Evidence map›Paper›PMID 41928950›Full record

ArticlebioRxiv : the preprint server for biology2026

Variable Resolution Maps (VRM) in CCTBX and Phenix: Accounting For Local Resolution In cryoEM.

Pavel V Afonine, Paul D Adams, Alexandre G Urzhumtsev

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Pavel V AfonineMolecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA.ORCID 0000-0002-5052-991X
Paul D AdamsMolecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA.
Alexandre G UrzhumtsevCentre for Integrative Biology, Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104 / Institut National de la Santé de la Recherche Médicale (Inserm) U964 / Université de Strasbourg, Illkirch, France.

Funding

Phenix: providing high quality software to the research community for crystallography and cryo-EMR24GM141254 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI PAUL David ADAMS · 2021 to 2026
$9.2M
NIGMS NIH HHS R24 GM141254
6 · The paper itself

Abstract

Calculation of density maps from atomic models is essential for structural studies using crystallography and electron cryo-microscopy (cryoEM). These maps serve various purposes, including atomic model building, refinement, visualization, and validation. However, accurately comparing model-calculated maps to experimental data poses challenges, particularly because the resolution of cryoEM experimental maps varies across the map. Traditional crystallography methods generate finite-resolution maps with uniform resolution throughout the unit cell volume, while most modern software in cryoEM employ Gaussian-like functions to generate these maps, which does not adequately account for atomic model parameters and resolution. Recent work by Urzhumtsev & Lunin (2022,

Indexed as

analytic approximationsatomic imagesfinite resolutionFourier ripplesrefinementVariable resolution maps

Identifiers

PMID41928950
PMCPMC13041909

What OpenQuestion holds

Textmetadata
LicenceCC BY-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.