{"body":"{\n \"cells\": [\n  {\n   \"cell_type\": \"markdown\",\n   \"metadata\": {},\n   \"source\": [\n    \"# Load a PDB file and visualize it\"\n   ]\n  },\n  {\n   \"cell_type\": \"markdown\",\n   \"metadata\": {},\n   \"source\": [\n    \"Set up the AMBER paths.\"\n   ]\n  },\n  {\n   \"cell_type\": \"code\",\n   \"execution_count\": null,\n   \"metadata\": {},\n   \"outputs\": [],\n   \"source\": [\n    \"(setf (logical-pathname-translations \\\"amber\\\") \\n\",\n    \"      (list (list \\\"**;*.*\\\" (concatenate 'string (ext:getenv \\\"AMBERHOME\\\") \\\"/**/*.*\\\"))))\"\n   ]\n  },\n  {\n   \"cell_type\": \"code\",\n   \"execution_count\": null,\n   \"metadata\": {\n    \"scrolled\": true\n   },\n   \"outputs\": [],\n   \"source\": [\n    \"(leap.core:clear-path)\\n\",\n    \"(leap.core:add-path \\\"amber:dat;leap;prep;\\\")\\n\",\n    \"(leap.core:add-path \\\"amber:dat;leap;lib;\\\")\\n\",\n    \"(leap.core:add-path \\\"amber:dat;leap;parm;\\\")\\n\",\n    \"(leap.core:add-path \\\"amber:dat;leap;cmd;\\\")\"\n   ]\n  },\n  {\n   \"cell_type\": \"markdown\",\n   \"metadata\": {},\n   \"source\": [\n    \"Cando reads Leap scripts.\"\n   ]\n  },\n  {\n   \"cell_type\": \"code\",\n   \"execution_count\": null,\n   \"metadata\": {\n    \"scrolled\": false\n   },\n   \"outputs\": [],\n   \"source\": [\n    \"(source #P\\\"leaprc.protein.ff14SB\\\")\"\n   ]\n  },\n  {\n   \"cell_type\": \"markdown\",\n   \"metadata\": {},\n   \"source\": [\n    \"Load a PDB file - warn if there are any unbuilt heavy atoms and unbuilt hydrogens. Put the result in the global variable \\\\*pdb\\\\*.\"\n   ]\n  },\n  {\n   \"cell_type\": \"code\",\n   \"execution_count\": null,\n   \"metadata\": {\n    \"scrolled\": false\n   },\n   \"outputs\": [],\n   \"source\": [\n    \"(:= *pdb* (load-pdb \\\"data/pdbload/5t6o.pdb\\\"))\"\n   ]\n  },\n  {\n   \"cell_type\": \"markdown\",\n   \"metadata\": {},\n   \"source\": [\n    \"Use a simple builder that builds unbuilt atoms by building them a random direction and 1A away from their bonded neighbor.\"\n   ]\n  },\n  {\n   \"cell_type\": \"code\",\n   \"execution_count\": null,\n   \"metadata\": {},\n   \"outputs\": [],\n   \"source\": [\n    \"(simple-build-unbuilt-atoms *pdb*)\"\n   ]\n  },\n  {\n   \"cell_type\": \"code\",\n   \"execution_count\": null,\n   \"metadata\": {\n    \"scrolled\": false\n   },\n   \"outputs\": [],\n   \"source\": [\n    \"(count-unbuilt-atoms *pdb*)\"\n   ]\n  },\n  {\n   \"cell_type\": \"markdown\",\n   \"metadata\": {},\n   \"source\": [\n    \"Show the structure. Rotate using the left mouse button, scale using two finger dragging.\"\n   ]\n  },\n  {\n   \"cell_type\": \"code\",\n   \"execution_count\": null,\n   \"metadata\": {},\n   \"outputs\": [],\n   \"source\": [\n    \"(nglv:show-aggregate *pdb*)\"\n   ]\n  },\n  {\n   \"cell_type\": \"code\",\n   \"execution_count\": null,\n   \"metadata\": {},\n   \"outputs\": [],\n   \"source\": []\n  },\n  {\n   \"cell_type\": \"code\",\n   \"execution_count\": null,\n   \"metadata\": {},\n   \"outputs\": [],\n   \"source\": []\n  }\n ],\n \"metadata\": {\n  \"kernelspec\": {\n   \"display_name\": \"cando\",\n   \"language\": \"lisp\",\n   \"name\": \"cando\"\n  },\n  \"language_info\": {\n   \"codemirror_mode\": \"text/x-common-lisp\",\n   \"file_extension\": \".lisp\",\n   \"mimetype\": \"text/x-common-lisp\",\n   \"name\": \"common-lisp\",\n   \"pygments_lexer\": \"common-lisp\",\n   \"version\": \"X3J13\"\n  }\n },\n \"nbformat\": 4,\n \"nbformat_minor\": 2\n}\n","name":"","extension":"txt","url":"https://www.irccloud.com/pastebin/sfy0C9ML","modified":1535525013,"id":"sfy0C9ML","size":3076,"lines":153,"own_paste":false,"theme":"","date":1535525013}