User contributions

From Jacobson Lab Wiki

Jump to: navigation, search
Search for contributions 
 

(Newest | Oldest) View (Newer 50) (Older 50) (20 | 50 | 100 | 250 | 500)

  • 06:53, 11 November 2010 (hist) (diff) Plop Monte Carlo(removed wrong syntax for sidemc only) (top)
  • 00:46, 7 August 2010 (hist) (diff) Load
  • 00:45, 7 August 2010 (hist) (diff) ICDA(New page: Quick Start: To run ICDA pka clust beg end fastpka no adjust yes To get plop to recognize the altered protonation states, in load pdb .... load pdb mypdb.pdb pka frompdb [other o...)
  • 00:27, 7 August 2010 (hist) (diff) Pka
  • 00:26, 7 August 2010 (hist) (diff) Plop Monte Carlo
  • 00:26, 7 August 2010 (hist) (diff) Plop Monte Carlo
  • 00:25, 7 August 2010 (hist) (diff) Plop Monte Carlo
  • 00:25, 7 August 2010 (hist) (diff) Plop Monte Carlo
  • 00:19, 7 August 2010 (hist) (diff) Plop manual
  • 00:18, 7 August 2010 (hist) (diff) Plop Molecular Dynamics(New page: Processes the dynamics options in the .con file prefixed by 'dyn' Control Words: All normal commands for selecting residues are active dyn [residue selection] & tempi [real]...)
  • 00:16, 7 August 2010 (hist) (diff) Plop Monte Carlo(New page: Move types: -Side chain moves: select_chi: Perturbs one random chi angle, with optional screening. Note -- the number of side chains perturbed each round is an input parameter to side cha...)
  • 00:10, 7 August 2010 (hist) (diff) m PlopRotTemp.py
  • 00:10, 7 August 2010 (hist) (diff) PlopRotTemp.py
  • 00:07, 7 August 2010 (hist) (diff) Basics of Plop
  • 00:00, 7 August 2010 (hist) (diff) Loop
  • 23:59, 6 August 2010 (hist) (diff) PlopRotTemp.py
  • 23:58, 6 August 2010 (hist) (diff) PlopRotTemp.py(New page: For ligands: Reads in a maestro mae file and makes a "rotamer enabled" template and the rotamer library to accompany it. This consists of finding the backbone core that results in the le...)
  • 23:57, 6 August 2010 (hist) (diff) PELE ANM(New page: Possible parameters If it necessary to turn on anm moves with anm_freq 1 (or some other integer) to run anm steps anm_freq [integer] : Set frequency of an...) (top)
  • 23:57, 6 August 2010 (hist) (diff) PELE (top)
  • 23:56, 6 August 2010 (hist) (diff) PELE Tasks(New page: Conditional Paramters if [metric] [ > < = ] [value] then [set these parameters] else [ set these other parameters] endif Sets paramters based on the values of certain metrics. Note ...) (top)
  • 23:55, 6 August 2010 (hist) (diff) PELE
  • 23:54, 6 August 2010 (hist) (diff) PELE Metrics(New page: '''Possible Metrics''' steps : Number of Steps on this processor in this task all_steps : Total Number of Steps on all Processors in...) (top)
  • 23:54, 6 August 2010 (hist) (diff) PELE
  • 23:53, 6 August 2010 (hist) (diff) PELE(New page: Protein Energy Landscape Explorer (PELE) Victor Guallar Lab Possible Paramters res [2 word PLOP res list] : Define a ligand using either the first and last residue or any oth...)
  • 23:45, 6 August 2010 (hist) (diff) Calculating RMSDs(New page: The ability to calculate RMSDs in PLOP is provided as a convenience. Please note that it is only intended to compare structures with identical sequences (or at the very least, only mini...)
  • 23:44, 6 August 2010 (hist) (diff) Homology(New page: '''Homology Modeling''' Specifically, this section deals with constructing a homology model from a sequence alignment. It is possible to do some rather sophisticated things with PLOP, ...)
  • 23:42, 6 August 2010 (hist) (diff) Helix(New page: Sample run: Input Output Helix prediction in PLOP is designed to systematically explore the conformational space of a single alpha-helix in the protein (within an adjustable cutoff ...)
  • 23:42, 6 August 2010 (hist) (diff) m Loop
  • 23:41, 6 August 2010 (hist) (diff) m Loop
  • 23:41, 6 August 2010 (hist) (diff) Loop(New page: == Loop Prediction == loop predict residue selection & [many, many options, see below] Sample run: Input Output Options controlling generation of loop candidate st...)
  • 23:33, 6 August 2010 (hist) (diff) Side(New page: == Side Chain Prediction == The command structure is side predict residue selection & gridres real & ofac_init real & ofac_min real & iter[ations] integer & rand[omize] ''ye...)
  • 23:32, 6 August 2010 (hist) (diff) Minimize(New page: == Direct Minimization == minim atom/residue selection & rmsg[radient] real & mxitn integer & iter[ations] integer & niterup integer & nbup yes/no & gbup yes/no The...)
  • 23:29, 6 August 2010 (hist) (diff) Plop residues
  • 23:28, 6 August 2010 (hist) (diff) Plop residues(New page: == Standard amino acids:== All standard amino acids are referred to using their 3 letter codes. Note that specific protonation states for residues with titratable side chains can be ...)
  • 23:27, 6 August 2010 (hist) (diff) Pka(New page: == Protonation States == The protonation states of Asp, Glu, His, Tyr, Cys, Lys, and phosphorylated residue side chains can vary depending on the pH and the local environment of the ...)
  • 23:26, 6 August 2010 (hist) (diff) Write
  • 23:25, 6 August 2010 (hist) (diff) Write
  • 23:25, 6 August 2010 (hist) (diff) Write(New page: == Writing PDB Files == The main command is write pdb ''file'' where ''file'' is a filename you specify for writing out the structure in Protein Data Bank format...)
  • 23:23, 6 August 2010 (hist) (diff) Plop
  • 23:23, 6 August 2010 (hist) (diff) Load
  • 23:22, 6 August 2010 (hist) (diff) Load(New page: == Loading PDB Files == The main command is load pdb file where file is a structure in Protein Data Bank format. There are several options that can be speci...)
  • 23:20, 6 August 2010 (hist) (diff) Basics of Plop
  • 23:20, 6 August 2010 (hist) (diff) Basics of Plop
  • 23:19, 6 August 2010 (hist) (diff) Plop manual(New page: == Protein Local Optimization Program: Manual == This "manual" is a work in progress and will continue to evolve as I have bits of time to work on it. The Basics PLOP is primari...)
  • 23:15, 6 August 2010 (hist) (diff) The basics(The basics moved to Basics of Plop: better name) (top)
  • 23:15, 6 August 2010 (hist) (diff) m Basics of Plop(The basics moved to Basics of Plop: better name)
  • 23:14, 6 August 2010 (hist) (diff) Basics of Plop(New page: Basics of PLOP Specifying Residues Residues are specified using the format "chain:number" (e.g., "A:134" to specify residue 134 in chain A). The term “residues” refers to both ...)

(Newest | Oldest) View (Newer 50) (Older 50) (20 | 50 | 100 | 250 | 500)

Views
Personal tools
Toolbox