December 2023 - phenixbb - phenix-online.org

unassigned densities
by Dmitry Semchonok 18 Dec '23

18 Dec '23

Dear colleagues, Is there a way to assign cryo-EM densities not included in the model sequence? Do you have any tools that can help? More closely, is there a way to screen the cryo-EM map + model, point out the unassigned densities, and provide the possible structures to fit in (e.g., water molecules, etc.)? Thank you. Kind regards, Dmitry

2 1

math behind beamstop_shadow_outliers
by Gao, Yunyun 14 Dec '23

14 Dec '23

Hi everyone, While I can find references for other outlier rejection options in scaling.outlier_rejction, there is none for beamstop_shadow_outliers. I am wondering what is the math behind z_lim_ac and z_lim_c. Another question would be: Does the same criteria also apply for the medium-resolution (e.g. 6-8 A) reflections? (like reflections under the beamstop support) Thanks! Best regards, Yunyun ------------------------------------ Yunyun Gao, Dr HARBOR Universitaet Hamburg Tel +49 (0)40 42838-3685

1 0

Bug in optimize weights
by Mark Saper 08 Dec '23

08 Dec '23

I am running build 5156 on macOS 13.6.1. I am refining a multi-molecule with imperfect NCS. When I tried to use "Optimize X-ray/sterochemistry" and "Optimize X-ray/ADP weight” the program aborted with an error during the first cycle. The error was: ====================== XYZ individual (reciprocal space) ====================== AttributeError I submitted a bug report via the internal bug report system. I would appreciate how to get around this problem. Should I try the previous stable version? Many thanks, Mark _____________________ Mark A. Saper, Ph.D. Visiting Professor Dept of Microbiology and Molecular Genetics Hebrew University Faculty of Medicine Associate Professor Emeritus of Biological Chemistry University of Michigan Medical School saper(a)umich.edu <mailto:[email protected]> | +972 52 815-0480

1 0

Reference model problem
by Luca Pellegrini 07 Dec '23

07 Dec '23

I am trying to use a reference model in real_space_refinement, but phenix stops with the message: “Cannot not restrain working model to self and a reference model simultaneously” (see below). The reference and working models are identical but bound to different ligands. As far as a I can see, all I am doing is adding the reference model in the input window and ticking the box for reference model restraints (phenix 1.21rc1-4985). Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK [cid:[email protected]]

2 1

Error 1.21rc1-5156 macOS and cross special position
by Xavier Brazzolotto 02 Dec '23

02 Dec '23

Dear Phenix developers, I have recently updated to macOS Sonoma and updated Phenix to the latest RC (1.21rc1-5156). I do have recent data where a residue gets a bit too close to its symmetric mate. In order to be able to start the refinement, I have to select the model interpretation option « allow_polymer_cross_special_position=True » In this case, the refinement process starts and does my 3 refinement cycles. However, the UI gives me a final error message stating that I have to enable the « cross-special position » (which is already True). The refined data are present (pdb, mtz, log, cif, eff, geo) but I do not get any analysis on these data. No _info.txt, no .kin files. The log ends with a « Sorry » If I deliberately move the faulty residue a bit out of its position (no more clashing with its symmetric mate) and NOT allow the cross-special position, then the refinement ends well with the correct final data analysis. Not a big deal per se, but but I suspect a small issue in the initiation of the analysis programs (Molprobity / King / etc…). Xavier

2 1

Re: [phenixbb] CCP4 Study Weekend 2024 - Early bird registration including standard student bursary deadline coming soon!
by Karen McIntyre - STFC UKRI 01 Dec '23

01 Dec '23

Dear all, Registration is open for the 2024 CCP4 study weekend entitled "Decision making in MX - how to be a productive structural biologist". This year we are focusing on decision-making in macromolecular crystallography: when to use what automated tool, how to interpret the output and when you need to get your hands dirty instead. The frontiers of crystallography now involve massive multi-crystal and multi-dimensional experiments. This means the more that you can leave to the automated pipelines, the more you can focus on the novel elements of your experiment. Sometimes those automated tools work, and sometimes they fail (but have maybe not told you exactly why or how). Sometimes they don't even exist. In that case, how can you return to the basics and develop new strategies to break down the barriers to publication? Once again, this year the CCP4 Study Weekend will be held as a hybrid event from the 3rd to 5th January 2024, enabling people to choose whether to attend in-person or virtually. The in-person event will be held at the East Midlands Conference Centre, Nottingham, UK. We would like to invite you to another iteration of the ever-popular CCP4 Study Weekend - to start the year 2024 with a lot of fresh ideas, new insights and (hopefully) new friends and contacts to boost. As always it will be an eclectic mix of bleeding-edge science, in-depth presentations, discussion panel, poster-sessions, hands-on tutorials and plenty of opportunities for social interactions including the ceilidh. For full details, programme, logistics and registration, please visit the Study Weekend website<https://studyweekend.ccp4.ac.uk/>. Important Key Dates: * Early bird registration final date: 19 November 2023; * Standard Student bursaries are open to all students registering during early bird period i.e. now until 19 November which cover the cost of registration plus one night accommodation; * Registration for in-person delegates closes 4 December 2023 (or earlier if in-person places sell out although you will be able to join the in-person waitlist). We hope to see you there! Scientific Organisers: Helen Ginn (Deutsches Elektronen-Synchrotron, DESY, Germany) Nick Pearce (Linköping University, Sweden) Clemens Vonrhein (Global Phasing Ltd, UK) Administrative Organisers: Karen McIntyre (CCP4, UK)

1 5

The experiment is still very much needed (though AlphaFold helps a lot)
by Tom Terwilliger 01 Dec '23

01 Dec '23

Hi Structural biologist colleagues! Our article that helps you make the case that the experiment is still very much needed is now out: https://www.nature.com/articles/s41592-023-02087-4 "AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination." Nature Methods (2023) Also, here is a video on the Phenix Tutorials YouTube channel that describes this analysis: https://www.youtube.com/watch?v=ugMPYdPo8Bc (I hope you will be happy to see that you and your structural biology colleagues get the credit for making AlphaFold possible at 2:35 in the introduction of this video! Keep up the fantastic structural biology work!) All the best, Tom T -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

2 1