About the workshop
Workshop 1 : Open source molecular visualisation techniques for researcher
Workshop 2 : Open source molecular visualisation techniques for
researchers – Advanced
Important Note :Â
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Participants may choose to enroll only in Workshop 1 and receive certification upon successful completion.
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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.Â
Workshop 1
Module 1:
Introduction to molecular visualisation and theoretical concepts
Concepts Covered :Â
- Need of molecular visualisation tools
- Importance of correct tool in improving efficiency of researchers
- Overview of available tools
Learning Outcomes :Â
The attendees will develop an appreciation of theoretical foundations of tools available for molecular visualisation
Module 2 : Building molecules
Concepts Covered :Â
- Do’s and don’ts of molecule building
- Introduction to Avogadro
- Molecule building using Avogadro and details on its features and limitations
Learning Outcomes :Â
The attendees will learn to use the open source molecular visualisation tool Avogadro
Module 3 : More on molecular visualisation
Concepts Covered :Â
- Jmol as a new tool
- Comparative features of Avogadro and Jmol
- Analysing the output files from optimisation and transition state calculations
Learning Outcomes :Â
The attendees will learn to use the open source molecular visualisation tool Jmol
Module 4 : More complexities
Concepts Covered :Â
Preliminaries of handling crystals
Learning Outcomes :Â
Prepare more complex structure building
Workshop 2 : Day 1
Day 1 :Â
Module 1 : Quick review and overview
Concepts Covered :
- Review of key features of molecular visualisation
- Overview of new and advanced systems
Learning Outcomes :Â
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 :Â
- Handling crystalline systems
Module 3 : More on crystalline systems
Concepts Covered :
- More on crystals
- Visualisation beyond atoms
Learning Outcomes :Â
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 :Â
Quick overview of structural biology
Module 2 : Handling proteins
Concepts Covered :
Visualisation of proteins
Learning Outcomes :Â
Handling proteins
Module 3 : More on biomolecular systems
Concepts Covered :Â
- Good visualisation practices
- Good image rendering practices and techniques
Learning Outcomes :Â
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 :Â 10:00 a.m. – 01:00 p.m. & 02:00 p.m. – 04:00 p.m. (IST)
Mode of the Workshop :Â Online
Course 2
Date of the Workshop : 13th & 14th September, 2025
Timings :Â 10:00 a.m. – 01:00 p.m. & 02:00 p.m. – 04:00 p.m. (IST)
Mode of the Workshop :Â 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 StudentsÂ
Eligibility :Â
Students pursuing UG degree courses in Engineering/Physics/Chemistry/Bioscience or higherÂ
Certificate Criteria
Attendance and Assignment Submission is mandatory for certification
(Attendance + quizzes + activities)
Type of Assignments :Â
- Online MCQ quizÂ
- Google form based project activityÂ
Additional Requirements
Participants should intsall the following softwares before attending the workshop(all are opensource )
(i) Avogadro
(ii) Jmol
(iii) VMD
(iv) xcrysdenÂ
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