April 2025 - phenixbb - phenix-online.org

Simulate map from model
by Ricardo Righetto 10 Apr '25

10 Apr '25

Hi, Apologies if I'm missing something obvious, but I was not able to find this in the documentation: is there a PHENIX tool for simulating Coulomb potential maps (aka "cryo-EM maps") from atomic models? I'm looking for something like the molmap <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html> command in ChimeraX, but more accurate. One such alternative is the simulate program from cisTEM, but I figured PHENIX might also have something? Thank you! -- Ricardo Diogo Righetto

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Differential density peaks and hydrophobic residues
by Lucas Souza 04 Apr '25

04 Apr '25

Hi everyone, I am refining a ~3A structure using phenix 1.21.2-5419. I am at the final stages of the refinement but I am seeing some positive density on some hydrophobic residues (mainly Ile and Leu) together with a negative density around those residues (image attached). At first, I guessed that might be related to solvent mask, so I turned on optimize_mask. That did not solve the issue, although slightly decreased R values. Diffraction data was processed with autoproc+staraniso and does not seem to be twinned (normal intensity stats + map deteriorates if twinning refinement is applied). Does anyone have a guess about that? Best, Lucas -- Lucas Souza dos Santos Laboratório de Biologia Estrutural Aplicada (LBEA) Departamento de Microbiologia Instituto de Ciências Biomédicas II - USP Cidade Universitária - São Paulo - SP CEP 05508-000

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CBMS Structural Biology Workbench - May 27 through 30, 2025 - registration deadline approaching
by Stojanoff, Vivian 03 Apr '25

03 Apr '25

Dear Colleagues, The CBMS Structural Biology Workbench will take place May 27 through 30, 2025. The first two days, May 27 and 28, are dedicated to MX and the following days May 29 and 30 to Solution Scattering and X-ray Footprintig. This is an IN-PERSON workshop. DEADLINE to REGISTER APRIL 15 https://www.bnl.gov/cbmsworkbench/ PROGRAM Macromolecular Crystallography May 27 - MX data collection on participants samples and pre-analysis May 28 - Phenix workshop "The Phenix workshop will focus on crystallographic refinement using phenix.refine. The first lecture will introduce major features and best practices of reciprocal space refinement, followed by a basic tutorial demonstrating how to run phenix.refine with default options. The second lecture will cover strategies for low-resolution refinement, including the use of secondary structure restraints and reference models. Participants who so desire will have the opportunity to work on their own data with Phenix developers available to answer questions—on phenix.refine or any other Phenix tools in the afternoon. Solution Scattering - SAXS & Xray Footprinting - XFP May 29 - Introduction to SAXS & LIX; Data collection on participants samples May 30 morning - SAXS data analysis software May 30 afternoon - Introduction to XFP and hands-on tutorial Questions can be directed to Vivian Stojanoff (stojanof(a)bnl.gov).

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for autobuild full sequence?
by James Holton 03 Apr '25

03 Apr '25

Hey all, Don't worry, nothing is funny today. I have a real question: Is there a way to force phenix.autobuild to build in the entire sequence? As in: the full length of the actual molecule that is in the crystal, such as what is supposed to go into SEQRES, regardless of "visible" density? I am trying to come up with a pipeline for prepping MD simulations of protein crystals. It seems proper to me that the molecule being simulated should be the actual molecular species, disordered bits an all. However, we don't seem to have good technology for building protein chains into "nothingness". Yes, I know Alphafold is a thing, but it is rubbish at clashes in the context of a crystal. I mean, I could write something, but does this tool already exist? Cheers, and happy Tuesday, -James Holton MAD Scientist

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