User contributions for TBalius

19 April 2017

• 16:5216:52, 19 April 2017 diff hist 0‎ Tutorial on running DOCK3.7 with GIST ‎ →‎docking
• 16:5116:51, 19 April 2017 diff hist +350‎ Tutorial on running DOCK3.7 with GIST ‎ →‎prepare system for docking

18 April 2017

• 21:0021:00, 18 April 2017 diff hist +3,860‎ Tutorial on running DOCK3.7 with GIST ‎ →‎enrichment
• 17:5217:52, 18 April 2017 diff hist +5‎ DOCK 3.7 2015/04/15 abl1 Tutorial ‎ →‎set up directories and get databases
• 17:4817:48, 18 April 2017 diff hist +16‎ DOCK 3.7 2015/04/15 abl1 Tutorial ‎ →‎run enrichment calculations
• 17:3017:30, 18 April 2017 diff hist −4‎ Ligand preparation - 20170424 ‎ →‎3 ways to build ligands:
• 17:2917:29, 18 April 2017 diff hist +6‎ Ligand preparation - 20170424 ‎ →‎3 ways to build ligands:
• 17:2717:27, 18 April 2017 diff hist −4‎ Ligand preparation - 20170424 ‎ →‎3 ways to build ligands:
• 17:0917:09, 18 April 2017 diff hist +2,390‎ Ligand preparation - 20170424 ‎No edit summary
• 15:5515:55, 18 April 2017 diff hist +306‎ Tutorial on running Molecular Dynamics for GIST grid generation with scripts ‎ →‎Run GIST post processing
• 15:1415:14, 18 April 2017 diff hist +288‎ Tutorial on running Molecular Dynamics for GIST grid generation with scripts 2 ‎No edit summary

17 April 2017

• 23:2323:23, 17 April 2017 diff hist +6,859‎ Tutorial on running DOCK3.7 with GIST ‎ →‎docking
• 23:1823:18, 17 April 2017 diff hist 0‎ Tutorial on running DOCK3.7 with GIST ‎No edit summary
• 21:5521:55, 17 April 2017 diff hist +137‎ DOCK 3.7 2015/04/15 abl1 Tutorial ‎ →‎run enrichment calculations
• 21:3721:37, 17 April 2017 diff hist +118‎ DOCK 3.7 2015/04/15 abl1 Tutorial ‎ →‎Visualize the docking spheres
• 20:3220:32, 17 April 2017 diff hist +2,551‎ Tutorial on running DOCK3.7 with GIST ‎ →‎prepare system for docking (flex)
• 19:1719:17, 17 April 2017 diff hist +3,637‎ Tutorial on running DOCK3.7 with GIST ‎No edit summary
• 18:4818:48, 17 April 2017 diff hist +98‎ Tutorial on running Molecular Dynamics for GIST grid generation with scripts ‎No edit summary
• 18:4618:46, 17 April 2017 diff hist +4,353‎ N Tutorial on running Molecular Dynamics for GIST grid generation with scripts 2 ‎ Created page with "here is 003md.tleap_reduce.csh: #!/bin/csh # This script uses first reduce and then tleap to prepare a receptor for amber. # The outputs are: parameter topology file (prm7..."
• 18:4418:44, 17 April 2017 diff hist +2‎ Tutorial on running Molecular Dynamics for GIST grid generation with scripts ‎ →‎Prepare for AMBER
• 18:4318:43, 17 April 2017 diff hist +145‎ Tutorial on running Molecular Dynamics for GIST grid generation with scripts ‎ →‎Prepare for AMBER
• 18:1318:13, 17 April 2017 diff hist +20,538‎ Tutorial on running Molecular Dynamics for GIST grid generation with scripts ‎ →‎Run GIST post processing
• 17:4717:47, 17 April 2017 diff hist +17,769‎ Tutorial on running Molecular Dynamics for GIST grid generation with scripts ‎No edit summary
• 17:2417:24, 17 April 2017 diff hist +9,391‎ Tutorial on running Molecular Dynamics for GIST grid generation with scripts ‎ →‎Prepare for AMBER
• 17:0817:08, 17 April 2017 diff hist −27‎ Tutorial on running Molecular Dynamics for GIST grid generation with scripts ‎ →‎Set up directories
• 16:5916:59, 17 April 2017 diff hist +1,244‎ N Tutorial on running Molecular Dynamics for GIST grid generation with scripts ‎ Created page with "Tutorial written by Trent Balius (Jan. 9, 2017). Here are more GIST related tutorials: DOCK_3.7_with_GIST_tutorials == Disclaimer == This is foremost for training Shoic..."
• 16:5616:56, 17 April 2017 diff hist +83‎ DOCK 3.7 with GIST tutorials ‎No edit summary
• 16:5516:55, 17 April 2017 diff hist +73‎ Tutorial on running DOCK3.7 with GIST ‎No edit summary
• 16:5416:54, 17 April 2017 diff hist +72‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎No edit summary

14 April 2017

• 22:1022:10, 14 April 2017 diff hist +121‎ DOCK 3.7 2015/04/15 abl1 Tutorial ‎ →‎run be_blasti.py
• 21:4221:42, 14 April 2017 diff hist +136‎ DOCK 3.7 2015/04/15 abl1 Tutorial ‎No edit summary

12 April 2017

• 15:2815:28, 12 April 2017 diff hist +1‎ Ligand preparation - 20170424 ‎No edit summary

28 February 2017

• 00:1400:14, 28 February 2017 diff hist +64‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Prepare for AMBER
• 00:1200:12, 28 February 2017 diff hist +96‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Prepare for AMBER
• 00:0100:01, 28 February 2017 diff hist +14‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎No edit summary

30 January 2017

• 16:3616:36, 30 January 2017 diff hist +2‎ Tutorial on running DOCK3.7 with GIST ‎No edit summary
• 16:3516:35, 30 January 2017 diff hist −5‎ Tutorial on running DOCK3.7 with GIST ‎No edit summary
• 16:3516:35, 30 January 2017 diff hist +357‎ Tutorial on running DOCK3.7 with GIST ‎No edit summary
• 16:2816:28, 30 January 2017 diff hist +195‎ N Tutorial on running DOCK3.7 with GIST ‎ Created page with " This tutorial assumes that you have already completed the MD tutorial [Tutorial on running Molecular Dynamics for GIST grid generation]. # use the align the receptor and lig..."

24 January 2017

• 18:1918:19, 24 January 2017 diff hist −79‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Run convergence analysis
• 18:1518:15, 24 January 2017 diff hist +2,704‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Run convergence analysis
• 17:4617:46, 24 January 2017 diff hist −1‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Run convergence analysis
• 17:4617:46, 24 January 2017 diff hist −154‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Run convergence analysis
• 17:4517:45, 24 January 2017 diff hist +2‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Run convergence analysis
• 17:4417:44, 24 January 2017 diff hist +330‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Run GIST post processing
• 17:1317:13, 24 January 2017 diff hist +146‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Run convergence analysis
• 17:1117:11, 24 January 2017 diff hist +1,193‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Run convergence analysis
• 17:0417:04, 24 January 2017 diff hist +84‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Combining GIST grids
• 17:0217:02, 24 January 2017 diff hist +4‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Combining GIST grids
• 17:0217:02, 24 January 2017 diff hist +1,191‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Combining GIST grids

23 January 2017

• 19:5719:57, 23 January 2017 diff hist +20‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Disclaimer
• 17:5317:53, 23 January 2017 diff hist +201‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Combining GIST grids
• 17:3317:33, 23 January 2017 diff hist +1,327‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Run GIST post processing
• 17:3017:30, 23 January 2017 diff hist −1‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Run GIST post processing
• 17:2917:29, 23 January 2017 diff hist +1,718‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Run GIST post processing
• 16:3416:34, 23 January 2017 diff hist +1‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎No edit summary
• 16:3316:33, 23 January 2017 diff hist −31‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎No edit summary
• 16:3116:31, 23 January 2017 diff hist +1,737‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎No edit summary

22 January 2017

• 18:3618:36, 22 January 2017 diff hist +10,057‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Run AMBER
• 02:2702:27, 22 January 2017 diff hist +41‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Run AMBER
• 02:2002:20, 22 January 2017 diff hist +1‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Prepare for AMBER
• 02:1902:19, 22 January 2017 diff hist +92‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Prepare for AMBER
• 02:1502:15, 22 January 2017 diff hist −18‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Prepare for AMBER
• 02:1202:12, 22 January 2017 diff hist +708‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Prepare for AMBER
• 01:5701:57, 22 January 2017 diff hist +1,854‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Prepare for AMBER
• 01:3401:34, 22 January 2017 diff hist +60‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Set up environment
• 01:3401:34, 22 January 2017 diff hist +78‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Prepare for AMBER
• 01:2901:29, 22 January 2017 diff hist +77‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎ →‎Prepare for AMBER
• 01:2701:27, 22 January 2017 diff hist +1,496‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎No edit summary

20 January 2017

• 17:2117:21, 20 January 2017 diff hist +166‎ Tutorial on running Molecular Dynamics for GIST grid generation ‎No edit summary

9 January 2017

• 19:4019:40, 9 January 2017 diff hist +817‎ N Tutorial on running Molecular Dynamics for GIST grid generation ‎ Created page with " Tutorial written by Trent Balius (Jan. 9, 2017). == Disclaimer == This is foremost for training in house Shoichet lab members. But we hope that the community finds this us..."
• 18:1918:19, 9 January 2017 diff hist +134‎ Chimera ‎No edit summary current
• 18:1618:16, 9 January 2017 diff hist +1,383‎ N Chimera Tutorial (Delta opioid receptor) ‎ Created page with "Delta opioid receptor By Reed Stein, 2016 PSPG bootcamp at UCSF. 1. Open Chimera 2. Select an atom or residue by holding CTRL and clicking 3. Rotate the protein by clickin..."
• 18:1318:13, 9 January 2017 diff hist +27‎ Useful chimera commands ‎No edit summary
• 18:1218:12, 9 January 2017 diff hist −1‎ Chimera Tutorial (AMPC) ‎No edit summary current

7 January 2017

• 18:1518:15, 7 January 2017 diff hist +8‎ Chimera Tutorial (AMPC) ‎No edit summary
• 18:1418:14, 7 January 2017 diff hist +41‎ Chimera Tutorial (AMPC) ‎No edit summary
• 18:1118:11, 7 January 2017 diff hist +2,041‎ N Chimera Tutorial (AMPC) ‎ Created page with "Based on Powers & Shoichet 2002 paper on characterizing the AMPC binding site: Characterizing the β-lactamase binding site Chimera tutorial 1. Open Chimera 2. Select an at..."
• 18:0518:05, 7 January 2017 diff hist +19‎ Useful chimera commands ‎ →‎Command line
• 18:0318:03, 7 January 2017 diff hist +55‎ Useful chimera commands ‎No edit summary

6 January 2017

• 22:5522:55, 6 January 2017 diff hist −2‎ Using thin spheres in DOCK3.7 ‎ →‎Tutorial for using Thin Spheres in DOCK 3.7
• 22:5422:54, 6 January 2017 diff hist +104‎ Using thin spheres in DOCK3.7 ‎ →‎Tutorial for using Thin Spheres in DOCK 3.7
• 22:4922:49, 6 January 2017 diff hist +229‎ Using thin spheres in DOCK3.7 ‎No edit summary
• 22:3722:37, 6 January 2017 diff hist +68‎ Using thin spheres in DOCK3.7 ‎ →‎Tutorial for using Thin Spheres in DOCK 3.7
• 22:2422:24, 6 January 2017 diff hist +87‎ Using thin spheres in DOCK3.7 ‎ →‎Tutorial for using Thin Spheres in DOCK 3.7
• 22:1622:16, 6 January 2017 diff hist +42‎ Using thin spheres in DOCK3.7 ‎ →‎Tutorial for using Thin Spheres in DOCK 3.7
• 22:1522:15, 6 January 2017 diff hist +488‎ Using thin spheres in DOCK3.7 ‎No edit summary

5 January 2017

• 23:4623:46, 5 January 2017 diff hist −3‎ DOCK 3.7 with GIST tutorials ‎No edit summary
• 23:4323:43, 5 January 2017 diff hist +256‎ N DOCK 3.7 with GIST tutorials ‎ Created page with " To docking with GIST, you must generate gist grids using molecular dynamics to generate a trajectory and this post process it with cpptraj. * Tutorial on running Molecula..."
• 23:4023:40, 5 January 2017 diff hist +35‎ DOCK 3.7 ‎No edit summary

14 December 2016

• 21:1921:19, 14 December 2016 diff hist 0‎ Using thin spheres in DOCK3.7 ‎No edit summary
• 00:5600:56, 14 December 2016 diff hist +54‎ Useful chimera commands ‎No edit summary
• 00:5400:54, 14 December 2016 diff hist −3‎ Using thin spheres in DOCK3.7 ‎No edit summary
• 00:5300:53, 14 December 2016 diff hist −4‎ Using thin spheres in DOCK3.7 ‎No edit summary

7 December 2016

• 01:5901:59, 7 December 2016 diff hist +20‎ Calculate volume of the binding site and molecules ‎No edit summary
• 01:5801:58, 7 December 2016 diff hist +1,474‎ Calculate volume of the binding site and molecules ‎No edit summary

4 December 2016

• 22:3122:31, 4 December 2016 diff hist +166‎ Calculate volume of the binding site and molecules ‎No edit summary
• 22:2622:26, 4 December 2016 diff hist +681‎ Calculate volume of the binding site and molecules ‎ →‎Calculating the volume of a binding site.
• 22:1722:17, 4 December 2016 diff hist −1‎ Calculate volume of the binding site and molecules ‎ →‎how the volume calculation works.
• 22:0522:05, 4 December 2016 diff hist +51‎ Calculate volume of the binding site and molecules ‎ →‎Calculating the volume of a small molecule.