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Final reminder: 11th CCP4/APS Crystallographic School in the US June 18 through 25, 2018
by Qingping Xu 16 Apr '18

16 Apr '18

Dear Colleagues, This is a reminder for the upcoming CCP4/APS school. The deadline for registering is coming up soon, please register if you plan to attend. Thanks. Charles, Garib and Qingping ====original announcement ==== Dear Colleagues, We are pleased to announce the *11th annual CCP4 crystallographic school *“From data collection to structure refinement and beyond” will be held on June 18-25, 2018 at Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at http://www.ccp4.ac.uk/schools/APS-2018/index.php. *Dates*: June 18 through 25, 2018 *Location*: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: *data collection workshop* and *crystallographic computing workshop*. Data collection workshop includes beamline training, 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 (see 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 *Wednesday May 2nd, 2018*. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2018/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 and lodging. The workshop organizers can assist in making the lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, Garib and Qingping

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Running on Windows 10
by Plínio Salmazo Vieira 15 Apr '18

15 Apr '18

Dear all I'm having issues on running Phenix. It installs smoothly (I downloaded the point-and-click 64-bit version), but when I try to open, the prompt writes very fast and closes by itself. I tried installing and running on administrator mode and on compatibility mode for Windows 7, but still no good. Below are my laptop configuration: Processor: Intel Core it-7500U CPU @ 2.70 GHz 2.90 GHz RAM: 8 GB System: Operational based on 64 bits, processor x64 Please, could anyone help me? Any guesses? If you need any more information, let me know. Best Regards, Plínio. -- Dr. Plínio Salmazo Vieira Laboratório Nacional de Ciência e Tecnologia do Bioetanol Centro Nacional de Pesquisa em Energia e Materiais Campinas - São Paulo

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Polder comment
by Patrick Loll 14 Apr '18

14 Apr '18

What does it mean when a Polder map calculation finishes with the comment "The polder map is more likely to show bulk-solvent or noise instead of the ligand” ? Thx, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pjloll(a)gmail.com pjl28(a)drexel.edu

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Unflagging accidental "Mark as Failed" in GUI
by Shane Caldwell 13 Apr '18

13 Apr '18

Hi phenixbb, I have a mostly inconsequential and hopefully simple problem to solve, but I can't find info about it online. I accidentally flagged a good run as "failed" in the Phenix GUI, and I can't figure out how to remove that tag. It's possible I'm overlooking something extremely obvious and if so apologies for the spam. How can I reset this marker? Shane Shane Caldwell shane.caldwell17(a)gmail.com

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AsCA 2018/CRYSTAL 32: Registration Open!
by Christopher Squire 11 Apr '18

11 Apr '18

? [https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-pub…] Dear Colleagues, Registration for the AsCA 2018/CRYSTAL 32 Conference (2 - 5 December 2018 at the University of Auckland, New Zealand) is now open! Please follow this link to register http://asca2018.org/registration/ Workshop registration is not yet open, however please use the voting function here<http://asca2018.org/workshops/> to advise which of the four potential workshops would be of most interest to you. Finally, a reminder that submissions are now open. Please visit the Call for Abstracts<http://asca2018.org/call-for-abstracts/> page for more information and to submit an abstract. Should you have any queries regarding the AsCA 2018/CRYSTAL 32 Conference, please do not hesitate to contact us using the email address listed below. Kind regards, Event Services University of Auckland Email: asca2018(a)auckland.ac.nz<mailto:[email protected]> [https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-pub…]

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Phenix video tutorials
by Dorothee Liebschner 10 Apr '18

10 Apr '18

Dear Phenix users, This is an update for the Phenix video tutorials. There are now 25 videos, explaining Phenix tools for X-ray crystallography and cryo-EM. New videos include topics such as model and data validation (Xtriage, Molprobity), phasing (Phaser, AutoSol) and tools for cryo-EM. A categorized overview is on the phenix homepage: https://www.phenix-online.org/documentation/reference/tutorial_channel.html You can also browse the videos directly on the Phenix Tutorial YouTube channel: https://www.youtube.com/c/phenixtutorials (To see subtitles, hit the cc (closed captions) button in the right bottom of the video screen. Subscribe to see the tutorial videos in your YouTube subscription feed. To get notifications about new videos, tap the bell button, which is next to the "subscribe" button.) Feedback about the videos is very welcome. Write an email to tutorials(a)phenix-online.org or use the comment section on YouTube. If you want to see a tutorial about a certain (Phenix-related) topic, don't hesitate to tell us. Best wishes, The Phenix team

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9th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 09 Apr '18

09 Apr '18

Second announcement 9th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 11 - June 15, 2018 Travel and accommodation expenses are supported for selected participants. No registration fee. Detailed information can be found on the workshop web page: 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 Neutron Scattering Scientist, Neutron Sciences Directorate Oak Ridge National Laboratory Associate Professor, Molecular and Structural Biochemistry North Carolina State University

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FW: Announcement of European Crystallographic Computing Forum 2018 in Mieres, Spain
by Tom Terwilliger 09 Apr '18

09 Apr '18

Registration for the European Crystallographic Computing Forum is open: https://www.mrc-lmb.cam.ac.uk/harry/ecacomsig/mieres.html A poster for print can be downloaded here: https://we.tl/CyPFzYvorG Spread the word! The Forum will be held in Mieres, Spain, 18th - 22nd August 2018 (preceding the ECM). We invite both beginners (from graduate level) and experienced software developers from all crystallographic disciplines. Participants can bring their own software development project to work on it in teams, interspersed with tutorials and lectures. There will be opportunity to exchange and connect with other crystallographic software developers. The registration fee (360 €) includes: accommodation (4 nights), full board and refreshments and transfer to the ECM. We offer childcare and family rooms. Bursaries are available. We hope to see you there! The Organisers Andrea Thorn, Harry Powell, Laura Roces Fernandez We would like to thank our kind sponsors! - CCP4 - Dectris - Rigaku - Bruker -

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TaBr SAD Autosol and Phaser
by Ian S 09 Apr '18

09 Apr '18

Hi Phenixbb, I trying to phase a structure soaked in TaBr and am running into some technical problems. My anomalous signal goes out to about 4.5 and I have a 1.9A native data set. SIR hasn't worked so far. Autosol SAD has given me several convincing solutions when searching for Tantalum (not TX), finding 11 sites (not clustered) at 6 angstroms: FOM =0.478, map=0.1.3, and corr of 0.82 and a final score of 37+-15.71. By only playing around with the sites I can get an overall score of 73 +- 4.58, map skew to 0.5, and a RMS density to 0.79, thought the R-factor increases to .43 and the FOM . Perhaps not suprisingly at this resolution, the map is uninterpretable (maybe some helices) so I'm trying to improve the phases by model building and by using Phaser and giving it TX sites. If I put the Ta sites in Phaser with the same dataset as Autosol, I get a FOM of .342. If I use the TX label it drops to 0.143. What is happening here? I know that typically TaBr has one or two major sites (my protein isnt massive, only about 1200 aa predicted in the ASU) , so I use only the top two major sites and have the same problem. Does this indicate that the Ta sites Autosol found are not in fact the sites I'm looking for? Or maybe that there really are 10 TaBr sites all with low occupancy? Any suggestions would be appreciated. Thank you. Best, Ian

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linking only one conformer to a thiol
by Krzysztof Bzymek 06 Apr '18

06 Apr '18

Hi, I'm trying to refine a structure with a disulfide bond between a cysteine and a thiol-containing peptide. There are two conformations for the thiopeptide, in one of them the thiol is facing away from SG of the cysteine (~7 A away). I defined the link as: refinement.pdb_interpretation { apply_cif_link { data_link = DRG-CYS residue_selection_1 = chain A and resname DRG and resid 10 residue_selection_2 = chain B and resname CYS and resid 20 } } I also tried: refinement.pdb_interpretation { apply_cif_link { data_link = DRG-CYS residue_selection_1 = chain A and resname DRG and resid 10 and altloc A residue_selection_2 = chain B and resname CYS and resid 20 } } After refinement (with a corresponding data_link.eff file defining the bonds and angles), the thiol of the other conformer that was facing away from the cysteine moves out of the electron density and now faces the cysteine (still about ~5.7 A away). Is there a way to define a link between only one conformer and have the other refine independently? I did try refinement without the above link definition (relying on the proximity of the two cysteines and automatic linking in phenix) but some of the bond and dihedral angles showed higher deviation from ideal values expected for disulfide bonds. Thanks, Chris

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