User contributions for Inchoate

12 September 2008

• 16:0816:08, 12 September 2008 diff hist −152‎ TOPTOC ‎No edit summary
• 15:4115:41, 12 September 2008 diff hist +321‎ TOPTOC ‎No edit summary
• 15:1915:19, 12 September 2008 diff hist +33‎ Displaying Biochemical Properties ‎ →‎Contact Potential
• 15:1815:18, 12 September 2008 diff hist +187‎ Displaying Biochemical Properties ‎ →‎Native Nucleic Acid Rendering in PyMol
• 15:1515:15, 12 September 2008 diff hist +36‎ Nuccyl ‎No edit summary current
• 15:1515:15, 12 September 2008 diff hist +36‎ Surfaces and Voids ‎No edit summary current
• 15:1515:15, 12 September 2008 diff hist +36‎ Caver ‎No edit summary
• 15:1415:14, 12 September 2008 diff hist +36‎ Dss ‎No edit summary
• 15:1415:14, 12 September 2008 diff hist +14‎ Displaying Biochemical Properties ‎ →‎Cavities
• 15:1415:14, 12 September 2008 diff hist +146‎ Displaying Biochemical Properties ‎ →‎Surface Area
• 15:1315:13, 12 September 2008 diff hist +36‎ Get area ‎No edit summary
• 15:1115:11, 12 September 2008 diff hist +13‎ Displaying Biochemical Properties ‎No edit summary
• 15:1015:10, 12 September 2008 diff hist 0‎ m Protein contact potential ‎No edit summary
• 15:0915:09, 12 September 2008 diff hist +37‎ Protein contact potential ‎No edit summary
• 15:0915:09, 12 September 2008 diff hist +55‎ Talk:Displaying Biochemical Properties ‎ New section: Organization
• 15:0615:06, 12 September 2008 diff hist +307‎ Protein contact potential ‎No edit summary
• 15:0515:05, 12 September 2008 diff hist 0‎ N File:Prot contact APBS.png ‎No edit summary current
• 14:5314:53, 12 September 2008 diff hist +1,722‎ N Protein contact potential ‎ New page: Protein_Contact_Potential is an automated PyMOL representation where the false red/blue charge-smoothed surface is shown on the protein. The rule of thumb with respect to PyMOL's inte...
• 14:5314:53, 12 September 2008 diff hist 0‎ N File:Prot contact pot.png ‎No edit summary current
• 14:4814:48, 12 September 2008 diff hist +272‎ APBS ‎No edit summary
• 14:4414:44, 12 September 2008 diff hist +1,194‎ Command Line Options ‎No edit summary
• 14:1514:15, 12 September 2008 diff hist +113‎ N Talk:Launching PyMOL ‎ Cleanup current
• 14:1414:14, 12 September 2008 diff hist −5‎ Launching PyMOL ‎No edit summary
• 14:1414:14, 12 September 2008 diff hist +2‎ Launching PyMOL ‎No edit summary
• 14:1314:13, 12 September 2008 diff hist +891‎ Launching PyMOL ‎No edit summary
• 14:0314:03, 12 September 2008 diff hist +873‎ N Inchoates pymolrc ‎ New page: Here's my example '''~/.pymolrc''' file. <source lang="python"> # sets first residue to 0 on load run ~/playground/pymol_scripts/oload.py # for cealign; optimal superposition run ~/playgr... current
• 13:5613:56, 12 September 2008 diff hist +23‎ MacOSX-specific .pymolrc file ‎No edit summary current
• 13:5613:56, 12 September 2008 diff hist +52‎ Launching From a Script ‎No edit summary
• 09:0109:01, 12 September 2008 diff hist +99‎ Visualizing a computed structure - a commented example ‎No edit summary

11 September 2008

• 16:5416:54, 11 September 2008 diff hist +349‎ Unbond ‎No edit summary
• 16:3916:39, 11 September 2008 diff hist +15‎ N File:Unbond2.png ‎ Unbond example. current
• 16:3916:39, 11 September 2008 diff hist +15‎ N File:Unbond1.png ‎ Unbond example. current
• 16:3716:37, 11 September 2008 diff hist +507‎ N Ray trace gain ‎ New page: = Overview = When ray tracing, PyMOL knows the Z-depth of coordinates. The ray_trace_gain setting darkens pixels based on their Z-depth. <gallery> Image:Ray trace gain0.png|ray_trace... current
• 16:3416:34, 11 September 2008 diff hist 0‎ N File:Ray trace gain20.png ‎No edit summary current
• 16:3316:33, 11 September 2008 diff hist 0‎ N File:Ray trace gain8.png ‎No edit summary current
• 16:3316:33, 11 September 2008 diff hist 0‎ N File:Ray trace gain2.png ‎No edit summary current
• 16:3316:33, 11 September 2008 diff hist 0‎ N File:Ray trace gain0.png ‎No edit summary current
• 16:1216:12, 11 September 2008 diff hist +4‎ Settings ‎No edit summary
• 15:5415:54, 11 September 2008 diff hist −60‎ m Objects and Selections ‎No edit summary current
• 15:1315:13, 11 September 2008 diff hist +198‎ Set Symmetry ‎No edit summary

10 September 2008

• 17:4717:47, 10 September 2008 diff hist +21‎ Load traj ‎No edit summary
• 17:4617:46, 10 September 2008 diff hist +520‎ N Defer builds mode ‎ New page: = Overview = The defer_builds_mode setting for improved performance with long trajectories. This now makes it possible to work with files containing thousands of states, and to render...
• 17:4217:42, 10 September 2008 diff hist +4‎ Settings ‎No edit summary

9 September 2008

• 17:3517:35, 9 September 2008 diff hist +497‎ H Add ‎No edit summary
• 10:2310:23, 9 September 2008 diff hist +135‎ Main Page ‎No edit summary
• 10:2210:22, 9 September 2008 diff hist +1,074‎ N Removealt ‎ New page: = Overview = removeAlt removes all atoms from '''obj''' that have alternate locations but aren't altloc '''keep'''. = The Code = <source lang="python"> def removeAlt(obj="", keep="A")...
• 10:1910:19, 9 September 2008 diff hist +57‎ Property Selectors ‎ →‎Select All Alternate Locations Except the A-Locations
• 10:0210:02, 9 September 2008 diff hist +1,876‎ Property Selectors ‎ →‎User Notes
• 09:5309:53, 9 September 2008 diff hist +150‎ Property Selectors ‎ →‎User Notes

8 September 2008

• 12:2912:29, 8 September 2008 diff hist +212‎ N CASTp ‎ New page: = Overview = The CASTpyMOL plugin allows for the visualization of surfaces and voids identified from CASTp using pyMOL. For more information see the [http://sts-fw.bioengr.uic.edu/castp/p...