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"*": "Subscribe to the mediawiki-api-announce mailing list at <https://lists.wikimedia.org/mailman/listinfo/mediawiki-api-announce> for notice of API deprecations and breaking changes."
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"*": "Because \"rvslots\" was not specified, a legacy format has been used for the output. This format is deprecated, and in the future the new format will always be used."
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"title": "Tracking Systems",
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"*": "{{TOCright}}\n=Recommendations=\nThere are three specific Position Tracking systems that are recommended.\nChoosing a particular model depends on the factors described below, as well as availability.\n\n\n''Recommendations:''\n* '''NaturalPoint Tracking Tools Plus''' package provides 6 IR cameras plus the reflective balls, and calibration tools requied for a good tracking environment. This has been the traditional system of the IQ-station community, so there is a lot of experience with it.\n* '''NaturalPoint Trio''' system provides 3 IR cameras in a fixed bar arrangement. This saves from having to do calibration for the camera arrangements. These are just now being tested for use with IQ-stations.\n* '''AR-Tracking SmartTrack''' system provides 2 IR cameras in a fixed bar arrangement, also saving from calibration. These too are just now being tested for use with IQ-stations. Note that these are slightly pricier than the other two options.\n\n=Position Tracking Technologies=\nThere are many different technologies can can be employed to provide full '''six [http://en.wikipedia.org/wiki/Degrees_of_freedom_(mechanics) Degrees of Freedom]''' position tracking — three translational degrees and three rotational degrees — a requirement for physical immersion.\nThree common techniques for low-cost systems are:\n* Optical\n* Sonic\n* Electromagnetic\nEach method has it's own pros & cons.\nWe recommend the book [http://www.amazon.com/Understanding-Virtual-Reality-Interface-Application/dp/1558603530/ ''Understanding Virtual Reality''] for details on these technologies.\n\nAll three of our recommended technologies use optical tracking methods in the infrared spectrum (IR).\n\n=Experience with Specific Models=\n\n==Optical Tracking==\n* [http://www.naturalpoint.com/optitrack/products/tracking-tools-bundles/ NaturalPoint OptiTrack 6-camera TrackingTools Bundle]\n** {{Pro|'''Pro:''' Complete Hardware/Software solution}}\n** {{Pro|'''Pro:''' Moderate Cost — '''~$5600'''}}\n** {{Pro|'''Pro:''' Uses standard VRPN interface}}\n** {{Con|'''Con:''' Requires MS-Windows-based PC for software}}\n** {{Con|'''Con:''' Requires Lengthy calibration when cameras are re-adjusted (or accidentally moved)}}\n** used at Indiana University\n** used at Desert Research Institute\n** used at UC-Davis\n** used at INL\n* [http://www.naturalpoint.com/optitrack/products/v120-trio/ NatrualPoint OptiTrack Trio]]\n** {{Pro|'''Pro:''' Complete Hardware/Software solution}}\n** {{Pro|'''Pro:''' Low Cost — '''~$2500'''}}\n** {{Pro|'''Pro:''' Uses standard VRPN interface}}\n** {{Pro|'''Pro:''' No Calibration required}}\n** {{Con|'''Con:''' Requires MS-Windows-based PC for software}}\n** tested at INL\n** tested at Indiana University\n* [http://www.ar-tracking.de/SMARTTRACK.347.0.html A.R.T. SMARTTRACK]\n** {{Pro|'''Pro:''' Complete Hardware/Software solution}}\n** {{Pro|'''Pro:''' No Calibration required}}\n** {{Pro|'''Pro:''' No additional PC required}}\n** {{Con|'''Con:''' Somewhat higher cost ('''~$10000''' — '''~$7500''' academic)}}\n** in use at Indiana University\n** in use at Idaho National Laboratory\n\n==Electromagnetic Tracking==\n* [http://polhemus.com/?page=Motion_PATRIOT%20Wireless Polhemus Patriot Wireless]\n** {{Pro|'''Pro:''' No line-of-sight limitations — uses EM tracking technology}}\n** {{Con|'''Con:''' Not very robust}}\n** {{Con|'''Con:''' tracking ''markers'' are somewhat bulky}}\n** {{Con|'''Con:''' metal in the vicinity negatively affects performance}}\n** {{Con|'''Con:''' Somewhat higher cost ('''~$9000''' for a two-marker system)}}\n**: NOTE: price reflects that the system effectively needs two \"receivers\"\n** tested at Indiana University\n\n==Game Technology Tracking==\nWhile the example game system technologies listed here both use optical means of tracking,\nwe include them as a separate category due to the clear qualitative differences with\n''professional'' tracking systems.\n* MicroSoft Kinect\n** {{Pro|'''Pro:''' really, really low-cost ('''$150''')}}\n** {{Con|'''Con:''' not sufficiently robust for a research workflow}}\n** {{Con|'''Con:''' requires extra technical expertise to setup}}\n* Nintendo WiiMote\n** {{Pro|'''Pro:''' really, really low-cost ('''$50''')}}\n** {{Con|'''Con:''' not sufficiently robust for a research workflow}}\n** {{Con|'''Con:''' requires extra technical expertise to setup}}"
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"27": {
"pageid": 27,
"ns": 0,
"title": "VMD",
"revisions": [
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"*": "{{TOCright}}\n'''Visual Molecular Dynamics (VMD)'''\n\n[http://www.ks.uiuc.edu/Research/vmd VMD] is a good visualization tool for visualizing large molecular systems (typically used for large biomolecular systems). VMD has a long history of being interfaced to immersive technologies, including haptic devices and CAVE VR displays. There is also a section on the usage of VMD for HPC systems.\n\n=Immersive Mode VMD=\nInformation specific to the usage and setup of VMD for immserive systems such as the\n[http://en.wikipedia.org/wiki/Cave_automatic_virtual_environment CAVE virtual reality display].\n\n\n==How to Run VMD in Immersive Mode==\n\nIf VMD with the FreeVR interface is installed and properly configured, follow these steps to run in immersive mode:\n\n#<CODE>% module load freevr vmd</CODE>\n#<CODE>% vmd -dispdev freevrforms <path>/proteins/brH.pdb</CODE>\n#*This alone should be sufficient to render the molecule in the VR system, with joystick-controlled travel\n# In order to grab and move an object, the <CODE>grab</CODE> tool must be initialized:\n#:# →<CODE>Graphics</CODE> →<CODE>Tools</CODE>\n#:# →<CODE>Create</CODE> a <CODE>grab</CODE> style tool\n#:# set <CODE>Position</CODE> to <CODE>FreeVRTracker</CODE>\n#:# set <CODE>Buttons</CODE> to <CODE>FreeVRButtons</CODE>\n#:: The wand avatar will now appear in the scene\n# Now touch an object with the wand avatar and press <CODE>Button-1</CODE> to move it.\n\n==How to Configure VMD for Immersive displays==\n\nThere are two stages of configuration required for the overall configuration of VMD for immersive displays.\nThe first step is to configure FreeVR for the specific hardware setup of the immersive facility. This is explained in the FreeVR documentation.\nThe second stage is to link the FreeVR inputs to VMD \"sensors devices\".\n\nVMD \"sensor devices\" are specified in the <CODE>.vmdsensors</CODE> file.\nThe format of this file is described in the [http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug/node49.html VMD User's Guide: Tool Window] documentation.\n\n* Create a <CODE>.vmdsensors</CODE> file in your <CODE>$HOME</CODE> directory or the local directory:\n*: Here is a sample <CODE>.vmdsensors</CODE> file for use with FreeVR:\n<BLOCKQUOTE>\n<PRE>\n### \n### Configuration for the FreeVR trackers\n### \ndevice freevrtracker freevrtracker://local/freevr\nscale 0.5\noffset 0.9 -4.0 -1.0\ndevice freevrbuttons freevrbuttons://local/freevr:0,1,2,3\n## uncomment the following if you have more than one wand:\n#device vrtracker2 freevrtracker://local/freevr:1\n#scale 1.0\n#offset 0.9 -4.0 -1.0\n</PRE>\n</BLOCKQUOTE>\n\n\n==How to Build VMD w/ Immersive features==\n\nThis section specifically instructs on how to compile VMD using the [[FreeVR]] immersive interface library.\n\n# Install missing dependencies\n#: Commonly needed packages include:\n#:* tcl-devel (8.5 -- 8.6 works with edits to <CODE>Makefile</CODE>)\n#:* tk-devel (8.5 -- 8.6 works with edits to <CODE>Makefile</CODE>)\n#:* fltk-devel\n#:* netcdf-devel\n#:\n# Download the latest source (version 1.9.4a57 as of this writing [12/21/23])\n#:: [http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD]\n#: NOTE: there is a (free) registration process required\n#: NOTE: the pre-built packages may not contain the Immersive features \n# Untar the source ball\n#: E.g. <CODE>% tar -zxf vmd-<''version''>.src.tar.gz</CODE>\n#::(As of this writing [12/21/23] <CODE><''version''></CODE> is <CODE>1.9.4a57</CODE>)\n# Compile the plugins\n#: <CODE>% export PLUGINDIR=`pwd`/vmd-<''version''>/plugins</CODE>\n#: <CODE>% cd plugins</CODE>\n#: Ensure the Makefiles are set for the proper version of Tcl/Tk:\n#:: <CODE>% $EDITOR ./cionize/Makefile.specialbuilds ./Make-arch ./Make-arch.debug</CODE>\n#::: CHANGE: edit <CODE>{{Con|tcl8.5}}</CODE> and <CODE>{{Con|tk8.5}}</CODE> to be <CODE>tcl8.6</CODE> and <CODE>tk8.6</CODE> respectively if that's the version of Tcl/Tk installed on your system\n#: <CODE>% make <''architecture''></CODE> — E.g. LINUXAMD64\n#: <CODE>% make distrib</CODE>\n# Configure VMD\n#: <CODE>% cd ../vmd-<''version''></CODE>\n#: <CODE>% $EDITOR configure.options</CODE>\n#::Enter a list of desired options -- make sure to include <CODE>FREEVR</CODE>\n#::A sample list is:\n#::* <CODE>LINUXAMD64 OPENGL FREEVR FLTK TK TCL PTHREADS</CODE>\n#::An expanded list is:\n#::* <CODE>LINUXAMD64 OPENGL OPENGLPBUFFER FREEVR FLTK TK CXX11 XINERAMA XINPUT LIBPNG ZLIB VRPN NETCDF TCL PTHREADS SILENT</CODE>\n#::(I don't necessarily know what all those do and whether they help or not)\n#::(As of this writing [12/21/23] I was unable to get the <CODE>CUDA</CODE>, <CODE>Optix</CODE> or <CODE>Python</CODE> options to build.)\n#: <CODE>% $EDITOR configure</CODE>\n#:: CHANGE: <CODE>install_bin_dir=<''installation-path''>/bin</CODE>\n#:: CHANGE: <CODE>install_library_dir=<''installation-path''>/lib/$install_name</CODE>\n#: <CODE>% ./configure</CODE>\n# Compile VMD\n#: <CODE>% cd <path>/vmd-<''version''></CODE>\n#: <CODE>% export PLUGINDIR=`pwd`/plugins</CODE> — only if you're in a different shell from where this happened in step 4\n#: <CODE>% cd src</CODE>\n#: <CODE>% $EDITOR Makefile</CODE>\n#:: CHANGE: edit the values for <CODE>INCDIRS</CODE> and <CODE>LIBDIRS</CODE> to point to the correct directory for the '''FreeVR''' includes and library.\n#::* (UNLESS: you've configured <CODE>$CPATH</CODE> and <CODE>$LPATH</CODE>, perhaps through the \"modules\" system.)\n#:: CHANGE: edit <CODE>{{Con|tcl8.5}}</CODE> and <CODE>{{Con|tk8.5}}</CODE> to be <CODE>tcl8.6</CODE> and <CODE>tk8.6</CODE> respectively if that's the version of Tcl/Tk installed on your system\n#::* NOTE: Ideally the VMD build system would just specify <CODE>tcl8</CODE> and <CODE>tk8</CODE>.\n#: <CODE>% make veryclean</CODE>\n#: <CODE>% make -j 8</CODE>\n#:: NOTE: you will get a handful compiler warnings. As long as they are only warnings, you should be fine.\n# Install VMD\n#: <CODE>% sudo make install</CODE>\n# [Optional] Create a ''module'' file for VMD\n#: <CODE>% $EDITOR <''module-path''>/vmd/<''vmd-version''></CODE>\n#:: Set all the appropriate environment variables for VMD (<CODE>PATH</CODE>).\n\nAt this point you can now run VMD in standard desktop mode.\n* For example:\n*: <CODE>% vmd ../proteins/brH.pdb</CODE>\n\n\n=General Usage=\n==Usage Tidbits==\n\n* To place the FLTK menu interface on a screen separate from the immersive displays, use the <CODE>DISPLAY</CODE> environment variable prior to running the <CODE>vmd</CODE> command.\n\n* To change the overall world transformation via the Tcl command shell, try these options:\n** <CODE>vmd > '''scale to .5'''</CODE>\n** <CODE>vmd > '''translate to 0 0 -3'''</CODE>\n** <CODE>vmd > '''rotate y by 5'''</CODE>\n\n* To modify the atomic/molecular representation:\n** <CODE>vmd > '''mol modstyle 0 0 CPK; puts \"CPK\"'''</CODE>\n** <CODE>vmd > '''mol modstyle 0 0 Licorice; puts \"Licorice\"'''</CODE>\n\n* To modify selected objects:\n** <CODE>vmd > '''set a [atomselect 0 all]'''</CODE>\n** <CODE>vmd > '''set xval 4'''</CODE>\n** <CODE>vmd > '''set yval 2'''</CODE>\n** <CODE>vmd > '''$a moveby [list $xval $yval 0]'''</CODE>\n\n* To connect VR and other inputs to TCL scripts:\n** <CODE>vmd > '''user add key Aux-5 { scale by 1.3 }'''</CODE>\n** <CODE>vmd > '''user add key Aux-7 { scale by 0.7 }'''</CODE>\n** <CODE>vmd > '''user add key Aux-6 { animate forward; puts \"play\" }'''</CODE>\n** <CODE>vmd > '''user add key Aux-8 { animate forward; puts \"pause\" }'''</CODE>\n** <CODE>vmd > '''user add key Aux-0 { mol modstyle 0 0 CPK; puts \"CPK\" }'''</CODE>\n** <CODE>vmd > '''user add key Aux-1 { mol modstyle 0 0 Licorice; puts \"Licorice\"'''</CODE>\n\n* To add new objects/annotations into the world:\n** <CODE>vmd > '''graphics top text { 0 0 0 } \"hello\"'''</CODE>\n** <CODE>vmd > '''graphics top cone { 40 0 0 } { 40 0 10 } radius 10 resolution 60'''</CODE>\n** <CODE>vmd > '''graphics top line { 10 0 0 } { 0 0 0 } width 5 style dashed'''</CODE>\n** <CODE>vmd > '''graphics top list'''</CODE> — output a list of object IDs ''(I think)''\n** <CODE>vmd > '''graphics top info 1'''</CODE> — or any of the ID numbers returned in the list\n\n* Useful system commands:\n** <CODE>vmd > '''logfile console'''</CODE> &mdash start recording interactions as TCL commands ''(like ParaView's trace)''\n** <CODE>vmd > '''logfile off'''</CODE> — stop the TCL command trace and output the results\n** <CODE>vmd > '''menu main off'''</CODE> — or <CODE>on</CODE>\n** <CODE>vmd > '''menu list'''</CODE> — list all the interface menus\n** <CODE>vmd > '''user print keys'''</CODE> — list all the keyboard shortcuts\n\n* To get information about the environment:\n** <CODE>vmd > '''vmdinfo arch'''</CODE>\n** <CODE>vmd > '''echo $auto_path'''</CODE> — lists the path whence plugins are searched\n\n* Commands that aren't useful in Immersive Mode:\n** <CODE>vmd > '''display resize 1920 1080'''</CODE>\n** <CODE>vmd > '''display projection orthographic'''</CODE>\n\n\n==Usage Issues==\n\n[NOTE: these issues are from tests with VMD version 1.9.2a15. (And need to be re-tested with version 1.9.4a57)]\n\n* I still need to figure out the proper scale and offset (this would/will be easier if we can avoid the use of Euler angles in \"<CODE>P_GrabTool.C</CODE>\").\n* The <CODE>grab</CODE> tool only grabs one molecule object at a time, so multiple molecules won't stay together.\n* The <CODE>grab</CODE> tool requires that the wand avatar be touching an object before it can be moved.\n* The <CODE>rotate</CODE> tool does not work\n* I don't know how to use the <CODE>joystick</CODE> tool — does it work with the VR interfaces?\n* I need to learn whether (and if so what) the command-line and/or tcl-shell options for setting up the graphics tools w/o the need for the interactive menu.\n* There are gimble lock issues when the wand points up or down.\n* The material colors of some/all of the objects in the scene are not always present.\n* Changes in representations seem to only have an effect on a single screen.\n\n==Build Issues==\n* VMD should compile with Tcl/Tk 8.6 (as mentioned above), probably better to just use the major version number\n* The CUDA option did not compile for me as it's hard-coded to Cuda version 10.2, and I have version 12.3.\n* Some of the plugins report as being broken when starting VMD -- but some of them work, so it's not a matter of improperly building/installing the \"plugins\".\n\n==Development Issues==\n===Immersive-mode development issues===\nThis section is for issues that are of interest to those working directly on the VMD code-base as it relates to immersive interfaces.\n\n* '''DONE:''' Need to figure out how to pass <CODE>RenderInfo *</CODE> argument to <CODE>FreeVRScene::draw()</CODE> in order to add the navigation controls to where the virtual world is rendered.\n* Need to go over the source code in \"<CODE>P_GrabTool.C</CODE>\" so that I can know how to improve it (and I'll add comments as we go.) My goal is to avoid the use of Euler angles, since there are gimble lock issues in the interface.\n* Consider adding a <CODE>grab-world</CODE> tool that allows the entire world to be grabbed with the wand. '''An alternative was done — an always active \"Grab-World\" operation.''' \n* Determine whether there is a mechanism to enable an X11 window always-on-top property for the FLTK control menu.\n** Alternatively, a command that returns the X11 id of a menu's window could be used by a tool like <CODE>xdotool</CODE> to manipulate the window however is desired.\n\n===Non-immersive development issues===\n* Can FLTK menus work without OPENGL enabled?\n* Running <CODE>./configure</CODE> should report installation directories — since those are options we may want to change (otherwise one may not know where these can be configured).\n* Is there a command (if not, can one be added) that reports the configuration options of the compiled VMD?\n* <S>\"Lines\" and \"Points\" representations don't seem to work when rendering from BigRedII to the desktop.</S>\n** (I don't care about the BigRedII HPC system anymore, but this issue may also exist when using VNC, etc.)\n\n===ANARI development issues===\n* Using the \"standard\" <CODE>ANARI_LIBRARY</CODE> environment variable to specify the backend would be preferred.\n* Outputting a still-render to ''ImageMagick'' at the end of a <CODE>ANARI (interactive)</CODE> session should be optional — perhaps generated by a keyboard shortcut.\n\n\n=VMD with ANARI=\nNOTE: presently the VMD ANARI build is under development, but if you happen to have a working binary, here are some instructions:\n==Running VMD with ANARI==\n# <CODE>% module load cuda anari vmd</CODE>\n# <CODE>% export VMDANARIDEVICE=<''backend-library''></CODE> (e.g. <CODE>visrtx</CODE>)\n#* NOTE: It would be better if VMD used the \"standard\" <CODE>ANARI_LIBRARY</CODE> environment variable.\n# <CODE>% vmd <''options''></CODE>\n# Start ANARI rendering:\n#* File Menu -> Render\n#*# Select: Render the current scene using: <CODE>ANARI (interactive)</CODE>\n#*# Use mouse to interact\n#*# To end interactive session: Type <CODE>q</CODE> in the window\n#*# This will render and display a still image using ''ImageMagick''\n#*# Again type <CODE>q</CODE> to quit ''ImageMagick'' window\n\n\n=HPC Usage of VMD=\nThis section describes specific usage and compiling issues related the VMD\non HPC systems such as the Indiana University [http://kb.iu.edu/data/bcqt.html BigRedII supercomputer].\n\n==Running VMD via command-driving interactions on BigRedII==\nPresently, the VMD installed on BigRedII can be used interactively via the TCL command language.\nOnce running in an interactive shell, a molecule can be loaded and rendered with these simple\ncommands:\n\n#Load the <CODE>vmd</CODE> module:\n#:<CODE>% module load vmd</CODE>\n#Start VMD:\n#:<CODE>% vmd</CODE>\n#Load an example molecule:\n#:<CODE>vmd > mol new <''path''>/brH.pdb</CODE>\n#Render the current \"view\" to an image file:\n#:<CODE>vmd > render TachyonInternal <''filename''>.ppm</CODE>\n#Quit VMD\n#:<CODE>vmd > quit</CODE>\n\nThen, perhaps in another shell, an image viewer program can be used to see the rendered text.\n[NOTE: this requires logging on from an X11-cabable desktop system and using the <CODE>-X</CODE>\nflag to <CODE>ssh</CODE>.]\n* Use the FEH image viewer:\n*:<CODE>% module load imlib2 feh</CODE>\n*:<CODE>% feh --reload 1 <''filename''>.ppm</CODE>\n* or use the Eye-of-Gnome viewer:\n*:<CODE>% eog <''filename''>.ppm</CODE>\n\n\n==Links to Old Immersive Mode VMD wiki pages==\nHere are links to previous versions of this page that were designed for older VMD releases:\n* [https://wiki.iq-station.com/index.php?title=VMD&oldid=197 VMD 1.9.1 instructions (April 2014)]\n* [https://wiki.iq-station.com/index.php?title=VMD '''Return to current version''']"
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