{"id":644,"date":"2019-04-13T02:31:46","date_gmt":"2019-04-13T02:31:46","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/agfr\/?page_id=644"},"modified":"2019-04-26T22:19:59","modified_gmt":"2019-04-26T22:19:59","slug":"appendix","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/agfr\/appendix\/","title":{"rendered":"Appendix"},"content":{"rendered":"

This page was last updated on April 26th, 2019 at 10:19 pm<\/p>

APPENDIX<\/h1>\n

<\/a>Toolbar buttons<\/h1>\n
\n\n\n\n\n\n\n\n\n\n\n\n
<\/td>\nFocus the view on the current docking box<\/td>\n<\/tr>\n
<\/td>\nShow\/Hide the receptor line representation. This button cycles through 3 mode: 1) display entire receptor; 2) display receptor atoms inside the current docking box; 3) hide the receptor line representation.<\/td>\n<\/tr>\n
<\/td>\nShow\/Hide the receptor surface representation. This button cycles through 3 modes: 1) display the surface for the entire receptor; 2) display the surface for atoms inside the docking box; 3) hide the surface representation.<\/td>\n<\/tr>\n
<\/td>\nShow\/Hide residue labels. This button cycles through 3 modes: 1) label residues of the entire receptor; 2) label residues that have at least one side chain atom within the box; 3) hide the residue labels.<\/td>\n<\/tr>\n
<\/td>\nShow\/Hide the ligand.<\/td>\n<\/tr>\n
<\/td>\nShow\/Hide the ligand anchor atom. The anchor atom is the ligand atom that the AutoDockFR will be translate to binding pocket fill points to generate an initial pool of solutions to be optimized by its Genetic Algorithm.<\/td>\n<\/tr>\n
\"\"<\/td>\nShow\/Hide atoms forming covalent bond.<\/td>\n<\/tr>\n
<\/td>\nShow\/Hide the docking box.<\/td>\n<\/tr>\n
<\/td>\nShow\/Hide map visualization widget for displaying ortho-slices and iso-contours.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Parameter panel buttons<\/h1>\n\n\n\n\n\n\n\n
<\/td>\nDefine docking box to enclose the receptor<\/td>\n<\/tr>\n
<\/td>\nDefine docking box to enclose the ligand<\/td>\n<\/tr>\n
<\/td>\nDefine docking box to enclose the binding pocket fill points<\/td>\n<\/tr>\n
<\/td>\nDefine docking box to enclose user selected receptor amino acids<\/td>\n<\/tr>\n
<\/td>\nManually define the docking box and set grid point spacing and smooth factor<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Validity status lights (disabled, invalid, valid)<\/h1>\n\n\n\n\n\n\n
<\/td>\nThe box status light is red if the box does not overlap with the receptor, i.e.<\/em> no receptor atom is found to be inside the box. This light is never disabled and the condition applied to any docking calculation.<\/td>\n<\/tr>\n
<\/td>\nThe \u201cPocket\u201d validity status light is enabled unless a receptor is prepared for covalent docking, in which case the light becomes disabled. The light will be red if none of the currently selected\/displayed fill points is located within the box.<\/td>\n<\/tr>\n
<\/td>\nThe validity status light for Flexible Residues \u201cFR\u201d is only enabled when receptor amino acid side chain have been selected to be flexible during docking. The light will be red if at least one atom in these side chain is outside the docking-box.<\/td>\n<\/tr>\n
<\/td>\nThe covalent docking validity status light is only enabled if the covalent docking check button is checked. It will turn green after 2 atoms forming the covalent bond in the receptor have been selected.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

 <\/p>\n","protected":false},"excerpt":{"rendered":"

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