{"id":15696817,"url":"https://github.com/danmichaelo/crystallography","last_synced_at":"2026-02-03T06:39:18.362Z","repository":{"id":140199440,"uuid":"1576259","full_name":"danmichaelo/crystallography","owner":"danmichaelo","description":"A VMD plugin for drawing crystallographic vectors and aligning the view to a crystallographic view direction","archived":false,"fork":false,"pushed_at":"2022-10-19T17:03:39.000Z","size":1656,"stargazers_count":7,"open_issues_count":1,"forks_count":2,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-11-08T07:20:49.705Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Tcl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/danmichaelo.png","metadata":{"files":{"readme":"README.markdown","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2011-04-06T08:38:15.000Z","updated_at":"2022-10-20T01:23:10.000Z","dependencies_parsed_at":null,"dependency_job_id":"f80bcc12-7722-4cff-81ce-d479783eaded","html_url":"https://github.com/danmichaelo/crystallography","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/danmichaelo/crystallography","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/danmichaelo%2Fcrystallography","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/danmichaelo%2Fcrystallography/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/danmichaelo%2Fcrystallography/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/danmichaelo%2Fcrystallography/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/danmichaelo","download_url":"https://codeload.github.com/danmichaelo/crystallography/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/danmichaelo%2Fcrystallography/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29035844,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-03T06:11:29.234Z","status":"ssl_error","status_checked_at":"2026-02-03T06:11:03.146Z","response_time":96,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-10-03T19:10:02.270Z","updated_at":"2026-02-03T06:39:18.347Z","avatar_url":"https://github.com/danmichaelo.png","language":"Tcl","funding_links":[],"categories":[],"sub_categories":[],"readme":"# About\n\n[VMD](http://www.ks.uiuc.edu/Research/vmd/) plugin written primarily to make it \neasier to align the view direction along specific crystallographic directions. \nIt also includes commands to convert vectors between crystallographic and cartesian \ncoordinates, and to draw arrows indicating the crystallographic axes arrows and/or \nthe current view direction.\n\nThe plugin can be used either from the command line or from a GUI, inspired in part\nby the \"Orientation\" window of the program VESTA and the \"Set View Direction\" window \nof CrystalMaker.\n\nFor the plugin to work, the loaded molecule must contain unit cell information.\nIf VMD can not read this from your file, it can be set manually using the \npbctools plugin. Note that pbctools also provide the nice command `pbc box' to draw\nthe unit cell.\n\n# Installation\n\nPut the crystallography folder in a folder searched by VMD, that is, a folder\nlisted in `auto_path`. For instance, you may put it in `~/vmd/plugins`, and add\n\n    set auto_path [concat \"{$env(HOME)/vmd/plugins}\" $auto_path] ;\n\nto your `~/.vmdrc` (or `vmd.rc' on Windows) file. To add the plugin to the Plugins-menu, add the following\nto your `~/.vmdrc` file (or just type it in VMD when needed):\n\n    vmd_install_extension crystallography cryst_tk \"Crystallography\"\n\n# Example usage\n\nTo view along the [111] direction, type `view_along {1 1 1}` (list notation) or `view_along 111` (short-hand notation)\nTo view towards the (100) plane, type `view_towards {1 0 0}` or `view_towards 100`.\nTo show crystal axes, type `crystal_axes on -position lower-left`, say. \nSimilarly, type `view_vectors on` to show the vectors of the current viewing plane. \nThe plugin tries to show these as properly formatted Miller indices when a crystal plane is in focus.\n\nThe commands `cart2dir` and `cart2rec` transforms a vector from a cartesian basis {**i**,**j**,**k**} to a \nreal space lattice basis {**a**,**b**,**c**} and a reciprocal space lattice basis {**a**\\*,**b**\\*,**c**\\*}, respectively. \nAnd `dir2cart` and `rec2cart` transforms the other way around. \n\nAll the above can also be carried out using the GUI, that can be opened by using the menu item or by typing `cryst_tk`.\n\nSee `crystallography.tcl` for more information.\n\n![Vector drawing](https://github.com/danmichaelo/crystallography/raw/master/samples/vmdscene.png)\n\n# GUI\n\nThe font rendering on Linux is probably better if VMD is built with Tcl 8.5 instead of 8.4.\nSeems to be encoding issues on Windows.\n\n\n![GUI on Mac OS X](https://github.com/danmichaelo/crystallography/raw/master/samples/gui_mac.png)\n\n![GUI on Linux/Gnome](https://github.com/danmichaelo/crystallography/raw/master/samples/gui_gnome.png)\n\n![GUI on Windows XP](https://github.com/danmichaelo/crystallography/raw/master/samples/gui_windows.png)\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdanmichaelo%2Fcrystallography","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdanmichaelo%2Fcrystallography","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdanmichaelo%2Fcrystallography/lists"}