - phenixbb - phenix-online.org

r_work and r_free from an .mtz file containing Fobs and Fcalc
by Andre LB Ambrosio 01 Jul '19

01 Jul '19

Dear colleagues, Can Phenix calculate r_work and r_free from a .mtz file containing FP and FC_ALL (from PDB_REDO), without inputing the matching .pdb file? Many thanks in advance, -- Andre LB Ambrosio

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PEG as a polymer
by Felix Cat 30 Jun '19

30 Jun '19

Hi all, I'm working on a structure where I see extensive interaction of the protein with PEG (polyethylene glycol). The largest PEGs I can find in structures in the PDB with a quick search are around 12 EDO subunits long, and they're called "dodecaethanediol" or the like. I am seeing at least 20. Currently, I've built the PEG as a giant, single ligand, and generated a viable cif file for it using eLBOW with a SMILES string (very simple for PEG, you can imagine). I'm wondering if I might rather be able to handle it as a polymer of EDO subunits. I started to dig into that but got lost pretty quickly. I can't figure out how to create an automatically link-able EDO molecule, all with proper geometry, and I don't want to have to tell phenix.refine about 19+ custom linkages every time. (I've had to do that with N-linked acetylglucosamine moieties in the past.) Nate NUNC

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Real space refinement with helical symmetry
by Yangqi Gu 29 Jun '19

29 Jun '19

Hi all, I am trying to do a real space refinement with phenix and my map is a filament and I have monomer model and I would like to refine against my filament map. I am wondering how to impose the helical symmetry in this case? (I have a pseudo filament model by copying multiple subunits and aligned in Chimera using "fit in map"). Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

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CaBLAM fixing and interpretation in comprehensive validation for cryo-EM
by Ahmad Khalifa 28 Jun '19

28 Jun '19

Hello, I would appreciate some insights on how to interpret the validation results under the CaBLAM tab and how to use it to fix my structure in Coot? What are the CaBLAM score, the Ca geometry score, the helix score and the 3-10 score? How to use the information under the secondary structure tab? In my protein for example, I see a lot of "try beta sheets", should I try to refine that segment using beta sheets restraints? Best regards.

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(no subject)
by Pu Qian 28 Jun '19

28 Jun '19

Hi All I have a problem to do refinement for one of our cryo-em model caused by ligand of spirilloxanthin (wwPDB code CRT). I'm using phenix cryo-EM real-space refinement for one of my cryo-em models which contains a ligand called spirilloxanthin, a very common carotenoid molecule found in nature. Its code is CRT which can be found in wwPDB ligand dictionary and in COOT. However, when I run real-space refinement, I got a error message caused by this ligand "Fatal problem interpreting model file: Number of atoms with unknot non bonded type symbols: xxx please edit the model file to resolve the problem and /or supply a cis file with matching restrain definitions, along with apply_cif_modification and apply-cis-link parameter definitions if necessary". I checked my pdb file. All atom names and order are exactly same as that in wwPDB. I also try to insert it into map using COOT monomer find method. It does not work as well. It seems to me that Phenix can not recognise this ligand, CRT spirilloxanthin. Does anyone have an idea of how to deal with this issue. Or is it OK if I add CRT.cif into upload window of Phenix for refinement? Any suggestion is greatly appreciated. The version of Phenix I am using is Mac version recently downloaded from Phenix website. Best regards

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Position Opening: Synchrotron Macromolecular Crystallographer @ IMCA-CAT
by Lisa J. Keefe 28 Jun '19

28 Jun '19

Dear Colleagues, POSITION: Synchrotron Macromolecular Crystallographer LOCATION: IMCA-CAT at the Advanced Photon Source (near Chicago, IL) The Industrial Macromolecular Crystallography Association - Collaborative Access Team (IMCA-CAT) and the Hauptman-Woodward Medical Research Institute (HWI) seek an inventive macromolecular crystallographer to join the IMCA-CAT team in accelerating pharmaceutical drug discovery through synchrotron-based structural biology research. As an employee of HWI, you will be based at the center of the team’s operations at the Advanced Photon Source (APS), Argonne National Laboratory, near Chicago, IL. This is an ideal position for a motivated scientist who is passionate about delivering strategic value, developing new technologies, and working in a high- powered, collaborative environment. DESCRIPTION: This is an exciting time to join IMCA-CAT. Underway this summer is the first of a two-phase upgrade that will significantly increase throughput and establish a strong foundation upon which to build capacity. The second phase upgrade, currently in design, will profoundly increase capacity and dramatically expand capability for challenging research projects. The successful candidate will be an integral part of these upgrade activities while maintaining flow of diffraction data for pharmaceutical research projects. The candidate will work closely with IMCA-CAT colleagues in an inclusive and respectful environment, and is expected to take initiative and contribute to the team effort. On any given day, you will do one or all of these things: • Contribute to drug discovery research efforts using a growing portfolio of synchrotron sources. • Enhance the structural biology programs for pharmaceutical structure-based drug design. • Provide experiment support for scientists from the structural biology community who conduct research using the IMCA-CAT synchrotron beamlines. • Ensure beamline instrumentation is operational and produces data of the highest quality. • Expand the experiment envelope of the beamline. • Establish efficient protocols for accelerating data acquisition while enhancing data security. • Develop automated methods for acquiring quality data from challenging samples. • Participate in highly collaborative working groups. • Engage in the technical development of new strategies for ultra-high throughput. • Collaborate with staff on strategically-aligned research and development projects. • Communicate with researchers and present at meetings. • Conduct independent and/or collaborative research. DESIRED SKILLS and EXPERIENCE: • PhD in a relevant field. • Expertise in macromolecular crystallography. • Outstanding experimental skills. • Considerable mechanical skills. • Highly collaborative and team-oriented approach to conducting work and solving problems. • Excellent written and oral communication skills. • Deeply proactive approach to meeting and exceeding goals. • Ability to meet requirements for site access to Argonne National Laboratory. TO APPLY: Send an introductory email, cv, and contact information for three references to Lisa Keefe, IMCA-CAT Director and HWI Vice President of Advancing Therapeutics, at keefe(a)imca-cat.org. LEARN MORE: Visit our websites to learn more about IMCA-CAT (www.imca-cat.org) and HWI (www.hwi.buffalo.edu). HWI is an equal opportunity employer. Lisa J Keefe, PhD Director IMCA-CAT <http://www.imca-cat.org/> Industrial Macromolecular Crystallography Association - Collaborative Access Team 630.252.0544 • Sector 17 @ Advanced Photon Source, Argonne National Laboratory Vice President for Advancing Therapeutics Hauptman-Woodward Medical Research Institute <http://hwi.buffalo.edu/> Past-President American Crystallographic Association <http://www.amercrystalassn.org/> .

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Copying mtz file
by Cygler, Miroslaw 25 Jun '19

25 Jun '19

Hi Phenixers, I have copied mtz file to a new file with a lower resolution limit using the "Reflection file editor” tool. I copied all arrays to the output file. When I attempted to continue refinement with the new mtz file, a message appears saying that there are no R-free flags in the mtz file. Yet, the new file contains the R-free-flags column but the values are inverted, 1 is changed to 0 and 0 is changed to 1. In the output option dialog the box “Preserve original flag values” was checked. How to fix this? Thanks, Mirek

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Why the correlation coefficient of the electron density with the model is never 1?
by Murpholino Peligro 24 Jun '19

24 Jun '19

The links below show a plot of the results of phenix.real_space_correlation* for a nice lisozyme crystal and also the coot view. https://drive.google.com/open?id=0B9tqXyDsq9YIdkRhcVFXU2dEdnhINXR6Y3hza2Y5N… https://drive.google.com/open?id=0B9tqXyDsq9YIREd1OFZhNGZtRnN4aldtVU1mdk84N… As you can see the electron density fits very well the model. Why not a single residue gets a perfect correlation coefficient? (i.e. 1) Just curious. Thanks * phenix.real_space_correlation pdbfile mtzfile --detail="residue" > outpu

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New bug in phenix.refine
by Aaron Oakley 23 Jun '19

23 Jun '19

Phenix.refine used to be able to handle a ligand covalently bound to cysteine if an appropriate cif dictionary was provided. This now seems to be broken. Re-running a job that used to work now fails. KeyError : 'link_CYS-MPS' Traceback: File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/libtbx/runtime_utils.py", line 180, in run return_value = self.target() File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/libtbx/runtime_utils.py", line 75, in __call__ result = self.run() File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/runtime.py", line 79, in run refine_object = self._run(args, callback) File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/runtime.py", line 92, in _run call_back_handler=callback) File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/command_line.py", line 106, in run log=log) File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/driver.py", line 224, in __init__ run_clash_guard=False) File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/model/model.py", line 1124, in setup_restraints_manager assume_hydrogens_all_missing = not self.has_hd()) File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5509, in geometry_restraints_manager log=self.log) File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5154, in construct_geometry_restraints_manager log=log, File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/monomer_library/linking_mixins.py", line 751, in process_nonbonded_for_links origin_id = origin_ids['link_%s' % key] File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/cctbx/geometry_restraints/linking_class.py", line 35, in __getitem__ raise e

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Refining alternate conformation of duplex DNA
by ABHISHEK SUMAN 20 Jun '19

20 Jun '19

Hello All, I am solving a X-ray crystal structure of protein-DNA complex at 2.3 Angs. In my structure, it seems like the the duplex DNA is bound in two different conformations, and both the conformations are occupied in same density. I wish to know how to refine the alternative conformations of the DNA duplex in Phenix. In am using Phenix GUI. Thanks Abhishek *______________________________________________* *Abhishek Suman* *Research Scholar, PhD* C/o, Dr. Rajakumara Eerappa Macromolecular Structural Biology Group Department of Biotechnology R# 517,315, Academic Block - A Indian Institute of Technology Hyderabad Kandi 502 285 Sangareddy Telangana INDIA Contact: +91 91002 74548 (O) +91 80843 11898 (R) Email: abhisheks.iith(a)gmail.com ----------------------------------------------------------------- *Please don't print this e-mail or attachment unless necessary. Preserve trees on the planet.*

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