{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T01:54:56Z","timestamp":1776045296395,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2018,1,11]],"date-time":"2018-01-11T00:00:00Z","timestamp":1515628800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100002809","name":"Generalitat de Catalunya","doi-asserted-by":"publisher","award":["2014SGR989"],"award-info":[{"award-number":["2014SGR989"]}],"id":[{"id":"10.13039\/501100002809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002809","name":"Generalitat de Catalunya","doi-asserted-by":"publisher","award":["2017FI_B2_00168"],"award-info":[{"award-number":["2017FI_B2_00168"]}],"id":[{"id":"10.13039\/501100002809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>UCSF Chimera is a powerful visualization tool remarkably present in the computational chemistry and structural biology communities. Built on a C++\u2009core wrapped under a Python 2.7 environment, one could expect to easily import UCSF Chimera\u2019s arsenal of resources in custom scripts or software projects. Nonetheless, this is not readily possible if the script is not executed within UCSF Chimera due to the isolation of the platform. UCSF ChimeraX, successor to the original Chimera, partially solves the problem but yet major upgrades need to be undergone so that this updated version can offer all UCSF Chimera features.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>PyChimera has been developed to overcome these limitations and provide access to the UCSF Chimera codebase from any Python 2.7 interpreter, including interactive programming with tools like IPython and Jupyter Notebooks, making it easier to use with additional third-party software.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>PyChimera is LGPL-licensed and available at https:\/\/github.com\/insilichem\/pychimera.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty021","type":"journal-article","created":{"date-parts":[[2018,1,9]],"date-time":"2018-01-09T21:39:22Z","timestamp":1515533962000},"page":"1784-1785","source":"Crossref","is-referenced-by-count":22,"title":["PyChimera: use UCSF Chimera modules in any Python 2.7 project"],"prefix":"10.1093","volume":"34","author":[{"given":"Jaime","family":"Rodr\u00edguez-Guerra Pedregal","sequence":"first","affiliation":[{"name":"InsiliChem, Departament de Qu\u00edmica, Universitat Aut\u00f2noma de Barcelona, Barcelona, Spain"}]},{"given":"Jean-Didier","family":"Mar\u00e9chal","sequence":"additional","affiliation":[{"name":"InsiliChem, Departament de Qu\u00edmica, Universitat Aut\u00f2noma de Barcelona, Barcelona, Spain"}]}],"member":"286","published-online":{"date-parts":[[2018,1,11]]},"reference":[{"key":"2023012713525862400_bty021-B1","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1021\/ct300857j","article-title":"OpenMM 4: a reusable, extensible, hardware independent library for high performance molecular simulation","volume":"9","author":"Eastman","year":"2013","journal-title":"J. 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