Open source molecular visualisation techniques for researchers

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Last date of Registration : 20th August, 2025

 

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SKU: IIT Jodhpur | Date : 23rd Aug, 2025 Categories: ,

About the workshop

Workshop 1 : Open source molecular visualisation techniques for researcher

Workshop 2 : Open source molecular visualisation techniques for
researchers – Advanced

Important Note : 

  1. Participants may choose to enroll only in Workshop 1 and receive certification upon successful completion.

  2. Participants cannot enroll in Workshop 2 without first enrolling in Workshop

Profile of the Instructor

Parag A. Deshpande is a Professor and the Head of the Department of Chemical  Engineering at the Indian Institute of Technology Jodhpur. He served as a faculty in  the Department of Chemical Engineering IIT Kharagpur between 2012 and 2023  before assuming the current position. He is a recipient 2015 and 2019 DAAD  fellowship and Fulbright-Nehru professional and academic excellence fellowship  2020-21. He advises a research group which specialises in computational analysis of chemical and biochemical systems, employing DFT and QMMM calculations to understand the underlying materials science, catalysis and biophysical-biochemical  behaviour with specific interest in carbon capture, NOx abatement, and protein  engineering. 

Workshop 1

Module 1:

Introduction to molecular visualisation and theoretical concepts

Concepts Covered : 

  • Need of molecular visualisation tools
  • Importance of correct tool in improving efficiency of researchers
  • Overview of available tools

Learning Outcomes : 

The attendees will develop an appreciation of theoretical foundations of tools available for molecular visualisation

Module 2 : Building molecules

Concepts Covered : 

  • Do’s and don’ts of molecule building
  • Introduction to Avogadro
  • Molecule building using Avogadro and details on its features and limitations

Learning Outcomes : 

The attendees will learn to use the open source molecular visualisation tool Avogadro

Module 3 : More on molecular visualisation

Concepts Covered : 

  • Jmol as a new tool
  • Comparative features of Avogadro and Jmol
  • Analysing the output files from optimisation and transition state calculations

Learning Outcomes : 

The attendees will learn to use the open source molecular visualisation tool Jmol

Module 4 : More complexities

Concepts Covered : 

Preliminaries of handling crystals

Learning Outcomes : 

Prepare more complex structure building

 

Workshop 2 : Day 1

Day 1 : 

Module 1 : Quick review and overview

Concepts Covered :

  • Review of key features of molecular visualisation
  • Overview of new and advanced systems

Learning Outcomes : 

Recapitulation of the previously learnt concepts and importance of advanced methods

Module 2 : Handling crystalline systems

Concepts Covered :

  • Preliminaries of crystal systems
  • Do’s and don’ts while handling crystals

Learning Outcomes : 

  • Handling crystalline systems

Module 3 : More on crystalline systems

Concepts Covered :

  • More on crystals
  • Visualisation beyond atoms

Learning Outcomes : 

Visualisation of properties like electron density

Module 4 : More on crystalline systems

Concepts Covered :

Some examples from crystalline systems

Learning Outcomes : Quizzes, activities and competition

 

Workshop 2 : Day 2

Module 1 : Handling biomolecular systems

Concepts Covered :

  • Review of key features of biomolecular systems
  • Overview of new and advanced systems

Learning Outcomes : 

Quick overview of structural biology

Module 2 : Handling proteins

Concepts Covered :

Visualisation of proteins

Learning Outcomes : 

Handling proteins

Module 3 : More on biomolecular systems

Concepts Covered : 

  • Good visualisation practices
  • Good image rendering practices and techniques

Learning Outcomes : 

Good visualisation and reporting practices

Module 4 : More on biomolecular systems

Concepts Covered :

Some examples from biomolecular systems

Learning Outcomes :

Quizzes, activities and competition

Session Details

Course 1

Date of the Workshop : 23rd August, 2025

Timings : 10:00 a.m. – 01:00 p.m. & 02:00 p.m. – 04:00 p.m. (IST)

Mode of the Workshop : Online

Course 2

Date of the Workshop : 13th & 14th September, 2025

Timings : 10:00 a.m. – 01:00 p.m. & 02:00 p.m. – 04:00 p.m. (IST)

Mode of the Workshop : Online

Fee Structure

Course 1

Student : Rs. 1180 (Rs. 1000 + 18% GST)

Faculty : Rs. 2360 (Rs. 2000 + 18% GST)

Industry : Rs. 5900 (Rs. 5000 + 18% GST)

 

Course 2

Student : Rs. 2590 (Rs. 2500 + 18% GST)

Faculty : Rs. 5900 (Rs. 5000 + 18% GST)

Industry : Rs. 11800 (Rs. 10000 + 18% GST)

 

Intended Audience & Eligibility

Intended Audience :

Masters and PhD Students 

Eligibility : 

Students pursuing UG degree  courses in Engineering/Physics/Chemistry/Bioscience or higher 

Certificate Criteria

Attendance and Assignment Submission is mandatory for certification

(Attendance + quizzes + activities)

Type of Assignments : 

  • Online MCQ quiz 
  • Google form based project activity 

Additional Requirements

Participants should intsall the following softwares before attending the workshop(all are opensource )

(i) Avogadro

(ii) Jmol

(iii) VMD

(iv) xcrysden 

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