PyMoL – A molecular graphics tool

PyMoL – A molecular graphics tool, a free cross-platform molecular graphics system to visualize molecules in a better way.

PyMoL - A molecular graphics tool

Docking of small molecule compounds into the binding site of a receptor and estimating the binding affinity of the complex is an important part of the structure-based drug design process.

For a thorough understanding of the structural principles that determine the strength of a protein/ligand complex both, an accurate and fast docking protocol and the ability to visualize binding geometries and interactions are mandatory.

About PyMol

Virtual screening of compound libraries has become a standard technology in modern drug discovery pipelines. If a suitable structure of the target is available molecular docking can be used to discriminate between putative binders and non-binders in large databases of chemicals and to reduce the number of compounds to be subjected to experimental testing substantially.

Visual examination of predicted binding geometries (docking poses) thereby contributes crucially to the further development of a lead compound either towards enhanced binding affinity, towards reduced side effects or towards reduced susceptibility to drug resistance-related mutations.

Over the last years, the PyMOL molecular graphics system has evolved from being a powerful molecular viewer with exceptional 3D-capabilities into a platform for several programs and applications which make use of PyMOL’s versatile visualization properties.

PyMol Bioinformatics tool

PyMOL is a free cross-platform molecular graphics system made possible through recent advances in hardware, internet, and software development technology.

PyMOL provides most of the capabilities and performance of traditional molecular graphics packages written in C or Fortran. However, its integrated Python interpreter endows it with features and expandability unmatched by any traditional package.

PyMOL has been released under a completely unrestrictive open-source software license 5 so that all scientists and software developers can freely adopt PyMOL and then distribute derivative works based on it without cost or limitation.

Molecular Graphics Representations

PyMOL supports most of the common representations for macromolecular structures: wire bonds, cylinders, spheres, ball-and-stick, dot surfaces, solid surfaces, wire mesh surfaces, backbone ribbons, and cartoon ribbons which are comparable to those generated by Molscript.

Molecular Graphics Representations

Labels can be displayed for atoms, and dashed bonds can be used to indicate hydrogen-bonding interactions and distances. Surfaces can be transparent, and molecules can be loaded from PDB files as well as several other common file formats.

Labels

Crystallographic Visualization

PyMOL reads CCP4 and X-PLOR 7 map files and can display multiple arbitrary bricks of electron density within each map. PyMOL also has the ability to “carve” out electron density around any selection of atoms to create figures which show only localized electron density.

This example shows the clarity of "carved" electron density compared with a standard cartesian brick.
This example shows the clarity of “carved” electron density compared with a standard cartesian brick.

Provided that a structure has been loaded from a PDB file with correct unit cell and space group parameters, PyMOL can generate symmetry-related molecules. This was made possible by R.W. Grosse-Kunstleve’s generous contribution to the SgLite package.

Electron density and models showed about a two-fold axis of symmetry

At present, symmetry-related molecules are treated as independent objects, not as virtual images of the original object. Electron density and models shown about a two-fold axis of symmetry. PyMOL contains a rudimentary electron density “wizard” (written in Python) which can be used to quickly navigate through one or more electron density maps surrounding an atomic model. This wizard enables one to move and regenerate multiple meshes merely by CTRL-middle-clicking on the atom to center. PyMoL – A molecular graphics tool

Although PyMOL’s built-in ray-tracer is quite good, PovRay support has recently been added, and it can now be used as a replacement renderer for the generation of the highest quality images. Both OpenGL and ray-traced images can be output from PyMOL using standard Portable Network Graphics (PNG) files.

PyMOL’s native cartoon ribbons are very similar to Molscript’s, but if genuine Molscript output is required, PyMOL can read Molscript output in Raster3D format to perform rendering. The advantage of using PyMOL instead of Raster3D is that it allows users to orient and combine multiple objects in real-time 3D prior to rendering. The quality of the resulting images is comparable using either approach.

PyMOL
Models

A standalone program

  • Atom Selections
  • Molecular Editing
  • Animations
  • Batch Processing and Command-Line Only Mode

Strengths

  • Cross−Platform. A single code base supports both Unix, Macintosh, and Windows, using OpenGL and Python and a small set of Open−source external dependencies.
  • Command−Line and GUI Control Real-world applications require both. • Atom Selections. Arbitrary logical expressions facilitate focused visualization and editing. Molecular Splits/Joins. Structures can be sliced, diced, and reassembled on the fly and written out to standard files (i.e. PDB).
  • Movies. Creating movies is as simple as loading multiple PDB files and hitting play.
  • Surfaces. As good if not better than Grasp, and mesh surfaces are supported too. Cartoon Ribbons. PyMOL’s cartoons are almost as nice as Molscript but are much easier to create and render.
  • Scripting. The best way to control PyMOL is through reusable scripts, which can be written in the command language or in Python.
  • Rendering. A built−in ray tracer gives you shadows and depth on any scene. You also render externally.
  • Output. PNG files output from PyMOL can be directly imported into PowerPoint. Conformational Editing. Click and drag interface allows you to edit conformations naturally. Sculpting allows the molecule to adapt to your changes.
  • Expandability. The PyMOL Python API provides a solid way to extend and interface.

Weaknesses

  • User Interface. Development has been focused on capabilities, not on easy−of−use for new users.
  • Documentation. Only recently has any documentation become available.
  • Object−Orientation. There is a single monolithic, functional API.
  • Electrostatics. PyMOL is not yet a replacement for Delphi/Grasp. No Mechanics Engine Although PyMOL sports potent molecular editing features, you can’t yet perform any “clean−up”.

Find the user guide.

PyMoL – A molecular graphics tool – Download at https://pymol.org/2/

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