User contributions for Oliv Eidam
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6 May 2013
- 22:5422:54, 6 May 2013 diff hist +2,893 N Filter.py: Created page with "=Filter.py: search a substructure in DOCK poses and calculate atom distances= Sometimes it is interesting to search for a substructure in your DOCK output poses and calculate..."
- 22:0322:03, 6 May 2013 diff hist −118 Calculate DOCK6 RMSD No edit summary
- 21:4821:48, 6 May 2013 diff hist +849 Screen3d No edit summary
- 21:4421:44, 6 May 2013 diff hist +1 Omega.parm No edit summary
- 21:4321:43, 6 May 2013 diff hist +20 Omega.parm No edit summary
- 21:4121:41, 6 May 2013 diff hist +1,019 Omega.parm No edit summary
- 21:3321:33, 6 May 2013 diff hist 0 N File:Omega1.png No edit summary current
- 21:3221:32, 6 May 2013 diff hist 0 N File:Dock4 noEstat.png No edit summary current
- 21:2321:23, 6 May 2013 diff hist +4 Plop No edit summary
- 21:1821:18, 6 May 2013 diff hist +886 Plop No edit summary
- 21:0821:08, 6 May 2013 diff hist +249 Plop No edit summary
- 21:0821:08, 6 May 2013 diff hist 0 N File:Map.png No edit summary current
- 21:0721:07, 6 May 2013 diff hist 0 N File:Plop960.png No edit summary current
- 21:0721:07, 6 May 2013 diff hist 0 N File:Xtal.png No edit summary current
30 April 2013
- 23:5523:55, 30 April 2013 diff hist +1 Phenix No edit summary
- 23:5423:54, 30 April 2013 diff hist 0 N File:Sa omit map2.png No edit summary current
- 23:4423:44, 30 April 2013 diff hist +13 Phenix No edit summary
- 23:3823:38, 30 April 2013 diff hist +1,201 Phenix No edit summary
- 23:3023:30, 30 April 2013 diff hist 0 N File:Sa omit map.png No edit summary current
- 23:1823:18, 30 April 2013 diff hist +1,019 Phenix No edit summary
- 20:4020:40, 30 April 2013 diff hist +487 Phenix No edit summary
- 18:2818:28, 30 April 2013 diff hist 0 N File:Pdb sf download.jpg No edit summary current
- 18:2118:21, 30 April 2013 diff hist +577 N Phenix Created page with "==Calculate electron densities using Phenix== Here are a couple of useful phenix commands to calculate electron densities. In docking, it is often useful to have a look at el..."
29 April 2013
- 22:5222:52, 29 April 2013 diff hist +19 Calculate DOCK6 RMSD No edit summary
- 22:5022:50, 29 April 2013 diff hist +3,005 N Calculate DOCK6 RMSD Created page with "==Calculate ligand RMSDs using DOCK6== Calculating ligand RMSDs is a tricky thing, but DOCK6 does this quite well. All you need is two ligands (with the same number of atoms..."
- 22:0822:08, 29 April 2013 diff hist +4 Tools for protein and ligand analysis No edit summary
- 22:0722:07, 29 April 2013 diff hist +2,855 N Omega.parm Created page with "==Changing settings for OMEGA (OpenEye)== You may be interested to change the default settings for OMEGA (defined in omega.py) when generating conformations for docking. Maby..."
- 22:0422:04, 29 April 2013 diff hist +145 Omega.py No edit summary
- 22:0022:00, 29 April 2013 diff hist −1,654 Omega.py No edit summary
- 21:4921:49, 29 April 2013 diff hist +495 Screen3d No edit summary
- 20:3820:38, 29 April 2013 diff hist +1,703 N Screen3d Created page with "==Sceen3d: Align ligands in 3D== This tool is useful if you want to align (superpose) conformations of a ligand (for example generated by OMEGA). Maybe you are interested to ..."
26 April 2013
- 23:4023:40, 26 April 2013 diff hist +68 Omega.py No edit summary
- 22:4222:42, 26 April 2013 diff hist +4,296 N Omega.py Created page with "==Changing settings for Omega (OpenEye)== You may be interested to change the default settings for Omega (defined in omega.py) when generating conformations for docking. Maby..."
- 19:0819:08, 26 April 2013 diff hist +156 Plop No edit summary
- 19:0319:03, 26 April 2013 diff hist +12 Plop No edit summary
- 19:0319:03, 26 April 2013 diff hist +6 Plop No edit summary
25 April 2013
- 21:3021:30, 25 April 2013 diff hist 0 Plop No edit summary
- 21:2621:26, 25 April 2013 diff hist 0 Plop No edit summary
- 21:2421:24, 25 April 2013 diff hist −40 Plop No edit summary
- 21:2321:23, 25 April 2013 diff hist +1 Plop No edit summary
- 21:2321:23, 25 April 2013 diff hist +322 Plop No edit summary
- 21:1521:15, 25 April 2013 diff hist −1 Plop No edit summary
- 21:1421:14, 25 April 2013 diff hist +276 Plop No edit summary
- 21:0821:08, 25 April 2013 diff hist +80 Plop No edit summary
- 21:0621:06, 25 April 2013 diff hist +2,908 N Plop Created page with "==Energy minimization using Plop== This page describes simple protocols for receptor/active site and ligand minimization using Plop.<br> Check also the Plop manual on the Jaco..."
18 April 2013
- 23:4523:45, 18 April 2013 diff hist +643 Tools for protein and ligand analysis No edit summary
- 18:1418:14, 18 April 2013 diff hist +71 Tools for protein and ligand analysis No edit summary
- 18:1118:11, 18 April 2013 diff hist −5 Tools for protein and ligand analysis No edit summary
- 18:1118:11, 18 April 2013 diff hist −2 Tools for protein and ligand analysis No edit summary
- 18:0818:08, 18 April 2013 diff hist +76 N Tools for protein and ligand analysis Created page with "- Plop - omega.py - screen3d - Phenix - filter.py - FlexPepDock - DOCK6 RMSD"