November 2019 - phenixbb - phenix-online.org

problems running refinement of shaken model against half map
by L. Hielkema 23 Nov '19

23 Nov '19

Hi all, For the validation of my model to my map in phenix 1.17.1 I tried to refine my shaken model (0.5Å) against my half map in phenix real space refine. However, whatever I try I get a weird behaviour in the FSC(Model-map), see the image below. It seems not to be able to reach 0 in the correlation, but keeps getting stuck at 0.1. I tried various things to solve this, but unfortunately nothing helps: - Using the other half map - Cut of the heterogeneous part of my model and map and refine this - Used refined data without using a mask for the last iterations - Used different resolutions to refine against - Tried data from someone else in the lab (same microscope, same imaging conditions), to check if I am doing something wrong (this gave good results) When doing the same refinement in Refmac5 in ccpem 1.4 it does seem to work, however I would not like to switch programs, because this will mess up my final model. Best, Lisa

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weight optimization in refinement
by Alexei Gorelik 23 Nov '19

23 Nov '19

Hi, Is there a setting to control the number of parallel weight optimization threads in phenix.refine? Also, is there a way to force phenix.refine to perform global real-space refinement (rsrg)? Most of the time, when the "real-space" option is selected, it only carries out rotamer fitting (rsrl). I do know there's a separate real-space refinement program in Phenix. Thanks!

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Secondary structure restraints
by Luca Pellegrini 21 Nov '19

21 Nov '19

I have a protein-DNA complex and would like to apply SS restraints. What is the best way to apply the SS restraints to the protein only, using the GUI? I have tried the following: Select ‘Use secondary structure restraints’ in the ‘Refinement Settings’ tab ‘Select Atoms’ In the Selection Editor window, 'Find Secondary Structures' Removed manually all nucleic acid restraints in ‘Base Pairs’ and Stacking Pairs’ tabs Save and close. However, phenix refinement keeps switching SS restraints for nucleic acids to True. Kind regards, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom lp212(a)cam.ac.uk tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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Molybdenum cofactor refinement
by Cristiano Mota 21 Nov '19

21 Nov '19

Hi all, I'm using phenix.refine to refine a structure of a Molybo-protein at 1.9Å. The MGD cofactors (molybdopterin guanine dinucleotide) are being refined with a weird distorted geometry causing some clashes. The Fo-Fc maps show that something is going wrong in the aromatic rings interatomic distances. I'm using the readyset to pick up MGD and metal restraints. Am I using the right protocol? Best regards, Cristiano Mota -- *Cristiano de Sousa Mota* Postdoctoral Researcher, Macromolecular Crystallography Group UCIBIO / FCT - Universidade Nova de Lisboa 2829-516 Caparica, Portugal (00351 212948300, ext 10962) http://xtal.dq.fct.unl.pt/

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Deadline Extended to December 9th
by Nick DeHaan 21 Nov '19

21 Nov '19

Hi PhenixBB, Thanks for sharing information about the AIMS Awards with your colleagues! Many have told us they really appreciated it. We’ve had requests for more time - so we extended the deadline to December 9th! For anyone with a protein target of interest, the AIMS Award program can help you discover new molecular tools, start new drug development efforts, and get published. The program is open to investigators, postdocs, and graduate students worldwide. We encourage you to check out our flyer for more information: Flyer <http://bit.ly/37oIrS3> You can apply directly on the website: atomwise.com/aims. Please don't hesitate to reach out with any questions! Best, Nick Nick DeHaan, MsE *Partnering Executive* *Atomwise* <http://www.atomwise.com/> | *Better Medicines Faster* ᐧ -- Confidentiality Notice: The information contained herein is for informational purposes only. This message is private and the information contained in this message, including any attachments, contains information that may be confidential, privileged and/or proprietary. It is intended to be read only by the individual or entity to whom it is addressed. If you are not the intended recipient, please notify the sender by replying to this message, delete the material immediately from your system and note that you must not review, disclose, copy, distribute or take any action in reliance on or in reference to this message, including any attachments. No confidentiality, privilege, or property rights are waived or lost by any errors in transmission. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.

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cryo-EM density modification
by Tom Terwilliger 19 Nov '19

19 Nov '19

Hi Phenix cryo-EM users, For those of you trying out density modification for cryo-EM (phenix.resolve_cryo_em), the automatic estimation of resolution in the current version uses unmasked resolution instead of masked, in some cases resulting in running density modification at too low a resolution. Consequently it is best with this version if you specify your nominal resolution. To run it you can type: phenix.resolve_cryo_em half_map_1.ccp4 half_map_2.ccp4 \ seq_file=seq.dat resolution=3.5 or something like that. It requires the current nightly build to run. You might also want to wait just a short while and a version that has this and a few other bugs fixed, a GUI, full documentation, and an example dataset will be out (hopefully this week). The full description of the method is at https://www.biorxiv.org/content/10.1101/845032v1 Let me know of any problems or suggestions! 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

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Differences in refinement statistics
by Chancievan Thangaratnarajah 19 Nov '19

19 Nov '19

Hello, I have noticed differences in the refinement statistics between two different Phenix versions (see attachments) even though I am using the same cryo-EM map and model as input. The most notable difference are rotamer outliers, which were 0 % in Phenix 1.16-3549 and now 6 % in Phenix 1.17-3660. I was wondering whether anyone has noticed a similar behaviour? Or is there something that I have missed? Best, Chancie.

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Error in sequence assignment
by Tom Terwilliger 18 Nov '19

18 Nov '19

Hi Nicholas, I'm afraid there isn't a way to say which sequence goes with which chain. I would suggest using the tool phenix.replace_side_chains. Give it 1 chain and 1 sequence and if they have the same length it should just put it in. If it doesn't work, try phenix.sequence_from_map which can do the same thing. Let me know if that doesn't do it! All the best, Tom T Date: Sun, 17 Nov 2019 17:07:16 -0500 From: Nicholas Gao <dominion146(a)GMAIL.COM> Subject: Specify chain assignment in sequence file for rebuild-in-place of phenix.autobuild Dear CCP4, I currently have an MR solution that has the wrong sequence. The pdb file of the solution contains 3 chains, and I'd like to use the rebuild-in-place functionality within phenix.autobuild to correct the sequence of all 3 chains. Phenix allows me to supply a sequence file as input for this job, it's not clear to me how I tell the program which sequence should be assigned to which chain. Anyone know how to do this? Sincerely, Nicholas Gao -- 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

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RapiData at SSRL 2020 - application deadline extended by one week!
by Smith, Clyde 16 Nov '19

16 Nov '19

Hi all, We have extended the deadline for applications for a place at the RapiData 2020 @ SSRL workshop to next Friday, November 22 2019! There are still a few spots left, so get your application in! The workshop will be held from March 30 - April 4 2020 on the SLAC campus in Menlo Park, California. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on the following topics: Specimen preparation, data collection strategies, X-ray light sources, X-ray detectors, data reduction, structure solution by MAD, SAD and molecular replacement, complementary methods (spectroscopy, small angle scattering and cryoEM). Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2020/ and use the links on the "registration" page to apply for the course. Successful applicants will be notified early in December 2019 and invited to register at that time. A limited amount of travel support funding may be available. We look forward to seeing you all out in sunny California in March 2020! Silvia Russi, Clyde Smith and Jeney Wierman (Organizers) srussi(a)slac.stanford.edu csmith(a)slac.stanford.edu jwierman(a)slac.stanford.edu

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General interest
by John R Helliwell 15 Nov '19

15 Nov '19

Dear Colleagues, I imagine the two articles that I describe in my posting at the IUCr’s Forum will be of interest to the MX community. See:- https://forums.iucr.org/viewtopic.php?f=39&t=427 All best wishes, John Emeritus Professor John R Helliwell DSc

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