[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"doc-detail-167133-en":3,"doc-seo-167133-105":30,"detail-sidebar-cat-1-en-105":96},{"code":4,"msg":5,"data":6},0,"success",{"doc_id":7,"user_id":8,"nickname":9,"user_avatar":10,"doc_module":11,"category_id":12,"category_name":13,"doc_title":14,"doc_description":15,"doc_content":16,"file_id":17,"file_url":18,"file_type":19,"file_size":20,"view_count":4,"is_deleted":4,"is_public":11,"is_downloadable":11,"audit_status":11,"page_count":21,"language":22,"language_code":23,"site_id":24,"html_lang":23,"table_of_contents":25,"faqs":26,"seo_title":27,"seo_description":15,"update_tm":28,"read_time":29},167133,962084925782,"Chloe Bennett","https://ap-avatar.wpscdn.com/davatar_9964176cb1d06d4a9deccf72a44ae3dc",1,158,"General","CAVER PyMOL plugin - Part 3 - 介绍","CAVER PyMOL plugin v3.0 provides tunnel calculation and visualization inside PyMOL by leveraging the CAVER 3.0 software package. The plugin is implemented in Python and runs across operating systems, with a recommended Python version of 2.7 or higher. CAVER 3.0 itself is Java-based and requires Java Runtime Environment 6.0 or higher. The guide explains plugin prerequisites, how to check Java versions, and compatibility notes for supported PyMOL releases. It also outlines basic installation sources and setup steps, including required executables and plugin installation workflow.","The CAVER 3.0 software package is distributed under the terms of the GNU General Public License v3.0. There is no warranty for the program, to the extent permitted by applicable law. Except when otherwise stated in writing the copyright holders and/or other parties provide the program “as is” without warranty of any kind, either expressed or implied, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. The entire risk as to the quality and performance of the program is with you. Should the program prove defective, you assume the cost of all necessary servicing, repair or correction.\nCitation:\nChovancova, E., Pavelka, A., Benes, P., Strnad, O., Brezovsky, J., Kozlikova, B., Gora, A., Sustr, V., Klvana, M., Medek, P., Biedermannova, L., Sochor, J. Damborsky, J. (2012). CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures. PLoS Comput Biol 8: e1002708.\ndoi:10.1371/journal.pcbi.1002708\nDeveloper Team:\nHuman Computer Interaction Laboratory\nFaculty of Informatics, Masaryk University\u000bBotanická 68a, 602 00 Brno, Czech Republic\u000bWebpage: http://decibel.fi.muni.cz\u000bPhone: +420 549 496 939, Fax: +420 549 491 820\nLoschmidt Laboratories, Department of Experimental Biology and\nResearch Centre for Toxic Compounds in the Environment\u000bFaculty of Science, Masaryk University\u000bKamenice 5, Bld. A13, 625 00 Brno, Czech Republic\u000bWebpage: http://loschmidt.chemi.muni.cz\u000bPhone: +420 549 493 467, Fax: +420 549 496 302\nWebpage: http://www.caver.cz\u000bE-mail: caver@caver.cz\n© Copyright 2005-2013\u000bHuman Computer Interaction Laboratory, Faculty of Informatics\nand Loschmidt Laboratories, Department of Experimental Biology and\nResearch Centre for Toxic Compounds in the Environment, Faculty of Science\u000bMasaryk University\u000bBrno, Czech Republic\nContents\n\u0013 TOC \\o \"1-3\" \\h \\z \\u \u0014\u0013 HYPERLINK \\l \"_Toc365899227\" \u0014A. ABOUT\t\u0013 PAGEREF _Toc365899227 \\h \u00144\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899228\" \u0014B. INSTALLATION\t\u0013 PAGEREF _Toc365899228 \\h \u00144\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899229\" \u0014C. RUNNING CAVER plugin\t\u0013 PAGEREF _Toc365899229 \\h \u00145\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899230\" \u0014D. CALCULATION SETTINGS\t\u0013 PAGEREF _Toc365899230 \\h \u00146\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899231\" \u0014Tunnel calculation\t\u0013 PAGEREF _Toc365899231 \\h \u00146\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899232\" \u0014Starting point optimization\t\u0013 PAGEREF _Toc365899232 \\h \u00149\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899233\" \u0014E. INPUTS\t\u0013 PAGEREF _Toc365899233 \\h \u001410\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899234\" \u0014PDB file\t\u0013 PAGEREF _Toc365899234 \\h \u001410\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899235\" \u0014Configuration file (config.txt)\t\u0013 PAGEREF _Toc365899235 \\h \u001410\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899236\" \u0014F. OUTPUTS\t\u0013 PAGEREF _Toc365899236 \\h \u001411\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899237\" \u0014summary.txt\t\u0013 PAGEREF _Toc365899237 \\h \u001411\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899238\" \u0014summary_precise_numbers.csv\t\u0013 PAGEREF _Toc365899238 \\h \u001411\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899239\" \u0014log.txt\t\u0013 PAGEREF _Toc365899239 \\h \u001411\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899240\" \u0014warnings.txt\t\u0013 PAGEREF _Toc365899240 \\h \u001411\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899241\" \u0014analysis directory\t\u0013 PAGEREF _Toc365899241 \\h \u001412\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899242\" \u0014pymol directory\t\u0013 PAGEREF _Toc365899242 \\h \u001415\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899243\" \u0014data directory\t\u0013 PAGEREF _Toc365899243 \\h \u001415\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899244\" \u0014inputs directory\t\u0013 PAGEREF _Toc365899244 \\h \u001416\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899245\" \u0014G. ADVANCED SETTINGS\t\u0013 PAGEREF _Toc365899245 \\h \u001417\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899246\" \u0014Advanced calculation settings\t\u0013 PAGEREF _Toc365899246 \\h \u001417\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899247\" \u0014Atomic radii settings\t\u0013 PAGEREF _Toc365899247 \\h \u001417\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899248\" \u0014Visualization settings\t\u0013 PAGEREF _Toc365899248 \\h \u001417\u0015\u0015\n\u0013 HYPERLINK \\l \"_Toc365899249\" \u0014H. Description of CAVER PLUGIN versions\t\u0013 PAGEREF _Toc365899249 \\h \u001418\u0015\u0015\n\u0015\nA. ABOUT\nThe CAVER PyMOL plugin v3.0 enables calculation and visualization of tunnels in PyMOL. For the calculation of tunnels, the plugin utilizes CAVER 3.0 software package.\nCAVER plugin is written in the P","cbCaijRjqnpyj6oN","https://ap.wps.com/l/cbCaijRjqnpyj6oN","docx",1718924,18,"English","en",105,"# A. ABOUT\n# B. INSTALLATION\n# C. RUNNING CAVER plugin\n# D. CALCULATION SETTINGS\n## Tunnel calculation\n## Starting point optimization\n# E. INPUTS\n## PDB file\n## Configuration file (config.txt)\n# F. OUTPUTS\n## summary.txt\n## summary_precise_numbers.csv\n## log.txt\n## warnings.txt\n## analysis directory\n## pymol directory\n## data directory\n## inputs directory\n# G. ADVANCED SETTINGS\n## Advanced calculation settings\n## Atomic radii settings\n## Visualization settings\n# H. Description of CAVER PLUGIN versions","[{\"question\":\"What does the CAVER PyMOL plugin v3.0 do?\",\"answer\":\"It enables tunnel calculation and visualization of tunnels in PyMOL. Tunnel calculations use the CAVER 3.0 software package.\"},{\"question\":\"What software requirements are needed to run the plugin?\",\"answer\":\"The plugin runs on all operating systems with Python 2.7 or higher. CAVER 3.0 requires Java Runtime Environment 6.0 or higher.\"},{\"question\":\"How do I install the CAVER plugin on Windows?\",\"answer\":\"Download the caver_3.0_plugin.zip archive, extract it, then run windows/setup_301.exe and follow the prompts. Ensure the PyMOL executable directory is specified correctly.\"},{\"question\":\"How is the Linux/MacOS installation performed?\",\"answer\":\"Move the linux_mac/Caver3 folder to a destination directory and edit linux_mac/Caver3_0_1.py to set the correct caver3 path. Then run PyMOL as root and install the plugin via the Plugin menu, selecting the edited script.\"}]","CAVER PyMOL plugin - Part 3 - 介绍 | DOCX",1788209332,6,{"code":4,"msg":31,"data":32},"ok",{"site_id":24,"language":23,"slug":33,"title":14,"keywords":34,"description":15,"schema_data":35,"social_meta":91,"head_meta":93,"extra_data":95,"updated_unix":28},"caver-pymol-plugin-part-3-introduction","",{"@graph":36,"@context":90},[37,54,69],{"@type":38,"itemListElement":39},"BreadcrumbList",[40,44,48,51],{"item":41,"name":42,"@type":43,"position":11},"https://docshare.wps.com","Home","ListItem",{"item":45,"name":46,"@type":43,"position":47},"https://docshare.wps.com/template/","Template",2,{"item":49,"name":13,"@type":43,"position":50},"https://docshare.wps.com/template/general/",3,{"item":52,"name":14,"@type":43,"position":53},"https://docshare.wps.com/template/caver-pymol-plugin-part-3-introduction/167133/",4,{"url":52,"name":14,"@type":55,"author":56,"headline":14,"publisher":58,"fileFormat":61,"inLanguage":23,"description":15,"dateModified":62,"datePublished":63,"encodingFormat":61,"isAccessibleForFree":64,"interactionStatistic":65},"DigitalDocument",{"name":9,"@type":57},"Person",{"url":41,"name":59,"@type":60},"DocShare","Organization","application/vnd.openxmlformats-officedocument.wordprocessingml.document","2026-09-01","2026-08-31",true,{"@type":66,"interactionType":67,"userInteractionCount":11},"InteractionCounter",{"@type":68},"ViewAction",{"@type":70,"mainEntity":71},"FAQPage",[72,78,82,86],{"name":73,"@type":74,"acceptedAnswer":75},"What does the CAVER PyMOL plugin v3.0 do?","Question",{"text":76,"@type":77},"It enables tunnel calculation and visualization of tunnels in PyMOL. Tunnel calculations use the CAVER 3.0 software package.","Answer",{"name":79,"@type":74,"acceptedAnswer":80},"What software requirements are needed to run the plugin?",{"text":81,"@type":77},"The plugin runs on all operating systems with Python 2.7 or higher. CAVER 3.0 requires Java Runtime Environment 6.0 or higher.",{"name":83,"@type":74,"acceptedAnswer":84},"How do I install the CAVER plugin on Windows?",{"text":85,"@type":77},"Download the caver_3.0_plugin.zip archive, extract it, then run windows/setup_301.exe and follow the prompts. Ensure the PyMOL executable directory is specified correctly.",{"name":87,"@type":74,"acceptedAnswer":88},"How is the Linux/MacOS installation performed?",{"text":89,"@type":77},"Move the linux_mac/Caver3 folder to a destination directory and edit linux_mac/Caver3_0_1.py to set the correct caver3 path. Then run PyMOL as root and install the plugin via the Plugin menu, selecting the edited script.","https://schema.org",{"og:url":52,"og:type":92,"og:title":14,"og:site_name":59,"og:description":15},"article",{"robots":94,"canonical":52},"index,follow",{"doc_id":7,"site_id":24},{"code":4,"msg":5,"data":97},[98,103,108,113,118,123,128,132,137],{"id":99,"doc_module":11,"doc_module_name":46,"category_name":100,"show_sort_weight":101,"slug":102},11,"Presentations",90,"presentations",{"id":104,"doc_module":11,"doc_module_name":46,"category_name":105,"show_sort_weight":106,"slug":107},12,"Resumes",80,"resumes",{"id":109,"doc_module":11,"doc_module_name":46,"category_name":110,"show_sort_weight":111,"slug":112},14,"Invoices",70,"invoices",{"id":114,"doc_module":11,"doc_module_name":46,"category_name":115,"show_sort_weight":116,"slug":117},15,"Posters",60,"posters",{"id":119,"doc_module":11,"doc_module_name":46,"category_name":120,"show_sort_weight":121,"slug":122},16,"Social Media",50,"social-media",{"id":124,"doc_module":11,"doc_module_name":46,"category_name":125,"show_sort_weight":126,"slug":127},17,"Forms",40,"forms",{"id":21,"doc_module":11,"doc_module_name":46,"category_name":129,"show_sort_weight":130,"slug":131},"Letters",30,"letters",{"id":133,"doc_module":11,"doc_module_name":46,"category_name":134,"show_sort_weight":135,"slug":136},21,"Paper Templates",5,"papers-templates",{"id":12,"doc_module":11,"doc_module_name":46,"category_name":13,"show_sort_weight":4,"slug":138},"general-158"]