What we have covered
1. Visualization fundamentals Beyond Ball -and -Stick 2. Basic chemistry data types and representations
Part 2: Practical Chemistry Visualization 3. Some ideas about breaking barriers and increase usefulness of visualization
Mario Valle Swiss National Supercomputing Centre (CSCS)
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
What we cover now Data issues
1. Data and data management Representation follows data logical structure and intended usage 2. Good visualization tool characteristics
3. Visualization tools here at CSCS Horror stories from not knowing the data
4. Digital storytelling tools and ideas One thing is logical data format, another the physical data file format
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005 Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Usual chemistry data types Non quantitative data
O
O
OH
1D and 2D O Structures tables Scalar volumes
Data from prof. A. Oganov – ETH Zürich
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005 Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
1 Structure Structure visualization goals
Atoms coordinates Show spatial configurations Atom types With time show peculiar movements Eventually bonds data Show correlation between position/structure and other quantities Optional scalar values (like charges) or vector Show matching or spatial related configurations values (like vibration modes)
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005 Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Basic structure representation High level structures
CPK
Surfaces
Ball and Stick
Licorice
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005 AccessibleBeyond Ball-and-Sticksurface Tutorial – Mario Secondary Valle – CSCS U serstructure Day 27/09/2005 Secondary structure
Less is more Problem: structures are too big
Data from prof. A. Oganov – ETH Zürich
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2 Related scalar quantities Vector data (vibration modes)
Static (arrows) Animated
Colored by atom type Colored by charge
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Visualization techniques Data formats
Select part of a structure Base for almost everything Show two or more structures together PDB Show surfaces Gaussian Cube Add high level “summary” geometries (polyhedrons, Etc. planes, etc.) But there are incomplete formats (missing atoms types, unit cell, etc.) Other?
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005 Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Time dependent data Frame -by -frame or summary?
Sergey Churakov – PSI Villigen
Summary over trajectory
Images from AmiraMol Frame-by-frame
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3 Time -dependent visualization goals Trajectory data formats
Show spatial configurations changing over time Kino Show phase transitions PDB List of PDB DCD Working around limitations: Kino + file with base vectors Other ?
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Volume data Volume data file formats
The following formats contains structure + uniform grid of scalar values: Gaussian Cube CHGCAR Other?
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1D data Choose the right mapping
ABC analyzer warm-up
33
31 33 29
31 27 temperature(°C)
25 29 temp 0 3 6 9 12 15 18 27 time from power-on (min)
32 25 25 0 3 6 9 12 15 time
27
32
29 31
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005 Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005 Davide Donadio – ETH Zürich
4 2D Tables 3D time dependent data
Trajectory in parameter space Added perceptual cues to help understand 3D trajectory in parameter space
COSY NMR Spectra
Dotplot for protein
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1D & 2D tools Trend in scientific data lifecycle
From this (publish and forget)…
Gnuplot Grace Scigraphica R Matlab Other?
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Trend in scientific data lifecycle Metadata are not evil!
…to this (use, reuse, recycle)… Metadata is information about data We often use metadata without even knowing it
If you had two cans without Tuna? labels, which would you eat?
Without a label, how would Cat Food? you know which was tuna and which was cat food?
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5 Metadata inside/outside data Multiple files, different parameters
Noise variance = 0 Inside the file • E.g. PDB TITLE (describe what the PDB is about) KEYWDS (some keywords to retrieve the file) 0.003 AUTHOR (who to blame for bad data) REMARK 6 – 99 (free form remarks) Encoded in the filename or file path /simulations/20050921/param1=0.033/result_run_1.pdb In a companion file • Protein.pdb + Protein.xml • Desc.xml for a set of files
0.010
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My chemistry file collection The quest for the perfect tool
Description file editor
The perfect tool makes everyone happy. But: Chemistry is a very wide design space No single definition of perfection Visualization is still an art
Generated page view in browser
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The visualization “Holy Grail” Perfect tools – somewhere else
Your data
Smart Perfect system visualizations!
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6 Chemistry visualization tools Difficulty 1: tools inflexibility
Nice crystallography programs, What a chemistry visualization tool should provide: but animation missing and no Load and display everything I’m working on way to extend them Enable exploration and comparison Produce high quality images and movies for publication Has flexibility in adding customizing visualization techniques or analysis scripts Let me experiment with techniques and rendering modes But there are difficulties…
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005 Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Difficulty 2: formats a gog ò Difficulty 3: minimal integration
PDB, Gaussian Log, Gaussian Cube, Plan coordinates, Kino, SHEL -X, VASP POSCAR, XDATCAR, ADF, DCD, DL_POLY, VASP XDATCAR, Concatenated VASP POSCAR
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ChemViz@CSCS STM3 toolkit
We do not endorse any specific program, but encourage you to use the tool best suited to you STM3 is a framework in research which to develop unusual and enhanced techniques We use the STM3 platform to implement unusual for molecular visualization and advanced techniques STM3 goal is not to The other two application we suggest (if you ask) supplant existing tools are: VMD The toolkit is built on top Molekel of the commercial visualization environment The OpenBabel file type converter could be useful AVS/Express for accessing strange file formats
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7 STM3 modules VMD
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(new) Molekel Tools resources
STM3 http://www.cscs.ch/~mvalle/ChemViz/ http://www.cscs.ch/projects/AVSChemistry.php VMD http://www.ks.uiuc.edu/Research/vmd/ http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/ Molekel http://www.cscs.ch/a-display.php?id=138 OpenBabel http://openbabel.sourceforge.net/
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Digital storytelling Different roles of visualization
1. Help understanding data www.smartmoney.com/marketmap
2. Communicate and present results www.peets.com/selector_coffee/coffee_selector.asp We “see” a good story develops in our mind
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8 Why scientists are often boring? A not so unusual presentation…
When we added no drug the viral infection spread and lead to cell death within 17 hours of the initial challenge. “...drawing graphs, like motor-car driving and When we added the drug at 5 nM the viral infection persisted and love-making, is one of those activities which spread in the culture leading to cell death within 18 hours post almost every researcher thinks he or she can challenge. do well without instruction.” When we added the drug at 5 nM levels the 78% of cells survived viral infection and grew slowly without cell division. When we added the drug at 10 nM levels 73% of cells survived viral Wainer & Thissen, 1991 infection and grew slowly without cell division. Annual Review of Psychology When we added the drug at 15 nM levels 6 % of the cells resisted viral infection but did not grow or divide. When we added the drug at >15 nM levels all of the cells died within 10 hours.
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005 Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
… that could be better Excellence in thinking
Protection from viral infection
Survival time Growth/ [Drug] post challenge division Toxicity “[…] clarity and excellence in thinking is very much like clarity and excellence in the display of data. When control 0 17 hrs +/+ 0% principles of design replicate principles of thought, the 1 5 nM 18 hrs +/+ 22% act of arranging information becomes an act of insight.”
2 10 nM ∞ +/- 27% 3 15 nM ∞ -/- 94% Edward Tufte 1998 p. 9
4 > 15 nM 10 hrs -/- 100%
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Visual messages capture attention Visual preempts verbal messages
105
PowerPoint 1.0 derives from a 104 product called “Presenter” developed by Forethought A verbal message 103 Inc. at the beginning of 1987. never dominates over a non verbal 102 Microsoft bought Presenter on one. 101 august 1987 for 14 millions of dollars. 100 1999 2000 Immagine da: albinoblacksheep.com We walk away from this chart thinking that 2000 results are twice the ones from 1999 (instead of a mere +2%).
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9 Visual messages capture attention 14 Ways To Say Nothing…
Do you remember how much Microsoft paid Presenter?
Do you remember what the guy was doing in the photo?
Right! Wrong (violates rules) “““14“14 Ways to Say Nothing with Scientific VisualizatioVisualization”n” Al GlobusGlobus,, Eric Raible ––– NASA –––July 1994
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14 Ways To Say Nothing… Siggraph 1993: VIZ -O-MATIC
1. Never Include a Color Legend 2. Avoid Annotation 3. Never Mention Error Characteristics 4. When in Doubt, Smooth 5. Avoid Providing Performance Data 6. Quietly Use Stop-Frame Video Techniques 7. Never Learn Anything About the Data or Scientific Discipline 8. Never Compare Your Results with Other Visualization Techniques 9. Avoid Visualization Systems (e.g. AVS) 10. Never Cite References for the Data 11. Claim Generality but Show Results from a Single Data Set 12. Use Viewing Angle to Hide Blemishes 13. If Viewing Angle Fails, Try Specularity or Shadows 14. “This is easily extended to 3-D”
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Why chemistry should be boring? It is not a media, but it is important
Design your presentation remembering that not all your readers are perfect: There are color blind people Don’t rely on color alone for decisions Use appropriate color schemes There are people with low sight Avoid low contrast in visualizations and icons Avoid tiny fonts
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10 Media and tools Images – usual concerns
Image file formats Images No JPEG, better using PNG Usual problems Leave TIFF for process printing Tools Images for the web: JPEG, PNG, Animated GIF Movies Quality Usual problems Antialiasing lines and borders Tools Resolution Web Screen 75dpi better than 1000dpi for printers New, unusual output platforms? Colors Unreadable colors (especially on conference beamers!) Bad colors in print vs. good on screen Black & White requested by some publications
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Image formats Image quality
Edges on printed paper looks terrible at the printer resolution
Screen Paper JPEG
PNG
“mosquitoes” around sharp edges
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Color gamut Swiss Knife for images
Each media has a Image Magick
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11 Other useful image tools LittleCMS example of processing
Color corrected for GIMP
Check
Original image
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Different rendering intents Movies – usual concerns
Codec availability Impact playability on different machines. Unfortunately there is no universal no-fuss coding method Codec and container file format are two distinct things Quality Depends strongly on bitrate and compression method (trades compression time for quality) Suggestions for natural movies did not apply to sharp edge ‘cartoon-like’ movies File size Related to bitrate (quality), frame size, compressibility Output usage Rendering for visualization Rendering for presentation Personal projection, web, TV program, DVD burning, etc.
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Input to movie creation Codecs and containers
Usually a set of frames (image files) Normally everything is perfect on your own workstation...... and nothing works on the conference room PC. Better if the images are uncompressed (not to lose quality) Codecs MPEG1 Should choose a framerate (usually 10-12 fps, but some MPEG4 (different implementations: MS Mpeg4 V2, Divx, xvid) standards have a fixed framerate) X264 Not too much frames! (500 frames @ 12 fps 42 sec) Containers AVI MOV MPEG MP4
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12 Movie tools Movie players
Mencoder Default ones My preferred workhorse Windows Media Player It has a myriad of options (difficult to master) Quick Time Player (a triumph of non-usability) Adobe Premiere Other ones Everything you can dream of Xine (plays AVI on Linux) Perfect for adding titles and transitions Mplayer (plays almost everything on Linux and Windows) VLC (quick and multiplatform) VirtualDub Simple editing Other MJPEG, transcode, ffmpeg, ffmpegX, etc.
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GUI for mencoder Web page
Has unique opportunity for more interactive experience. Applets can be used in place of static images. The browser is an universal user interface for data collections and some decision support systems. Limits are in the available screen space and the heterogeneity of the client browsers (for platform, type and installed plugins) Load time is a critical factor, if it is too long, the user is discouraged and can go away.
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Consider for web display Unusual media: PDA & cellphones
Movies Download time Provide more than one resolution Images Reduce number of colors Reduce size Applets Chime Currently very Animated GIF limited and not an Quick and light usual medium, but who know...
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13 Immersive visualization What we have covered
1. Data and data management Enhanced interaction experience: you are Know your data “inside” your data. Record useful metadata Needs special 2. Good visualization tool characteristics hardware to view, Do not search the perfect tool, but think about your goal interact and track user position 3. Visualization tools here at CSCS Besides stereo Ask and consult with us! projection it adds 4. Digital storytelling tools and ideas viewpoint change Present to persuade and communicate
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Beyond Ball -and -Stick
Thanks for your attention!
Mario Valle
[email protected] http://www.cscs.ch/~mvalle/
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