February 2017 - phenixbb - phenix-online.org

protein atom selection
by wtempel 03 Feb '17

03 Feb '17

Hello all, in my hands and to my surprise, PHENIX atom selections such as "protein" or "peptide" would include a co-factor like SAM. Did others notice that also? Is this behavior what most users would want or even expect? Best regards. Wolfram Tempel

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Refine a structure with a disconnected region
by Yasser Almeida Hernández 02 Feb '17

02 Feb '17

Hi all, I am refining a structure at 1.9A, which contains a 7 residues C-terminal region. The resolution of the map in that region is low but is clear enough to define some side chains and the backbone. I build this region manually in Coot. This region is disconnected from the core of the protein, since the connecting loop cannot be seen in the density map. After running phenix.refine (GUI) and playing with the options several times, the final model of this region is always out of the … [View More]

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10th CCP4/APS Crystallographic School in the USA
by Sanishvili, Ruslan 01 Feb '17

01 Feb '17

Dear Colleagues, We are pleased to announce the 10th annual CCP4 crystallographic school “>From data collection to structure refinement and beyond”, held at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2017/index.php Dates: June 19 through 26, 2017 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop: beamline training;… [View More] data collection on GM/CA@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 trouble-shooting 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 http://www.ccp4.ac.uk/schools/APS-school/publications.php Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 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 19. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2017/index.php Registration fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation, lodging and breakfast. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses. We hope to see you at the school. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov [View Less]

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Announcement: Phenix tutorial videos
by Dorothee Liebschner 31 Jan '17

31 Jan '17

Dear Phenix users, Video tutorials about Phenix tools are now available on the Phenix Tutorial YouTube channel <https://www.youtube.com/channel/UCcdI0hfHngWAZLJWynxPQWg>. The videos give a short introduction about a Phenix tool, summarize the required input files and parameters, explain how to run it and – when appropriate – discuss the results. So far, the following topics are covered: - How to run phenix.refine - How to calculate polder maps - How to run phenix.… [View More]

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