ContentsSubsectionsThis tutorial demonstrates how to use the VMD plugin Timeline to analyzeand identify events in molecular dynamics (MD) trajectories. Timeline createsan interactive 2D box-plot - time vs. structural component - that can showdetailed structural events of an entire system over an entire MD trajectory.Events in the trajectory appear as patterns in the 2D plot.The plugin provides several built-in analysis methods, and the means todefine new analysis methods. Timeline can read and write data sets, allowingexternal analysis and plotting with other software packages. Timeline includesfeatures to help analysis of long trajectories and trajectories with largestructures.
In the main 2D box-plot graph, users identify events by looking for patterns ofchanging values of the analyzed parameter. The user can visually identifyregions of interest - rapidly changing structure values, clusters of brokenbonds, differences between stable and non-stable values, and similar. The usercan explore the resulting structures by tracing the mouse cursor(``scrubbing') over the identified areas. The structure is highlighted andthe trajectory is moved in time to track the highlight.
If you have any questions or comments on this tutorial, please email theTCB Tutorial mailing list at tutorial-l@ks.uiuc.edu. The mailing list is archived at http://www.ks.uiuc.edu/Training/Tutorials/mailing_list/tutorial-l/.
Getting Started
If you downloaded the tutorial from the web, the files that you will be needing can be found in a directory called timeline-tutorial-files. If you received the files through a workshop, they can be found in the same directory under the path /Workshop/timeline-tutorial.
- Unix/Mac OS X Users:In a Terminal window type:
cd <path to timeline-tutorial-files directory>
You can list the content of this directory, by using the command ls.
- Windows Users:Navigate to the timeline-tutorial-files directory using Windows Explorer.
This will place you in the directory containing all the necessary files. In the figure below, you can see the structure of this directory.
Figure 1:Directory structure for tutorial exercises. Output for file-writing exercises is provided in the ``example_output' subdirectory.
Figure 2:Exploring a secondary structure event. Row a) shows the system beforethe local structure change, row b) shows the system afterwards. The left panels show the entire data plot. The middle panels shows a zoomed-inpart of the data plot, and the right panels shows the 3D structure of theselected trajectory frame. The vertical bar indicates the current frame. The purple oval, added for this figure, shows therough area of the identified event. See text for additional details.
Required Programs
The following programs are required for this tutorial:
Broken Timeline - Prologue Mac Os Catalina
- VMD: The tutorial assumes that you already have a working knowledge of VMD, which is available at http://www.ks.uiuc.edu/Research/vmd/(for all platforms)
- The VMD tutorial is available at
http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/
- a text editor of your choice (we offer a few easy-to-use recommendations):
- UNIX: nedit (www.nedit.org)
- Windows XP: WordPad (included with OS). We recommend using WordPad as opposed to NotePad for this tutorial. However, please ensure that you save any files in this tutorial as .txt format files, as opposed to .rtf or .doc files, and to use the file extensions specified in the exercise, e.g. .tml.
- Mac OS X: Smultron (smultron.sourceforge.net), TextEdit (included with OS)
- a command prompt, such as a terminal in UNIX, Terminal.app in Mac OS X, or the DOS command prompt in Windows. Windows users can obtain a command prompt by clicking Start Programs Accessories Command Prompt.
Timeline in action: examine events in titin domain extension
Broken Timeline - Prologue Mac Os 11
Thissubsection provides a short run-through of of Timeline features to provide ageneral idea of how the plugin is used. Later sections will introduce thedisplay and user interface in greater detail. Here, we look at an MDtrajectory of the I91 domain of the muscle protein titin. In the simulationtrajectory, an external force is applied to the I91 domain with the SteeredMolecular Dynamics method: one terminus of the domain is fixed and a harmonicrestraint moving with constant velocity is applied to the other terminus,causing the domain to extend, unfold, and unravel. The secondary structurechanges greatly as the domain unfolds; examining these changes will give us someinitial insight into how the domain architecture responds to applied force.
With the titin I91 extension trajectory loaded into VMD, the user starts Timeline byselecting Extension Analysis Timeline fromthe main VMD window, then generates the secondary structure plot by selectingCalculate Calc. Sec. Structure in the VMDTimeline window.
We examine trajectory events which appear as changes in value in the 2D plot.As the user moves the highlight cursor around the area of an event in the 2Dplot, she can explore the behavior of the 3D structure.Figure 2 illustrates examining an event in a Timelineplot of per-residue secondary structure. By moving the cursor around the eventarea indicated with a purple oval, the user observes a beta strand, depicted inyellow, losing its secondary structure as it peels away from another betastrand. Note that the purple oval is added for the purposes of this tutorial,the user must normally visually identify the event area. Here the event tonotice is the abrupt transition of a horizontal region of yellow to white: partof the domain losing the beta strand character (yellow) it had since the startof the trajectory and becoming random coil (white) as the domain extensionproceeds. A user would scrub the mouse highlight cursor around the area of thepurple oval, would produce the state shown inFigure 2a, before the local structure change, andexamine the steps needed to reach Figure 2b, after thelocal structure change has taken place. To ``scrub', click down the leftmouse button with the cursor in the area of interest in the 2D graph, then movethe cursor around the area of interest with the button still depressed - whilesplitting attention between the 2D graph, the changing 3D structure, and thechanging numerical values displayed in the Highlight Details panel (describedbelow).
Figure 3:Exploring a salt bridge breaking event. A Timeline plot of the saltbridges found throughout a trajectory. The structural elements in the vertical axis are selection groups, with each group being the pair ofresidues involved in a salt bridge. The leftpanels show the data plot, and the right panels show the 3D structure of theselected trajectory frame. The vertical bar indicates the current frame. The purple oval, added to this figure, shows therough area of the identified event. Row a) shows the system before the saltbridge breaks, row b) shows the system after the salt bridge breaks. See textfor additional details.
In Figure 3, a plot of salt bridge lifetimes during thetitin domain extension trajectory shown in Figure 2is displayed, illustrating moving the highlight cursor to examine a salt bridgebreaking event. This plot is per-selection; each selection is the pair ofresidues involved in a salt bridge. Only residue pairs that form a salt bridgefor at least one frame of the trajectory are listed. A highlighted salt bridgeis seen breaking between Figure 3a and3b. The Timeline highlighted representation can bemanipulated like any other VMD representation; here coloring of the highlightwas changed from the default ColorID 1/red to ResType toshow the different residue types of the salt bridge partners, and easily tracksalt bridge partners as they move apart.
Figure 4:Using the threshold count to find a color scaling range. The per-residue Root Mean Square Fluctuation (RMSF) plot in a) has color scale set to the default, i.e., full, data range. Adjusting the Threshold Count range sliders in b) shows multiple peaks in the for the displayed range in c). In d), the 2D plot coloring scale of has been set to the range that was found in c), revealing which structures contribute to the threshold count.
In Figure 4 Timeline's Threshold Count plot is used to help find asuitable color scaling for the plot shown (per-residue Room Mean SquareFluctuation (RMSF)). The Threshold Count is the number of residues or selections in each frame with a value within a given range. As the Threshold Count range controls are adjusted as shown in Figure 4b, a patternwith multiple peaks appears (Figure 4c), this range is thenused to change the color scale, with the result shown in Figure4d. The Threshold Count sliders allow the users to veryquickly scan through threshold ranges, without taking the time to redraw theentire 2D plot, while still giving an overview of theentire trajectory.
Per-residue vs. per-selection calculations
Timeline plots data about a list of structural elements vs. time. There are two ways of defining the list of structural elements to be analyzed in Timeline.
Per-residue: a list of residues; the protein and nucleotide residues in the user-defined selection. The default selection is ``all', so this defaults to being a list of all residues in the current molecule.
Per-selection: a list of any VMD selections. For example, a list ofsalt bridge pairs, a list of the segments in a large protein complex, a list of of favoritestructures in a molecule. These may be defined in built-in functions, listedexplicitly, or defined algorithmically in user scripts.
Next:Interface and controls
Up:Timeline Tutorial
Previous:Contents
Broken Timeline - Prologue Mac Os X
Contentsschool@ks.uiuc.edu
Broken Timeline - Prologue Mac Os Download
Introduction
This set of pages is dedicated to Rhapsody. Not only that, it will be produced using tools native to Rhapsody. I wanted a record of all the things that I learned over the years to make Rhapsody a very comfortable operating system to use. It seemed to me that the best way of doing that was to build a site using Rhapsody and Rhapsody native software*.
The hardware being used isn't top of the line by anyone's imagination. The bulk of the work is now being done on an Apple Power Macintosh 8600, which has a PowerPC 604ev at 300 MHz (with 1 MB of cache), with 416 MB of RAM and a 9 GB hard drive. This system is currently running Rhapsody 5.6. Additionally, a lot of work will be done using an IBM ThinkPad 760 ED which is running on a Pentium at 133 MHz and has 80 MB of RAM and a 6 GB hard drive. I've been using this system, unchanged, since the summer of 2000 (yes, it is still running on it's original installation of Rhapsody 5.1).
As I've been using Rhapsody for years, I have a pretty good idea what software I'll be using for this endeavor. The main app is going to be Stone Design's Create. I'll be using version 5.1 in Rhapsody 5.1 and both 5.2 and 10.0 in Rhapsody 5.6. I'll also be making use of Apple's HTMLEdit in Rhapsody 5.6 for some page formating/generation, and OmniWeb 3.0/3.1 for previewing pages and editing code (I use OmniWeb 5.1 in Mac OS X to do these tasks for most of the sites I work on these days). For image editing I'll be using Caffeine Software's TIFFany3 and PixelNhance, with additional help from CuttingRoom and ToyViewer. Word Processing is going to be done using Apple's TextEdit. In fact this is the one place I may slip from time to time when it comes to using only Rhapsody. Some of the text used is going to be typed in Mac OS X on my PowerBook, but it'll still be using TextEdit (my primary word processor). For uploading I'll be using the native version of RBrowser (I use the current version of this FTP client in Mac OS X for all my web work).
It should also be noted that I've started a similar site for NEXTSTEP and OPENSTEP (which can be found here). In the beginning I had thought about building that entire site using only OPENSTEP and OPENSTEP native apps, but as my only OPENSTEP system is set up mainly as a school system, I decided that I wasn't going to follow the same plan that I've used here. What was surprising was that even with the ability to use both Mac OS X and Rhapsody for the other site, most of the other site was still created (like this one) in Rhapsody. It just turns out that producing these types of pages is very easy in Rhapsody for me.
What is Rhapsody?
Rhapsody is the name given to the fifth major version of the Mach based operating system first made by NeXT computer back in the late 1980s. Originally called NEXTSTEP (until version 3.3) and then OPENSTEP (for versions 4.0-4.2), it was renamed again for version 5 after NeXT was acquired by Apple. The following table is all the versions of this operating system.
| OS Version | OS Name | OS Product Name | OS Code Name | | 0.8 | NeXTstep | NeXTstep 0.8 | Photon | | 0.9 | NeXTstep | NeXTstep 0.94 | Kodak | | 1.0 | NeXTstep | NeXTstep 1.0 | | 2.0 | NeXTSTEP | NeXTSTEP 2.0 | | 2.1 | NeXTSTEP | NeXTSTEP 2.1 | | 2.2 | NeXTSTEP | NeXTSTEP 2.2 | | 3.0 | NEXTSTEP | NEXTSTEP 3.0 | | 3.1 | NEXTSTEP | NEXTSTEP 3.1 | | 3.2 | NEXTSTEP | NEXTSTEP 3.2 | | 3.3 | NEXTSTEP | NEXTSTEP 3.3 | | 4.0 | OPENSTEP | OPENSTEP for Mach 4.0 | | 4.1 | OPENSTEP | OPENSTEP for Mach 4.1 | | 4.2 | OPENSTEP | OPENSTEP for Mach 4.2 | | 5.0 | Rhapsody | Rhapsody Developer Release | Grail1Z4 | | 5.1 | Rhapsody | Rhapsody Developer Release 2 | Titan1U | | 5.2 | Rhapsody | Rhapsody 1.0 | | 5.3 | Rhapsody | Mac OS X Server 1.0 | Hera1O9 | | 5.4 | Rhapsody | Mac OS X Server 1.0.1 | Loki1A2
(mislabeled
as Hera1O9) | | 5.5 | Rhapsody | Mac OS X Server 1.0.2 | Loki2G1
(labeled as
Hera1O9+Loki2G1) | | 5.6 | Rhapsody | Mac OS X Server 1.2 | Pele1Q10 | | 5.6 | Rhapsody | Mac OS X Server 1.2v3 | Medusa1E3 |
I assume that there have been seven versions of Rhapsody, version 5.0 through 5.6 (eight if you count both versions of Rhapsody 5.6), but I have never seen Rhapsody 5.2. This was to be the first public release, but was pulled by Apple at the last minute when they turned their energies towards the Mac OS X project.
Rhapsody 5.3 was given the product name Mac OS X Server. This was cosmetic as the system itself doesn't refer to itself as Mac OS X Server anywhere. In fact, as Apple realized they were going to have multiple versions of Mac OS X Server (given the product version numbers 1.0, 1.0-1, 1.0-2 and 1.2/1.2v3) they never changed anything about the GUI to show what version you had installed. The only way to find out which version of Mac OS X Server you had was to ask the system what version of Rhapsody it was (Rhapsody 5.3, 5.4, 5.5 and 5.6 would be shown when 'uname -sr' was entered into the terminal).
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Even though much of the technology of Rhapsody is still in Mac OS X today, they are not the same operating systems. Rhapsody is actually more like OPENSTEP in it's foundations than Mac OS X. This is mainly do to Apple's desire to remove any legacy elements which would have cumbersome licensing (like Adobe's Display Postscript) and replacing them with either Apple generated solutions or open source elements. The result was an operating system with many of the advantages of Rhapsody at a price that was only a fraction of what Rhapsody or OPENSTEP was going for when they were being sold.
Updates:
This site is in a constant state of construction (very much like my other site). I'll list additions here (from newest to oldest) as I finish them.
07-25-2009: Posted an updated page on TextEdit (here) and started fixing broken links on a number of pages
06-17-2007: Posted a page on Red Box (here)
10-12-2006: Posted a page on compatible Rhapsody laptops (here)
10-09-2006: Posted a page on modifying Rhapsody's Login window (here)
10-02-2006: Posted a page on running Rhapsody on a PowerBook G3 Kanga (here)
09-24-2006: Posted a page on software piracy (here)
08-24-2006: Posted a page on running Rhapsody on a PowerBook G3 Lombard (here)
08-07-2006: Posted a page on ToyViewer (here)
07-20-2006: Posted a page on Rhapsody compatible video cards for PowerPC systems (here)
04-23-2006: Posted the RhapsodyAnswers page (here) which is an archive of technical articles on Rhapsody, I also linked (in the System section) to a page of Fonts (here) on my NEXTSTEP and OPENSTEP Resource Page
03-09-2006: Posted a page on Rhapsody's timeline (here)
02-20-2006: Posted pages on Mac OS X Server and Rhapsody documentation and FAQs (here)
02-10-2006: Posted a page on running Rhapsody on a PowerBook 3400c (here) and on some of my other hardware experience with Rhapsody (here)
02-04-2006: Posted a page on benchmarking Blue Box (here) using Mathematica 2.2
08-21-2005: Posted a page on Applications Barrier to Entry (here) which includes Tevanian's testimony on Rhapsody
08-07-2005: Added a link on the Miscellaneous page to an article on porting OPENSTEP apps to Rhapsody (here)
07-23-2005: Posted a page on Id games for Rhapsody (here)
06-20-2005: Posted a page on Display Settings (here), which includes how to setup multiple monitors
01-05-2005: Posted Stone Design's Create 5: Online Manual (here)
12-16-2004: Posted a page on 'What is Rhapsody?' (here)
11-15-2004: Posted a page on making web pages in Rhapsody (here)
10-30-2004: Posted a page on Installing a 3Com EtherLinnk III card for Rhapsody (here)
07-08-2004: Posted a page on MailViewer for Rhapsody (here)
06-26-2004: Posted a page on PDF solutions for Rhapsody (here)
06-22-2004: Posted a page on getting started with Rhapsody 5.1 for Intel (here)
06-19-2004: Posted Create (10.0) portability test page (here), again this is not the full write up I am planning
06-10-2004: Posted a page on Rhapsody Applications (here), the first of a series of them
05-31-2004: Posted a page on OpenUp and PackUp&Go (here)
05-22-2004: Posted a page on Rhapsody Media (here) which covers identifying versions
05-12-2004: Posted pages on adding users and groups to Rhapsody (5.0, 5.1 and 5.3-5.6)
05-02-2004: Posted page on Rhapsody for NeXT users (here) which mainly looks at Fiend
04-16-2004: Posted page on Printing in Rhapsody (here)
04-15-2004: Posted a page on enlarging Blue Box (here), also added links to some Stepwise articles in the Hardware and Miscellaneous sections
04-13-2004: Posted an Apple Menu page (here), this is for both the Yellow Box and Blue Box version of the Apple Menu
04-10-2004: Posted Create (5.1) portability test page (here), this is not the full write up I am planning, which is why I put it in the Misc. section
04-10-2004: Posted Create (5.1) portability test page (here), this is not the full write up I am planning, which is why I put it in the Misc. section
04-08-2004: Posted page on installing Fonts (here) and on Caffeine Software's PixelNhnace (here)
04-07-2004: Posted page on Rhapsody's TextEdit (here)
04-02-2004: Posted page on Rhapsody's Universal Colors Palette (here)
03-29-2004: Posted page on installing Rhapsody (here) and on Rhapsody system requirements (here)
03-22-2004: Posted main section pages, page on installing software (here) and on OmniWeb (here)
* NOTE: Originally due to the sizes of images, I had ran most the images on early pages through ImageReady so I didn't run out of room. Since those early pages I've done most of the site using Create 10.0 which makes images that don't need to be optimized further. The images and illustrations were all made in Rhapsody or where left overs from previous writings on the subject. All HTML code was done using Rhapsody and Rhapsody native apps.
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