- phenixbb - phenix-online.org

hi please unsubscribe me
by Zhenwei Su 27 Feb '18

27 Feb '18

-- Zhenwei Su 4417 Spruce Street, APT 3A Philadelphia, PA 19104 email: zwsuustc(a)gmail.com cell phone: (608) 698-4156

1 0

hi please unsubscribe me
by Zhenwei Su 27 Feb '18

27 Feb '18

-- Zhenwei Su 4417 Spruce Street, APT 3A Philadelphia, PA 19104 email: zwsuustc(a)gmail.com cell phone: (608) 698-4156

1 0

Issues with refinement of cadmium
by Mohammad Khan 27 Feb '18

27 Feb '18

Dear all, I am trying to fit Cd ion in a protein structure using Phenix. However, the refinement transposes CD to DC and returns me a result with DC ( 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE) in the validation report and gives me the missing atoms accordingly. When I open the same structure in Coot, it shows me the ion Cd. Also, the .pdb file contains Cd. Cd is present in my crystallization condition and fits well into the density. Other metal atoms such as Zn and Cl have refined well. HETATM 5535 CD CD F 1 156.533 -64.594 138.360 1.00 76.11 CD HETATM 5536 CD CD F 2 119.954-111.545 105.562 1.00 35.85 CD HETATM 5537 CD CD F 3 152.936 -93.077 102.747 1.00 28.68 CD HETATM 5538 CD CD F 4 121.467 -96.375 128.574 1.00 72.24 CD Can someone suggest what may be wrong? Thanks in advance!

3 2

[Feature request] Exclude atoms outside user provided mask from refinement (in phenix.real_space_refine)
by Oliver Clarke 26 Feb '18

26 Feb '18

Hi, Often I would like to refine part of a model against a EM map generated by masked refinement. Such a map is typically better than the globally refined map in the region within the mask, and worse outside it. It would be useful to have the capacity to refine the same model first against the globally refined map, and then against the maps generated by masked refinement, but restricting refinement in the latter case to atoms/residues within the bounds of the mask. Is this something that could be maybe added in a future version of phenix.real_space_refine? This would mean allowing the user to provide a mask file, and setting an option to exclude all atoms/residues outside the mask boundaries from refinement. Cheers Oli

1 0

refining a covalent-bound ligand
by Sebastiano Pasqualato 26 Feb '18

26 Feb '18

Hi there, I have a pretty basic question. I am refining a structure in which a drug has been covalently linked to a Cys of the protein. I have generated the .cif fie for the ligand, but I don’t know how to tell the program that carbon C04 has to be covalently linked to the SG of the Cys. Is that sufficient to insert a LINK record in the pdb file? What is the correct syntax for that? Thanks a lot for the feedback and sorry for the naive question, ciao, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEOXtalUnit

5 5

Information regarding Anisotropic atoms
by pooja kesari 22 Feb '18

22 Feb '18

I observed that phenix.refine tool is adding anisotropic atoms to the pdb file by default even at resolution more than 2A. Can anyone please suggest why is it doing so?

2 1

lattice symmetry and free-set selection?
by Edward A. Berry 22 Feb '18

22 Feb '18

Where can I find description of the free-r selection parameters: refinement.input.xray_data.r_free_flags { lattice_symmetry_max_delta=5 use_lattice_symmetry=True } ?

1 0

Industrial Biostructures America 2018 conference
by Leonard,Paul G 20 Feb '18

20 Feb '18

Dear all, The inaugural Industrial Biostructures America conference will be held on 20-22 May 2018 at the Hilton La Jolla Torrey Pines Hotel in San Diego, California. Conference registration and accommodation information is available at: https://industrialbiostructuresamerica.org/ This conference brings together structural biologists from across the pharmaceutical and biotech industry to showcase their cutting-edge research. Scientific sessions will cover the following topics: * Cryo-EM * X-ray crystallography * Lead discovery using NMR * Protein design * Membrane crystallography The Abstract submission deadline is 23rd March 2018. We look forward to seeing you there, Paul Leonard Institute Research Scientist MD Anderson Cancer Center pleonard1(a)mdanderson.org<mailto:[email protected]> 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.

1 0

BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY
by Salbego, Cyndi 18 Feb '18

18 Feb '18

BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE TWO ID BEAMLINES OF NE-CAT AT APS. We currently have a number of days open in March. Below is a brief description of our beam lines, and links with more information. The 24-ID-C beamline can deliver X-rays in the range of 6 to 21 keV or ~2.1 to 0.5 Å. This covers most of the popular elemental edges for phasing. This wide energy-range also makes the beamline well suited for ultra high-resolution data collection and soft X-ray sulfur SAD phasing. The beamline is equipped with an optional kappa goniometer for optimal alignment of crystals. A Pixel Array Detector (PAD), Pilatus-6MF, installed on the 24-ID-C beamline helps measure very weak Bragg reflection intensities due to its noise-less readout technology and also provides a very fast data collection capability in shutter-less data collection mode. The 24-ID-E beamline is a fixed energy microdiffraction beamline delivering X-rays at 12.66 keV, optimized for Se-SAD experiments. It is equipped with an Eiger-16M Pixel Array Detector, offering advantages similar to those of the Pilatus-6MF. For more information on our beamlines (beamline and robot manuals): http://necat.chem.cornell.edu To ask about available time please contact Raj Rajashankar (rajashankar(a)anl.gov<mailto:[email protected]>) or Cyndi Salbego (csalbego(a)anl.gov<mailto:[email protected]>) for further information. To apply for General User Time (Rapid Access for current run cycle) please follow this link: https://beam.aps.anl.gov/pls/apsweb/gup0005.start_page Cyndi Salbego Administrator, NECAT 630.252.0689

1 0

9th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 14 Feb '18

14 Feb '18

First announcement 9th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 11 - June 15, 2018 Detailed information: https://conference.sns.gov/biologyneutrons18/ Application deadline: April 30, 2018 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Flora Meilleur, Ph. D Associate Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Scattering Scientist, Neutron Sciences Directorate Oak Ridge National Laboratory

1 0