Beyond Ball -and -Stick - Mario Vallemariovalle.name/ChemViz/TutorialChemViz2005.Part2.pdf ·...
Transcript of Beyond Ball -and -Stick - Mario Vallemariovalle.name/ChemViz/TutorialChemViz2005.Part2.pdf ·...
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Beyond BallBeyond Ball --andand --StickStickPart 2: Practical Chemistry VisualizationPart 2: Practical Chemistry Visualization
Mario ValleMario ValleSwiss National Supercomputing Centre (CSCS)Swiss National Supercomputing Centre (CSCS)
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
What we have coveredWhat we have covered
1. Visualization fundamentals
2. Basic chemistry data types and representations
3. Some ideas about breaking barriers and increase usefulness of visualization
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
What we cover nowWhat we cover now
1. Data and data management
2. Good visualization tool characteristics
3. Visualization tools here at CSCS
4. Digital storytelling tools and ideas
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Data issuesData issues
� Representation follows data logical structure andintended usage
� Horror stories from not knowing the data
� 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
Usual chemistry data typesUsual chemistry data types
O
O
O
OH
Data from prof. A. Oganov – ETH Zürich
Structures
Scalar volumes
1D and 2D tables
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Non quantitative dataNon quantitative data
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Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
StructureStructure
� Atoms coordinates
� Atom types
� Eventually bonds data
� Optional scalar values (like charges) or vector values (like vibration modes)
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Structure visualization goalsStructure visualization goals
� Show spatial configurations
� With time show peculiar movements
� Show correlation between position/structure and other quantities
� Show matching or spatial related configurations
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Basic structure representationBasic structure representation
Ball and Stick
Licorice
CPK
Surfaces
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
High level structuresHigh level structures
Accessible surface Secondary structure Secondary structure
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Less is moreLess is more
Data from prof. A. Oganov – ETH Zürich
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Problem: structures are too bigProblem: structures are too big
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Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Related scalar quantitiesRelated scalar quantities
Colored by atom type Colored by charge
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Vector data (vibration modes)Vector data (vibration modes)
� Static (arrows)
� Animated
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Visualization techniquesVisualization techniques
� Select part of a structure
� Show two or more structures together
� Show surfaces
� Add high level “summary” geometries (polyhedrons, planes, etc.)
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Data formatsData formats
Base for almost everything
� PDB
� Gaussian Cube
� 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
Time dependent dataTime dependent data
Frame-by-frame
Summary over trajectory
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
FrameFrame --byby --frame or summary?frame or summary?
Images from AmiraMol
Sergey Churakov – PSI Villigen
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Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
TimeTime --dependent visualization goalsdependent visualization goals
� Show spatial configurations changing over time
� Show phase transitions
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Trajectory data formatsTrajectory data formats
� Kino
� PDB
� List of PDB
� DCD
Working around limitations: Kino + file with base vectors
� Other ?
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Volume dataVolume data
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Volume data file formatsVolume data file formats
The following formats contains structure + uniform grid
of scalar values:
� Gaussian Cube
� CHGCAR
� Other?
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
1D data1D data
Davide Donadio – ETH ZürichBeyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Choose the right mappingChoose the right mapping
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Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
2D Tables2D Tables
COSY NMR Spectra
Trajectory in parameter space
Dotplotfor protein
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
3D time dependent data3D time dependent data
Added perceptual cues to help understand 3D trajectory in parameter space
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
1D & 2D tools1D & 2D tools
� Gnuplot
� Grace
� Scigraphica
� R
� Matlab
� Other?
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Trend in scientific data lifecycleTrend in scientific data lifecycle
From this (publish and forget)…
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Trend in scientific data lifecycleTrend in scientific data lifecycle
…to this (use, reuse, recycle)…
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Metadata are not evil!Metadata are not evil!
Metadata is information about data
We often use metadata without even knowing it
If you had two cans without labels, which would you eat?
Without a label, how would you know which was tuna and which was cat food?
Cat Food?
Tuna?
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Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Metadata inside/outside dataMetadata inside/outside data
� Inside the file• E.g. PDB
� TITLE (describe what the PDB is about)� KEYWDS (some keywords to retrieve the file)
� 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
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Multiple files, different parametersMultiple files, different parameters
Noise variance = 0
0.003
0.010
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
My chemistry file collectionMy chemistry file collection
Description file editor
Generated pageview in browser
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
The quest for the perfect toolThe quest for the perfect tool
The perfect tool makes everyone happy. But:
� Chemistry is a very wide design space
� No single definition of perfection
� Visualization is still an art
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
The visualization “Holy Grail” The visualization “Holy Grail”
Smartsystem
Your data
Perfectvisualizations!
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Perfect tools Perfect tools –– somewhere elsesomewhere else
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Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Chemistry visualization tools Chemistry visualization tools
What a chemistry visualization tool should provide:
� Load and display everything I’m working on
� 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
Difficulty 1: tools inflexibilityDifficulty 1: tools inflexibility
Nice crystallography programs, but animation missing and no way to extend them
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Difficulty 2: formats a Difficulty 2: formats a goggog òò
PDB, Gaussian Log, Gaussian Cube, Plan coordinates,PDB, Gaussian Log, Gaussian Cube, Plan coordinates,Kino, SHELKino, SHEL --X, VASP POSCAR, XDATCAR,X, VASP POSCAR, XDATCAR,
ADF, DCD, DL_POLY, VASP XDATCAR,ADF, DCD, DL_POLY, VASP XDATCAR,Concatenated VASP POSCARConcatenated VASP POSCAR
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Difficulty 3: minimal integrationDifficulty 3: minimal integration
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
ChemViz@CSCSChemViz@CSCS
� We do not endorse any specific program, but encourage you to use the tool best suited to you research
� We use the STM3 platform to implement unusual and advanced techniques
� The other two application we suggest (if you ask) are:� VMD� Molekel
� The OpenBabel file type converter could be useful for accessing strange file formats
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
STM3 toolkitSTM3 toolkit
STM3 is a framework in which to develop unusualand enhanced techniques for molecular visualization
STM3 goal is not to supplant existing tools
The toolkit is built on top of the commercial visualization environment AVS/Express
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Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
STM3 modulesSTM3 modules
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
VMDVMD
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
(new) (new) MolekelMolekel
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Tools resourcesTools 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/
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Digital storytellingDigital storytelling
We “see” a good story develops in our mindBeyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Different roles of visualization Different roles of visualization
2. Communicate and present results
1. Help understanding datawww.smartmoney.com/marketmap
www.peets.com/selector_coffee/coffee_selector.asp
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Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Why scientists are often boring?Why scientists are often boring?
“...drawing graphs, like motor-car driving and love-making, is one of those activities which almost every researcher thinks he or she can do well without instruction.”
Wainer & Thissen, 1991Annual Review of Psychology
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
A not so unusual presentation…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.
When we added the drug at 5 nM the viral infection persisted andspread in the culture leading to cell death within 18 hours postchallenge.
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 infection and grew slowly without cell division.
When we added the drug at 15 nM levels 6 % of the cells resistedviral 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
…… that could be betterthat could be better
-/-
-/-
+/-
+/+
+/+
Growth/division
100%10 hrs> 15 nM4
94%∞15 nM3
∞
18 hrs
17 hrs
Survival time post challenge
27%10 nM2
22% 5 nM1
0%0control
Toxicity[Drug]
Protection from viral infection
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Excellence in thinkingExcellence in thinking
“[…] clarity and excellence in thinking is very much like clarity and excellence in the display of data. When principles of design replicate principles of thought, the act of arranging information becomes an act of insight.”
Edward Tufte 1998 p. 9
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Visual messages capture attentionVisual messages capture attention
PowerPoint 1.0 derives from a product called “Presenter” developed by Forethought Inc. at the beginning of 1987.
Microsoft bought Presenter on august 1987 for 14 millions of dollars.
Immagine da: albinoblacksheep.com
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Visual preempts verbal messagesVisual preempts verbal messages
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A verbal message never dominates over a non verbal one.
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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Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Visual messages capture attentionVisual messages capture attention
Do you remember how much Microsoft paid Presenter?
Do you remember what the guy was doing in the photo?
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
““““14 Ways to Say Nothing with Scientific Visualization”14 Ways to Say Nothing with Scientific Visualization”14 Ways to Say Nothing with Scientific Visualization”14 Ways to Say Nothing with Scientific Visualization”Al Al Al Al GlobusGlobusGlobusGlobus, Eric , Eric , Eric , Eric RaibleRaibleRaibleRaible –––– NASA NASA NASA NASA –––– July 1994July 1994July 1994July 1994
14 Ways To Say Nothing…14 Ways To Say Nothing…
Right!Right!Right!Right! Wrong (violates rules)Wrong (violates rules)Wrong (violates rules)Wrong (violates rules)
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
14 Ways To Say Nothing…14 Ways To Say Nothing…
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”
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
SiggraphSiggraph 1993: VIZ1993: VIZ--OO--MATICMATIC
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Why chemistry should be boring?Why chemistry should be boring?
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
It is not a media, but it is importantIt 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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Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Media and toolsMedia and tools
� Images� Usual problems� Tools
� Movies� Usual problems� Tools
� Web
� New, unusual output platforms?
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Images Images –– usual concernsusual concerns
� Image file formats� No JPEG, better using PNG� Leave TIFF for process printing� Images for the web: JPEG, PNG, Animated GIF
� Quality� Antialiasing lines and borders
� Resolution� Screen 75dpi � better than 1000dpi for printers
� Colors� Unreadable colors (especially on conference beamers!)� Bad colors in print vs. good on screen� Black & White requested by some publications
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Image formatsImage formats
PNG
JPEG
“mosquitoes” aroundsharp edges
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Image qualityImage quality
Edges on printed paper looks terrible at the printer resolution
Screen Paper
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Color gamutColor gamut
Each media has aset of colors that can be reproduced
This set is called the device color gamut
The number of colors available quantize the color gamut. If the set is too small artifacts (color banding) arise
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Swiss Knife for imagesSwiss Knife for images
Image Magick <www.imagemagick.org>
convert img-from img-toconvert –scale 50% img-from img-toconvert –flip img-from img-toconvert img-from –colorspace Gray img-toconvert img-from –annotate 0x0+50+10 ‘© Mario Valle 2005’ img-toconvert img-from –draw ‘image Over 50,10 0,0 logo.tif’ img-to
montage –tile 2x2 –geometry 512x512 img[1234].png tot.png
identify –verbose image.jpg
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Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Other useful image toolsOther useful image tools
� GIMP <www.gimp.org>
� Littlecms <www.littlecms.com>
� Photoshop
Check <www.cscs.ch/~mvalle/postprocessing/>
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
LittleCMSLittleCMS example of processingexample of processing
Original image
Color corrected for HP1200PS
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Different rendering intentsDifferent rendering intents
Rendering for visualization Rendering for presentation
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Movies Movies –– usual concernsusual 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� Personal projection, web, TV program, DVD burning, etc.
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Input to movie creationInput to movie creation
� Usually a set of frames (image files)
� Better if the images are uncompressed (not to lose quality)
� Should choose a framerate (usually 10-12 fps, but some standards have a fixed framerate)
� Not too much frames! (500 frames @ 12 fps � 42 sec)
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
CodecsCodecs and containersand containers
Normally everything is perfect on your own workstation......and nothing works on the conference room PC.
Codecs� MPEG1� MPEG4 (different implementations: MS Mpeg4 V2, Divx, xvid)� X264
Containers� AVI� MOV� MPEG� MP4
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Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Movie toolsMovie tools
Mencoder� My preferred workhorse� It has a myriad of options (difficult to master)
Adobe Premiere� Everything you can dream of� Perfect for adding titles and transitions
VirtualDub� Simple editing
Other� MJPEG, transcode, ffmpeg, ffmpegX, etc.
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Movie playersMovie players
Default ones� Windows Media Player� Quick Time Player (a triumph of non-usability)
Other ones� Xine (plays AVI on Linux)� Mplayer (plays almost everything on Linux and Windows)� VLC (quick and multiplatform)
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
GUI for GUI for mencodermencoder
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Web pageWeb 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.
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Consider for web displayConsider for web display
Movies� Download time� Provide more than one resolution
Images� Reduce number of colors� Reduce size
Applets� Chime
Animated GIF� Quick and light
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Unusual media: PDA & Unusual media: PDA & cellphonescellphones
Currently very
limited and not an usual medium, but who know...
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Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
Immersive visualizationImmersive visualization
� Enhanced interaction experience: you are “inside” your data.
� Needs special hardware to view, interact and trackuser position
� Besides stereo projection it addsviewpoint change
Beyond Ball-and-Stick Tutorial – Mario Valle – CSCS User Day 27/09/2005
What we have coveredWhat we have covered
1. Data and data management
� Know your data
� Record useful metadata
2. Good visualization tool characteristics
� Do not search the perfect tool, but think about your goal
3. Visualization tools here at CSCS
� Ask and consult with us!
4. Digital storytelling tools and ideas
� Present to persuade and communicate
Beyond BallBeyond Ball --andand --StickStick
Thanks for your attention!Thanks for your attention!
Mario ValleMario Valle
[email protected]@cscs.chhttp://www.cscs.ch/~mvalle/ http://www.cscs.ch/~mvalle/