Changelog

From FoldX plugin for YASARA

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4.4.23

  • Fixed a bug that affected Alanine scan of object because FoldX version 3 beta 6 has some changes in the output files.

4.1.21

  • Fixed a bug that affected Burial of residue because FoldX version 3 beta 6 has some changes in the output files.

3.4.9

  • New command: Burial of residue calculates the sidechain and mainchain burial of one or more residues and provides a simple value between 0 and 1.

2.6.8

  • Fixed a bug where an error was raised during AnalyseComplex after using the Mutate Multiple Residues command.

2.3.21

  • New command: Hydrogen bonds of object draws all hydrogen bonds in an object with the ability to distinguish between weak and strong hydrogen bonds. It is also possible to draw only intermolecular hydrogen bonds.

1.4.22

  • Improved command: Mutate residue can now also handle the four DNA nucleotides A, G, C and T for mutating and free energy predictions. When a DNA nucleotide has been selected for mutation, its pairbase will also be mutated to the matching type.

1.4.21

  • New command: Energy analysis of object prints the per-residue energy contribution to the structure as well as a full per-residue energy decomposition to its separate terms.
  • Improved command: Alanine scan of object is now fully customizable by temperature, pH, ionic strength and Vander Waals penalty.

1.4.6

  • Fixed an issue in Build homology model where template structures with multiple residue types at the same position (e.g. 1EJG, residue 25) led to an error, even if the Repair option was checked. See the troubleshooting section for more information.

1.3.12

  • Improved command: All BuildModel and RepairPDB aided functionalities use the YASARA SupAtom command to superpose resulting models with the original structure. This is a substantial increase in superposition speed compared to the previous method that used the MUSTANG algorithm.

1.1.7

1.1.6

  • New feature: added support for Repairing Objects in the HUD context menu (right-click on an Object or Molecule in the HUD).
  • Fixed a problem where interaction energy calculations failed when some molecules were not recognized by FoldX.

0.11.22

  • Improved command: Interaction energy of molecules now also lists the residues at the interface.
  • Improved command: Mutate multiple residues now allows to select residues from different Molecules (still in the same Object). If Interaction energy is checked, the plugin will calculate this energy difference between all possible interfaces in the complex.
  • Fixed a bug in the homology modeling module where a faulty alignment file was passed to FoldX, leading to the substitution of the wrong residues.

0.11.5

  • New feature: added support for mutagenesis to phosphotyrosine, phosphothreonine, phosphoserine and sulphotyrosine. See the documentation for a table with residue codes.

0.10.31

  • Improved performance: Fixing and freeing a large amount of residues works significantly faster.

0.7.8

  • Adapted all scripts to work with Python 2 and Python 3. Needs YASARA 10.7.8 or higher to work properly.

0.5.7

  • Made some visualization improvements when showing h-bond differences and Van der Waals clashes upon mutation

0.4.22

  • Interaction energy calculation is not limited anymore to 2 molecules. In both selections you can select multiple molecules that are joined as a group in each selection. See the documentation for more info.

0.4.13

  • Changed the format of target sequence file in Build homology model. This has now become an 'alignment file' with (part of) the template sequence on the first line and (part of) the target sequence on the second line.

0.4.12

0.4.9 (beta)

  • New feature: Build homology model creates a model of a given target sequence using a selected object as template structure
  • New feature: Alanine scan of object mutates every residue in an object to alanine and calculates the energy difference
  • Improved performance: YASARA screen does not freeze anymore when running FoldX calculations
  • fixed a bug where a RepairPDB was executed twice (instead of once) when clicked Analyze > FoldX > Repair object
  • fixed a bug that made the plugin crash on paths with spaces
  • fixed a Windows specific Console bug
  • fixed a variable name bug in the main script

0.4.1 (beta)

  • New feature: added option to zoom in on mutation site after calculation to compare WT and mutant
  • New feature: added option to visualize steric clashes (C-C clashes only for now) around mutation site in WT and mutant after calculation
  • New feature: added option to show hydrogen bonds around mutation site in WT and mutant after calculation
  • New feature: added option to save last FoldX calculation (all FoldX raw output files) to a specific folder
  • it is now possible to repair more than one object
  • added Object number to FoldX input and output files for clarity

0.3.27 (beta)

  • New feature: added menu to mutate multiple residues (double, triple, ...)
  • New feature: added menu to calculate stability of object
  • New feature: added menu to calculate interaction energy between two selected molecules
  • New feature: added menu Configure the plugin to select FoldX executable and rotabase.txt. No need to manually edit the foldx.cnf file anymore
  • New features: Fix residues that should not move during RepairPDB of BuilModel. Free residues that were mistakenly fixed.
  • New feature: added FoldX options panel to select options. No need for preformatted options/commands files anymore.
  • the plugin is now platform-independent. Works on YASARA for Linux, MacOSX and Windows.
  • added FoldX menus/commands to AtomContext menus and ResidueContext menus (right-click on atom or residue in molecule or in sequence selector to apply FoldX to an object or residue)
  • added FoldX menus to HUD (head-up display) context menu (only supported in YASARA 10.3.24 or higher)
  • spread the plugin over multiple Python modules. Easier to maintain and debug
  • fixed a bug in buildmodel.py where some models were not superposed when superposing multiple FoldX models with numberOfRuns=1
  • known issue: turning off 'Move neighbours' will crash when 'Calculate interaction energy' is selected in 'Mutate residue'. Franz is working on a FoldX update.

0.3.18 (beta)

  • first FoldX plugin for Yasara released for beta-testing
  • commands: Repair object, Mutate residue (with repair, stablity change, interaction energy change)
  • customizable option: numberOfRuns
  • mutation to multiple substitutions
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