ArticleActa crystallographica. Section D, Structural biology2017
Polder maps: improving OMIT maps by excluding bulk solvent.
Article in Acta crystallographica. Section D, Structural biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 424 papers.
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.
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.
Who cites it
424 citing papers in PubMed.
- Structural and functional characterisation of the dextran utilisome fromJournal of structural biology: X · 2026Article
- A distinct gene expression mechanism for d-amino acid utilization in hyperthermophilic archaeon Pyrococcus horikoshii.The FEBS journal · 2026Article
- Snapshots From the Catalytic Landscape of Chalcone Isomerase.Plant direct · 2026Article
- Discovery and structural analysis of glycoside hydrolase family 176 α-1,2 glucosidase from Arthrobacter humicola A8F5.The Journal of biological chemistry · 2026Article
- Sterol binding mechanism of a plant START-like domain: A new sterol transport paradigm via an amphiphilic cavity.The FEBS journal · 2026Article
- Avoiding pitfalls when modelling ligands in macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2026Article
- Dual Inhibitors of p38α Mitogen-Activated Protein Kinase and Butyrylcholinesterase for the Modulation of Neuroinflammation and Cognitive Dysfunction.Journal of medicinal chemistry · 2026Article
- Modular Inhibitor Approach to Map the Catalytic Trajectory of an Iterative Siderophore Synthetase, DesD.ACS bio & med chem Au · 2026Article
- Saxiphilin is a broad-spectrum toxin sponge for C13-modified saxitoxins.Structure (London, England : 1993) · 2026Article
- A mechanistic framework for the recognition of chemically diverse brassinosteroids by BRI1-family receptor kinases.Nature plants · 2026Article
- The Novel Carbapenem, JDB/PQ-1-219, Has Potent Broad Spectrum Activity against Multi-Drug ResistantACS infectious diseases · 2026Article
- Volatile anaesthetics modulate voltage-gated sodium channel function at a site directly linked to channel gating.Nature communications · 2026Article
- Structural Basis of pppGpp Binding to the N-Terminal Domain of the Bifunctional RelA/SpoT Homolog RelInternational journal of molecular sciences · 2026Article
- Off-Target Binding of Miglustat to Glycogen Debranching Enzyme.International journal of molecular sciences · 2026Article
- Investigating the role of a conserved hydrophobic pocket of gp41 in the anti-HIV activity of fusion inhibitors.Protein science : a publication of the Protein Society · 2026Article
- Development and structure-guided characterization of a novel ACE2-binding macrocyclic peptide.Journal of structural biology: X · 2026Article
- Rapid evolution of a highly efficient RNA polymerase by homologous recombination.Nature chemical biology · 2026Article
- Structure of chloramphenicol-bound MexB reveals residues in the distal binding pocket that are critical for substrate recognition.Journal of biochemistry · 2026Article
- Crystal structure of the plant GABA aminotransferase AtGABA-T from Arabidopsis thaliana.Acta crystallographica. Section F, Structural biology communications · 2026Article
- Comment on Photosystem II: light-dependent oscillation of ligand composition at its active site: existence of O6 in SActa crystallographica. Section D, Structural biology · 2026Article
364 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factors and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. The tools described in this manuscript have been implemented and are available in PHENIX.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.