Advanced Visualization for Chemistry
Part 7 – Visualization tools survey
Mario Valle
March 7 – 8, 2006
The perfect tool does not exist
The perfect tool makes everyone happy, but:
Chemistry is a very wide design space There is no single definition of perfection Visualization is still an art Corporations does not make much money with visualization…
Advanced Visualization for Chemistry – Mario Valle – CSCS – March 7-8, 2006
Chemistry visualization tools
A chemistry visualization tool should: 1. Load and display everything I’m working on 2. Enable exploration and comparison 3. Produce high quality images and movies for publication 4. Has flexibility in adding customizing visualization techniques or analysis scripts 5. Let me experiment with techniques and rendering modes But there are difficulties…
Advanced Visualization for Chemistry – Mario Valle – CSCS – March 7-8, 2006
1 Difficulty 1: tools inflexibility
Nice crystallography programs, but animation is missing and there is no way to extend them
Advanced Visualization for Chemistry – Mario Valle – CSCS – March 7-8, 2006
Difficulty 2: formats a gog ò
PDB, Gaussian Log, Gaussian Cube, Plan coordinates, Kino, SHEL -X, VASP POSCAR, XDATCAR, ADF, DCD, DL_POLY, VASP XDATCAR, Concatenated VASP POSCAR
Advanced Visualization for Chemistry – Mario Valle – CSCS – March 7-8, 2006
Difficulty 3: minimal integration
Advanced Visualization for Chemistry – Mario Valle – CSCS – March 7-8, 2006
2 Difficulty 4: disjoint subfields
Macromolecules
Crystallography
Advanced Visualization for Chemistry – Mario Valle – CSCS – March 7-8, 2006
Waiting for the perfect tool?
But also waiting for the perfect tool creates problems It is better to start doing something There are around plenty of chemistry visualization tools to try And there is always the opportunity to succumb to the NIH (Not Invented Here) syndrome…
Advanced Visualization for Chemistry – Mario Valle – CSCS – March 7-8, 2006
Possible tools classification
Free 1 Cost Commercial Single architecture 2 Platform Multiplatform Viewer 3 Usage Molecular renders Analysis tool Specialized 4 Field Generalist End user 5 User type User extensible Development environment Visualization 6 Goal Visualization + modeling
Advanced Visualization for Chemistry – Mario Valle – CSCS – March 7-8, 2006
3 Add subjective constrains
1. Already known
2. Already available in the department
3. I’m used to it
4. …
Advanced Visualization for Chemistry – Mario Valle – CSCS – March 7-8, 2006
Some questions to ask
1. Which are the file formats accepted?
2. Which are the representations supported?
3. Is there a community behind the tool?
4. Is the development and support active ?
5. Which is the data model supported?
Advanced Visualization for Chemistry – Mario Valle – CSCS – March 7-8, 2006
Some tools
VMD Macromolecules, multiplatform, active community STM3 Almost CSCS specific, active development, dev environment Molekel Active and vocal user community, simple and fast PyMOL Interesting but contrived, extensible, some modeling Jmol Powerful applet See also
Advanced Visualization for Chemistry – Mario Valle – CSCS – March 7-8, 2006
4 And your preferred tool?
Do you have used other tools? Why you selected those particular tools?
Advanced Visualization for Chemistry – Mario Valle – CSCS – March 7-8, 2006
Next step: cover more in depth
VMD
STM3
Advanced Visualization for Chemistry – Mario Valle – CSCS – March 7-8, 2006
Advanced Visualization for Chemistry
Thanks for your attention!
Mario Valle
http://www.cscs.ch/~mvalle/ [email protected]
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