I think PyMol is more for rendering of nice pictures as its lacks trajecory reading capabilities. For example can it color front and back of secondary structure motifs in different colors, what VMD cannot.

VMD on the other hand can load huge amount of trajectory data and TCL scripts and plugins ca be used for analysation. Altough VMD can render nice Pictures, too, its main usage is probably MD visualisation, building and analysation.

Dear Denish,

I would like to add UCSF Chimera in your considerations (and in part give answer to your question).

Some interesting links and references:

https://clarafi.com/training/from-structural-data-to-3d-animation-software-introduction-to-chimera-pymol-and-vmd-for-preproduction/

(pros and cons of UCSF Chimera as example is for free)

A bit old but still informative:

http://rosettadesigngroup.com/blog/284/what-is-your-favorite-molecular-viewer/

An interesting introduction to UCSF Chimera (my personal favourite):

http://aidanbudd.github.io/course_EMBO_at_TGAC_PPI_Sep2015/trainingMaterial/scooterMorris/Molecular%20Visualization%20Tutorial.pdf

Hope this is of any help to you.

The main strength of PyMOL is the generation of high quality ray traced images and animations for publications. In addition, through Plug-ins it serves as a graphical front end for computational programs such as APBS (electrostatics). Easy scripting using Python allows for automation of routine tasks.

VMD (Virtual molecular dynamics) is primarily geared at the interpretation and visualization of data generated by molecular dynamics. It can handle the huge datasets generated by such tasks (trajectory files). A large number of available scripts facilitate the extraction of data from MD traces.

For homology modeling, you might want to use programs like Deep View and UCSF Chimera in conjunction with Modeller. Chimera is also used for the analysis of CryoEM volume Data.

For the interpretation of crystallographic electron density, you may want to use programs such a COOT.

If you are working in the biomolecular modeling, simulation and structural biology field in an academic environment, your lab or department might consider joining the SBgrid Consortium https://sbgrid.org for easy access to a huge collection of precompiled applications (>270) for linux and OSX, tutorials, webinars and support.

following