ArticleProtein science : a publication of the Protein Society2016
Simplifying and enhancing the use of PyMOL with horizontal scripts.
Article in Protein science : a publication of the Protein Society, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 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
26 citing papers in PubMed.
- From wireframes to immersive reality: a historical perspective on molecular visualization software.Briefings in bioinformatics · 2026Review
- Integrated computational and experimental benchmarking of Bacillus phage endolysins reveals the relationship between peptidoglycan-fragment recognition descriptors and antibacterial performance.Scientific reports · 2026Article
- Immunogenicity of Adalimumab in Bacterial Molecular Mimicry: In Silico Analysis.JMIR bioinformatics and biotechnology · 2025Article
- Molecular Mimicry BetweenInternational journal of molecular sciences · 2025Article
- Genome-wide identification of wheat Ubiquitin-conjugating enzyme gene family and its role in wheat powdery mildew disease resistance.BMC plant biology · 2025Article
- Exploring the Structural and Functional Consequences of Deleterious Missense Nonsynonymous SNPs in theJournal of personalized medicine · 2024Article
- Genome-wide identification of3 Biotech · 2024Article
- Computational exploration ofBiochemistry and biophysics reports · 2024Article
- A newly identified photosystem II Subunit P geneFrontiers in plant science · 2024Article
- Discovery of novel inhibitor of 11 beta-hydroxysteroid dehydrogenase type 1 usingJournal of diabetes and metabolic disorders · 2023Article
- The extremophileFrontiers in microbiology · 2023Article
- Physiological Responses of Cigar Tobacco Crop to Nitrogen Deficiency and Genome-Wide Characterization of thePlants (Basel, Switzerland) · 2022Article
- Immunopotentiating properties of chimeric OprF-OprI-PopB protein againstIranian journal of basic medical sciences · 2022Article
- Identifying the Novel Inhibitors Against the Mycolic Acid Biosynthesis Pathway Target "mtFabH" ofFrontiers in microbiology · 2022Article
- Structure ofLife science alliance · 2022Article
- Structure of Aedes aegypti carboxypeptidase B1-inhibitor complex uncover the disparity between mosquito and non-mosquito insect carboxypeptidase inhibition mechanism.Protein science : a publication of the Protein Society · 2021Article
- Nitrogen Assimilation Related Genes inPlants (Basel, Switzerland) · 2021Article
- Construction, petro-collecting/dispersing capacities, antimicrobial activity, and molecular docking study of new cationic surfactant-sulfonamide conjugates.Journal of molecular liquids · 2021Article
- Attacking COVID-19 Progression Using Multi-Drug Therapy for Synergetic Target Engagement.Biomolecules · 2021Article
- LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate.Nature communications · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
Abstract
Scripts are used in PyMOL to exert precise control over the appearance of the output and to ease remaking similar images at a later time. We developed horizontal scripts to ease script development. A horizontal script makes a complete scene in PyMOL like a traditional vertical script. The commands in a horizontal script are separated by semicolons. These scripts are edited interactively on the command line with no need for an external text editor. This simpler workflow accelerates script development. In using PyMOL, the illustration of a molecular scene requires an 18-element matrix of view port settings. The default format spans several lines and is laborious to manually reformat for one line. This default format prevents the fast assembly of horizontal scripts that can reproduce a molecular scene. We solved this problem by writing a function that displays the settings on one line in a compact format suitable for horizontal scripts. We also demonstrate the mapping of aliases to horizontal scripts. Many aliases can be defined in a single script file, which can be useful for applying costume molecular representations to any structure. We also redefined horizontal scripts as Python functions to enable the use of the help function to print documentation about an alias to the command history window. We discuss how these methods of using horizontal scripts both simplify and enhance the use of PyMOL in research and education.
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.