1. Rediscover the beauty of PyMOL Brought to you by Molecules Lim Ting Hong 086586J11 Tay Yong Ren 086520A11 Zhao Yang U0940261G PyMOL animate

2. Overview Introduction to PyMOL Objective Open Office Tool: Scratch Progress & Achievements Limitations of Scratch The Next Step: Improvements & Sustainability Our Tasks Summary Overview Introduction to PyMOLObjectivesScratch Progress Sustainability Summary

3. PyMOL Crystal structure of human neutrophil elastase Open-source visualization program Written mostly in Python Language Create images of biomolecules Biomolecular structures deposited in a database (Protein Data Bank - PDB) Overview Introduction to PyMOL Objectives ProgressScratch Sustainability Summary

4. Why is PyMOL chosen? Advantages Powerful molecular visualization Session files enables sharing of content with others. Pitfalls Hard to master Primitive and quirky user interface Wordy tutorials worsen learning experience ● http://www.pymolwiki.org/index.php/Practical_Pymol_for_Beginners http://www.pymolwiki.org/index.php/Practical_Pymol_for_Beginners Documentation currently limited and sometimes outdated Overview Introduction to PyMOL ObjectivesProgress Scratch Sustainability Summary

5. Objectives To enhance the documentation of PyMOL by creating an interactive teaching animation with the use of Scratch To benefit elementary users of PyMOL at the moment, due to time constraints Overview Introduction to PyMOL Objectives Progress Scratch Sustainability Summary

6. Progress and Achievements Overview Introduction to PyMOL Objectives Scratch Progress Sustainability Summary Problems we faced Given the 4week time-frame

7. Why did we choose Scratch? Programming language that helps create interactive stories and animations Allows sharing of the creations on the web OPEN SOURCE software Reasonable amount of skills needed to master Relatively manageable Overview Introduction to PyMOL Objectives Scratch Progress Sustainability Summary

8. Some Limitations of Scratch Authors of Scratch acknowledged the following limitations and promised that the upcoming version of Scratch launching in 2012 will enable these functions. Little or no user-input capability Lack of undo command Need to “Press a key” to enter into different sites Hyperlink to websites not allowed Poor resolution of imported backgrounds Default : 480 x 360 Overview Introduction to PyMOL Objectives Scratch Progress Sustainability Summary

9. The Next Step Overview Introduction to PyMOL Objectives Scratch Progress Sustainability Summary Build on intermediate and advanced levels Enable user-input capability Collate questions to generate a FAQ database and offer personalized learning experiences Serve as note-taking function Engage in a more professional recording Avoid the need to press a key before entering a new site. Creating a wiki page wiki page – http://pymolanimate.wikispaces.com/http://pymolanimate.wikispaces.com/ PyMOL animate now available at http://scratch.mit.edu/projects/sai831/1872091 - allows access to the original scratch file - allows modification according to changing needs of users Improvements Sustainability

10. Overview Introduction to PyMOL Objectives Scratch Progress Sustainability Summary

11. Significance of PyMOL animate Addition of more engaging and interactive elements into existing documentation of PyMOL. With Scratch, make PyMOL a less dreadful experience for students in the bioscience field. Overview Introduction to PyMOL Objectives Scratch Progress Sustainability Summary This work is licensed under a Creative Commons Attribution-NonCommercial 3.0 Singapore License.

12. Special Thanks to… Prof Harish for the valuable advice and feedback on our progress Authors of Scratch for their prompt replies on our queries Prof Mu Yuguang, our former tutor for PyMOL Prof Chang for his silent support! Thanks to our fellow classmates for the attention too!