Advanced 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, 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  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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