- phenixbb - phenix-online.org

side-chain on special position.
by Aaron Oakley 02 Feb '18

02 Feb '18

Hello fellow Phenix-ers, I have a structure I am trying to finish in Phenix.refine The is one problem: a glutamate residue sitting on a crystallography 2-fold axis with partial occupancy (picture attached). This residue and its symmetry mate appear to take turns sitting at this position: filling the density leads to severe collision with its symmetry mate. Building the side-chain with occupancy 0.5 doesn’t seem to help, as the residue is pushed out of density during refinement. Any work-arounds? Thanks all, Aaron [cid:[email protected]]

3 4

phenix auto sharpen local sharpening masking artifacts?
by Oliver Clarke 01 Feb '18

01 Feb '18

Hi, I’m trying to run phenix.auto_sharpen with local sharpening, because I have an EM map that has a reasonably substantial variation in local resolution. This is the command I used: phenix.auto_sharpen cryosparc_exp001049_008.mrc resolution=3.26 local_sharpening=true local_aniso_in_local_sharpening=true model.pdb nproc=4 seq_file=seq.fasta >& log & The resulting map looks beautiful (maybe a little too beautiful??) around the model, but shows some funky looking masking artifacts in the density further away from the model (in the micelle region) - see screenshot. Am I doing something wrong? And can I trust that the density is completely free of model bias? Cheers Oli

2 3

Unwanted LINK Records
by Whitley, Matthew J 26 Jan '18

26 Jan '18

Hello all, I am currently refining a structure using Phenix 1.13-2998. Present in this structure is a diphosphate-containing ligand. In the protein chain surrounding the binding site, there is an arginine side chain that points generally toward the diphosphate group, but I cannot define the specific location of the side chain because the side chain density is very poor. The density for the ligand is unambiguous. Upon refinement, Phenix places the Arg side chain so close to the ligand that it draws a covalent bond between the two, and the post-refinement PDB file contains a LINK record for this bond. In reality, the two are not covalently connected, and ideally Phenix would find a conformation for this side chain that is outside of covalent bonding distance. I have tried refining after manually moving the side-chain to a non-clashing position multiple times, but in every case the output PDB contains a LINK for a covalent bond between ligand and side chain. My question: How can I tell Phenix NOT to allow these atoms to come with covalent bonding distance? Is there some kind of "anti-LINK" information I can feed it that will force phenix.refine to select some other conformation for the side chain? Thanks for your advice. Sincerely, Matthew Whitley --- Matthew J. Whitley, Ph.D. Research Instructor Department of Pharmacology & Chemical Biology University of Pittsburgh School of Medicine

3 2

Open Research Positions: Structural Biophysics of Protein Allostery, in New York City
by Daniel Keedy 26 Jan '18

26 Jan '18

The Daniel Keedy Lab at the ADVANCED SCIENCE RESEARCH CENTER (ASRC) AT CUNY in New York City has available positions for a POSTDOCTORAL SCHOLAR and a LABORATORY TECHNICIAN starting in 2018. The lab’s goal is to elucidate the role of protein flexibility in allosteric regulation — and to use that knowledge to control the function of dynamic, biomedically important enzymes such as tyrosine phosphatases. To do so, we combine cutting-edge experimental and computational techniques in structural biology, including multitemperature X-ray crystallography, high-throughput protein:ligand structure determination, and new algorithms for modeling alternative protein conformations based on electron density maps. REQUIREMENTS FOR THE POSTDOCTORAL SCHOLAR POSITION: a PhD in structural biology, biophysics, computational biology, or a related field; multiple years of experience studying proteins or other macromolecules; and excitement to try new techniques at both the bench and the keyboard. Familiarity with X-ray crystallography, a programming language, and the command line are preferred. REQUIREMENTS FOR THE LABORATORY TECHNICIAN POSITION: an MS, BS, or similar degree in biochemistry, molecular biology, or a related field; experience conducting research in a laboratory setting; and excellent organizational and communication skills. Experience with cloning, protein purification, and/or X-ray crystallography are preferred. OFFICIAL APPLICATIONS: For the postdoctoral scholar position, please apply here: https://cuny.jobs/new-york-ny/research-associate-structural-biology-advance… For the laboratory technician position, please apply here: https://cuny.jobs/new-york-ny/research-assistant-laboratory-technician-stru… ABOUT THE ASRC: The ADVANCED SCIENCE RESEARCH CENTER (ASRC) at the Graduate Center of the City University of New York (CUNY) elevates scientific research and education at CUNY through initiatives in five distinctive, but increasingly interconnected disciplines: STRUCTURAL BIOLOGY, NANOSCIENCE, PHOTONICS, NEUROSCIENCE, and ENVIRONMENTAL SCIENCES. The ASRC promotes a collaborative, interdisciplinary research culture with researchers from each of the initiatives working side-by-side in the ASRC’s core facilities, sharing equipment that is among the most advanced available. The ASRC is next-door to the cutting-edge inter-institutional NEW YORK STRUCTURAL BIOLOGY CENTER (NYSBC), and is also just 70 miles from the newly-constructed NATIONAL SYNCHROTRON LIGHT SOURCE II (NSLS-II), now the brightest synchrotron light source in the US. — Daniel A. Keedy, Ph.D. Assistant Professor Structural Biology Initiative, CUNY Advanced Science Research Center Department of Chemistry and Biochemistry, City College of New York Biochemistry and Chemistry Ph.D. Programs, CUNY Graduate Center http://www.keedylab.com // daniel.keedy(a)asrc.cuny.edu<mailto:[email protected]> // 212-413-3246

1 0

Amber force field for phenix.real_space_refinement?
by Sebastian Eustermann 24 Jan '18

24 Jan '18

Dear All, I just wondered whether/how one can use the Amber force field also for phenix.real_space_refinement? I tried “use_amber=True” as it is implemented for phenix.refine but that option does exists for phenix.real_space_refinement … Thanks for your help BW Sebastian -------------------------------------- Sebastian Eustermann, PhD Gene Center LMU Munich, Germany

2 1

phenix.auto_sharpen expected filtration of input map
by Ricardo Righetto 24 Jan '18

24 Jan '18

Hi, So far I have liked very much the results of phenix.auto_sharpen, but one thing is not yet clear to me: how does it expect the input map to be filtered? Would be something like: a) Unsharpened, unfiltered map (e.g. the simple average of the half-maps) b) Unsharpened, SSNR-weighted (Cref) (Rosenthal & Henderson, JMB 2003) c) Doesn't matter / other? Thanks in advance! Best wishes, -- Ricardo Diogo Righetto

2 2

Error with Phenix refine after adding ligand
by Mian-Chee Gor 23 Jan '18

23 Jan '18

Hello all, I run into this problem when I tried to refine my protein structure after adding ligand. The ligand that I am adding is a malonate, and the 3-letter chemical code is MLI. I add the ligand using Coot and it fit perfectly into the electron density map. I then tried to run phenix.refine by giving the protein structure pdb file, the original mtz file and the protein sequence fasta file. However, there was an error message saying missing restraints for the ligand. So I generate the CIF file for the ligand using the Ready Set icon in the toolbar. The ligand CIF file and a updated protein structure pdb file was generated and automatically added to the refinement windows. However, when I run the refinement, I saw this error message: Number of nonbonded interaction distances <0.001:2. Please inspect the output above (or in the log window) and correct the input model file. When I inspect the log window, the error is due to the oxygen atoms in the ligand being too close to each other. Why is there an error if the ligand was generated automatically in Phenix? Has anyone encounter this problem before? How do you solve that? Many thanks in advance! -- Dr Mian-Chee Gor Research Fellow Griffith Institute for Drug Discovery (GRIDD) Don Young Road, Nathan, QLD 4111 Mobile: +61 4 2084 7785 Email: m.gor(a)griffith.edu.au

3 2

Neutron diffraction protein refinement with Phenix
by Rex Palmer 22 Jan '18

22 Jan '18

I would like to contact someone based in or near London whois familiar with Phenix refinement of neutron diffraction protein structures and interpretation of the results. Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://www.springer.com/978-1-4641-3954-7

2 1

secondary structure presentation in VMD
by CPMAS Chen 22 Jan '18

22 Jan '18

Hi, Phenix users, This may be a little off-topic. I have posted this in VMD users mail list. I want to try here too to see if anyone experienced similar issue. VMD and pymol gave different presentation on the secondary structure of a protein. During phenix.refinement, I added secondary structure restraints and correctly labelled all helices and sheets. However, VMD does not correctly present the secondary structure in cartoon/new-cartoon presentation. A little more detail. In VMD-1.9.4a12, after I loaded the pdb, I chose new cartoon to present the secondary structure. All chains are presented as random coil, the same as tube representation. However, pymol correctly shows the secondary structure of the same pdb file in cartoon representation. Has anyone encountered similar situation? what would be the fix? Thanks! Best Regards, Charles -- *************************************************** Charles Chen Research Instructor University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

3 3

Refining a neutron structure
by Rex Palmer 19 Jan '18

19 Jan '18

When refining a neutron structure with Phenix why would the program appear to think it was an X-ray structure? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://www.springer.com/978-1-4641-3954-7

2 1