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CHANGELOG.md

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PyMod 3 Changelog

This file contains descriptions of changes of new PyMod 3 releases.

Version 3.0.2 (17/8/2020)

  • Added the possibility to import results from HH-suite output files (HHR and A3M).
  • Added compatibility for pyside2 (thanks to Thomas Holder).
  • Fixed the requirements for fully compatible PyMOL versions (see the README.md file).

Version 3.0.1 (15/6/2020)

  • Fixed the PDB fetching functionality (updated to HTTPS urls on RCSB).

Version 3.0.0 (22/5/2020)

  • Updated the PyMod GUI using PyQt5.
  • Homology modeling using MODELLER. Implemented various changes, some of them are:
    • Customize the optimization schedule of MODELLER.
    • Customize the MODELLER objective function terms.
    • Added the GA341 scoring function for model evaluation.
    • When building oligomeric models, added the SOAP-PP scoring function for interfaces evaluation.
    • Added sortable tables for model evaluation.
    • Added the possibility to use parallel jobs when building multiple models.
    • Solved a series of bugs which did not allow to use some PDB structures as templates.
  • Added the possibility to perform loop modeling (with MODELLER) for elements that have a 3D structure loaded in PyMod/PyMOL.
  • Added the SCR_FIND protocol (for analyzing the conservation in multiple structural alignments).
  • Added the possibility to use the following HMMER programs:
    • phmmer, jackhmmer, hmmsearch (for searching protein sequence databases)
    • hmmscan (for searching profile HMM databases). hmmscan can be used as a tool to assign Pfam domain families.
  • Added an easy-to-use dialog to install all PyMod external tools.
  • Added an easy-to-use dialog to update the sequence databases for the external tools of PyMod.
  • Added a contact/distance map viewer feature.
  • Added a series of other small functionalities and fixes (please refer to the updated PyMod manual for a full list of them).

Version 2.0.8 (2/11/2017)

  • Introduced a series of fixes to add compatibility to PyMOL 2.0.

Version 2.0.7 (2/12/2016)

  • Fixed a bug that changed the atom order of structures when performing CE alignments with PyMOL.

Version 2.0.6 (21/11/2016)

  • When coloring structures by residue properties, all atom types of a residue are now colored with the same color, allowing better visualization of surfaces.

Version 2.0.5 (13/11/2016)

  • Added back the possibility to use the NCBI QBLAST server to perform a BLAST search after the NCBI switched its services to the HTTPS protocol.

Version 2.0.4 (7/11/2016)

  • Added the possibility to save and load PyMod projects.