{"id":975,"date":"2024-05-24T13:01:01","date_gmt":"2024-05-24T10:01:01","guid":{"rendered":"https:\/\/www.bioeng.ru\/structbiotech\/?page_id=975"},"modified":"2025-09-16T22:21:44","modified_gmt":"2025-09-16T19:21:44","slug":"programs","status":"publish","type":"page","link":"https:\/\/www.bioeng.ru\/structbiotech\/en\/programs\/","title":{"rendered":"Software"},"content":{"rendered":"<div data-elementor-type=\"wp-page\" data-elementor-id=\"975\" class=\"elementor elementor-975\">\n\t\t\t\t<div class=\"elementor-element elementor-element-37865fc6 e-con-full e-flex e-con e-parent\" data-id=\"37865fc6\" data-element_type=\"container\">\n\t\t\t\t<div class=\"elementor-element elementor-element-604b5b99 elementor-invisible elementor-widget elementor-widget-elementskit-heading\" data-id=\"604b5b99\" data-element_type=\"widget\" data-settings=\"{&quot;_animation&quot;:&quot;fadeIn&quot;}\" data-widget_type=\"elementskit-heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<div class=\"ekit-wid-con\" ><div class=\"ekit-heading elementskit-section-title-wraper text_left   ekit_heading_tablet-   ekit_heading_mobile-\"><h1 class=\"ekit-heading--title elementskit-section-title\">Software<\/h1><div class=\"ekit_heading_separetor_wraper ekit_heading_elementskit-border-divider elementskit-style-long\"><div class=\"elementskit-border-divider elementskit-style-long\"><\/div><\/div><\/div><\/div>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-d06b32f e-flex e-con-boxed e-con e-parent\" data-id=\"d06b32f\" data-element_type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-25db2a6 elementor-widget elementor-widget-text-editor\" data-id=\"25db2a6\" data-element_type=\"widget\" data-settings=\"{&quot;_animation&quot;:&quot;none&quot;,&quot;_animation_mobile&quot;:&quot;none&quot;}\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<style>\/*! elementor - v3.21.0 - 30-04-2024 *\/\n.elementor-widget-text-editor.elementor-drop-cap-view-stacked .elementor-drop-cap{background-color:#69727d;color:#fff}.elementor-widget-text-editor.elementor-drop-cap-view-framed .elementor-drop-cap{color:#69727d;border:3px solid;background-color:transparent}.elementor-widget-text-editor:not(.elementor-drop-cap-view-default) .elementor-drop-cap{margin-top:8px}.elementor-widget-text-editor:not(.elementor-drop-cap-view-default) .elementor-drop-cap-letter{width:1em;height:1em}.elementor-widget-text-editor .elementor-drop-cap{float:left;text-align:center;line-height:1;font-size:50px}.elementor-widget-text-editor .elementor-drop-cap-letter{display:inline-block}<\/style>\t\t\t\t<p>List of programs we use to process data obtained from cryo-electron microscopes<\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-4a24268e e-flex e-con-boxed e-con e-parent\" data-id=\"4a24268e\" data-element_type=\"container\" data-settings=\"{&quot;animation_mobile&quot;:&quot;none&quot;}\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-ed3ade8 elementor-widget elementor-widget-text-editor\" data-id=\"ed3ade8\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ol><li><b>Ctffind <\/b>\u2013 <span style=\"font-size: 16px;\">determination of CTF params (astigmatism defocus) for untilted micrographs.<\/span><\/li><li><b>Ctftilt <\/b>\u2013 <b><\/b>same program, but for tilted images. Additional input parameters: PAve \u2013 pixel average, TiltA \u2013 expected tilt angle, TitlR \u2013 deviation of tilt angle.<\/li><li><b>Signature <\/b>\u2013 <b><\/b>particle picking program.<\/li><li><b>EMAN <\/b>\u2013 <b><\/b>3DEM suit for single particle analysis.<\/li><li><b>Chimera <\/b>\u2013 visualization software with many EM formats support.<\/li><li><b>ChimeraX <\/b>\u2013 new generation of Chimera. Supports Python3, integrations with modern web-services.<\/li><li><b>FReAlign<\/b> \u2013 3D reconstruction refinement program. In last versions of the program conversion to and from Imagic format is available. EMAN2 includes Frealign scripts, also.<\/li><li><b>IMAGIC-5<\/b> \u2013 one more software package for 3DEM data analysis.<\/li><li><strong>DireX<span style=\"font-style: inherit; color: var( --e-global-color-text ); font-family: var( --e-global-typography-text-font-family ), Sans-serif; text-align: var(--text-align);\">,\u00a0<\/span>Rosetta<span style=\"font-style: inherit; color: var( --e-global-color-text ); font-family: var( --e-global-typography-text-font-family ), Sans-serif; text-align: var(--text-align);\">,\u00a0<\/span>Gorgon<span style=\"font-style: inherit; color: var( --e-global-color-text ); font-family: var( --e-global-typography-text-font-family ), Sans-serif; text-align: var(--text-align);\">,\u00a0<\/span>Situs<\/strong> \u2013\u00a0software for 3DEM model validation and docking<\/li><\/ol>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>","protected":false},"excerpt":{"rendered":"<p>\u041f\u0440\u043e\u0433\u0440\u0430\u043c\u043c\u043d\u043e\u0435 \u043e\u0431\u0435\u0441\u043f\u0435\u0447\u0435\u043d\u0438\u0435 C\u043f\u0438\u0441\u043e\u043a \u043f\u0440\u043e\u0433\u0440\u0430\u043c\u043c, \u043a\u043e\u0442\u043e\u0440\u044b\u0435 \u043c\u044b \u043f\u0440\u0438\u043c\u0435\u043d\u044f\u0435\u043c \u0434\u043b\u044f \u043e\u0431\u0440\u0430\u0431\u043e\u0442\u043a\u0438 \u0434\u0430\u043d\u043d\u044b\u0445, \u043f\u043e\u043b\u0443\u0447\u0430\u0435\u043c\u044b\u0445 \u0441 \u043a\u0440\u0438\u043e\u044d\u043b\u0435\u043a\u0442\u0440\u043e\u043d\u043d\u044b\u0445 \u043c\u0438\u043a\u0440\u043e\u0441\u043a\u043e\u043f\u043e\u0432. Ctffind \u2013 \u043f\u0440\u043e\u0433\u0440\u0430\u043c\u043c\u0430 \u0434\u043b\u044f \u043e\u043f\u0440\u0435\u0434\u0435\u043b\u0435\u043d\u0438\u044f \u043f\u0430\u0440\u0430\u043c\u0435\u0442\u0440\u043e\u0432 CTF (\u0430\u0441\u0442\u0438\u0433\u043c\u0430\u0442\u0438\u0437\u043c, \u0434\u0435\u0444\u043e\u043a\u0443\u0441) \u0434\u043b\u044f untilted \u043c\u0438\u043a\u0440\u043e\u0444\u043e\u0442\u043e\u0433\u0440\u0430\u0444\u0438\u0439. Ctftilt \u2013 \u0442\u0430 \u0436\u0435 \u043f\u0440\u043e\u0433\u0440\u0430\u043c\u043c\u0430, \u043d\u043e \u0434\u043b\u044f \u043e\u043f\u0440\u0435\u0434\u0435\u043b\u0435\u043d\u0438\u044f CTF \u043f\u043e tilted \u0438\u0437\u043e\u0431\u0440\u0430\u0436\u0435\u043d\u0438\u044f\u043c. \u0412\u0445\u043e\u0434\u043d\u044b\u0435 \u043f\u0430\u0440\u0430\u043c\u0435\u0442\u0440\u044b \u0442\u0435 \u0436\u0435, \u0447\u0442\u043e \u0438 ctffind. \u0414\u043e\u0431\u0430\u0432\u043b\u044f\u044e\u0442\u0441\u044f \u0442\u043e\u043b\u044c\u043a\u043e PAve &#8212; pixel average, TiltA &#8212; \u043e\u0436\u0438\u0434\u0430\u0435\u043c\u044b\u0439 tilt [&hellip;]<\/p>","protected":false},"author":10,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"elementor_header_footer","meta":{"site-sidebar-layout":"no-sidebar","site-content-layout":"page-builder","ast-site-content-layout":"full-width-container","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"disabled","ast-breadcrumbs-content":"","ast-featured-img":"disabled","footer-sml-layout":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"set","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-gradient":""}},"footnotes":""},"class_list":["post-975","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.bioeng.ru\/structbiotech\/en\/wp-json\/wp\/v2\/pages\/975","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.bioeng.ru\/structbiotech\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.bioeng.ru\/structbiotech\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.bioeng.ru\/structbiotech\/en\/wp-json\/wp\/v2\/users\/10"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bioeng.ru\/structbiotech\/en\/wp-json\/wp\/v2\/comments?post=975"}],"version-history":[{"count":50,"href":"https:\/\/www.bioeng.ru\/structbiotech\/en\/wp-json\/wp\/v2\/pages\/975\/revisions"}],"predecessor-version":[{"id":3203,"href":"https:\/\/www.bioeng.ru\/structbiotech\/en\/wp-json\/wp\/v2\/pages\/975\/revisions\/3203"}],"wp:attachment":[{"href":"https:\/\/www.bioeng.ru\/structbiotech\/en\/wp-json\/wp\/v2\/media?parent=975"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}