Advanced Visualization for Chemistry

Transcription

1 Advanced Visualization for Chemistry Part 9 Tools in depth Mario Valle March 7 8, 2006 Plan 1. Introduce two tools 1. STM3 the tool used at CSCS (more developer oriented) 2. VMD widely used free tool (more end-user tool) 2. Overview the most common operations 3. Review their support to: 1. Target users 2. Chemistry support 3. Data model 4. File formats read 5. Flexibility and extensibility 4. Use them as an example for attacking other tools STM3 is a framework for the development of unusual and enhanced techniques for chemistry visualization 1

2 A little history Standard Chemistry Visualization tools are very good, but it s hard to include unusual or advanced functionalities. It is too expensive to develop -and maintain!- a new tool from scratch (the NIH syndrome!). Also you, the users, are really creative in requesting peculiar functionalities. So two years ago at CSCS Jean Favre introduced and adapted an existing toolkit (STM: See The Molecule from NCSC) built on top of AVS/Express. Later I have engineered and enhanced the toolkit to obtain the actual STM3. STM3 platform STM3 is built on top of the commercial visualization environment AVS/Express STM3 modules 2

3 STM3 modules Full module list with documentation on: STM3 modules Readers Readers for various, static and dynamic, chemical file formats. Molecular Modules Modules that computes various derived structures. Utility Modules Manipulation of molecules, like atom selection. Crystallography Modules Unit cells, periodic lattices and symmetries support. Gaussian Cube Utility Modules Gaussian output density cubes visualization and manipulation. Display Final rendering of molecular data, legends and interaction. Output Output to image files, movies and other formats. Full Applications Ready to run applications. Module list definition The list of modules has been defined incrementally answering requests and solving real user problems. That means: Interesting problems But also: Disorder Things learned on the job Discontinuous development Not every case covered (e.g. multi-component PDB) 3

4 AVS/Express STM3 data types Molecular Data Type Standard AVS Field Display Parameters Screen Image Geometries Getting started 1 Launch AVS/Express Linux Windows $ cd CSCSlib $./go $./go-viz $./go nohw (special cases) C:\> cd CSCSlib C:\CSCSlib> go.bat C:\CSCSlib> go-viz.bat C:\CSCSlib> go.bat -nohw 4

5 Getting started 2 1. Go To Libraries Chemistry 2. Then go to the rightmost column (Full Apps) 3. Drag the MolDisplayApp block in the area below marked Applications 4. In the window that pops up select the file format (e.g. PDB) and read a file. 5. Mouse rotate. Middle Mouse Button+Shift: Zoom. +Ctrl: Pan. Reset with the button. 6. With the Modules drop down menu select Display Molecule and change the molecule appearance. STM3 resources STM3 overview and image gallery page The list of current STM3 modules A (marketing) brochure on AVS/Express A user level AVS/Express course M. Valle: STM3: a chemistry visualization platform Zeitschrift für Kristallographie Vol. 220 (2005) Issue 5-6 Pages Review STM3 features 1. Target users More aimed to the developer Not an end user tool 2. Chemistry support It is not a complete {MD, crystallography, biomolecular, } visualization tool But has quite good support for MD and Crystallography 3. Data model Simple and evolving 4. File formats read What the user asks for 5. Flexibility and extensibility Maximal, but does not support end user extensibility (like plugins) 5

6 VMD VMD is a versatile, modifiable, fully documented molecular visualization program, and is freely distributed. VMD facilitates the study of macromolecules in an immediate and visual way. VMD benefits research and training in biology, physics, chemistry, biochemistry, and biophysics. VMD supports Microsoft Windows 95/98/NT, MAC and a wide variety of UNIX platforms VMD pages on: < VMD features Flexible atom selections Tcl based command and scripting language Static docking and structure alignment Display of multiple molecules simultaneously PDB, PSF, DCD and CRD file reading support Automatic conversion from other file formats Accelerated 3D rendering and stereoscopic display Scene export to external ray tracers Start VMD Viewer window VMD main window VMD console 6

7 Then 1. Load data 2. Select draw style 3. Select and create representations 4. Create subsets of atoms Create representation Classical representations Custom material definition Volumetric data visualization Create selection For each representation you can select all the atoms of the molecule or create a selection of them You can use one of the prebuild (singlewords) queries or build a query from a list of elementary conditions 7

8 Review VMD features 1. Target users It is an end user tool 2. Chemistry support Supports mostly biochemistry, but no Crystallography support 3. Data model Quite complete (for proteins) 4. File formats read A lot (again in the biomolecular area) 5. Flexibility and extensibility Very good extensibility, but only through TCL, no C++ API Something to take home 1. Do not theorize too much, start trying using a tool! 2. You can apply the same review questions to any tool Next step: CSCS experiences 8

9 Advanced Visualization for Chemistry Thanks for your attention! Mario Valle 9