Hi Masako, You cannot measure distances on the VRML object directly in Chimera. However, you could use the Volume Path Tracer tool to place markers at the ends of the object, then measure the distance between the markers. Volume Path Tracer: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ volumepathtracer/framevolpath.html measuring distances: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ structuremeas/structuremeas.html#distances Or, for an indication of scale rather than a measurement, you could use the Scale Bar tool: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/scalebar/ scalebar.html All these ways will show numbers based on the units of the VRML input. So you would need to know whether those units were angstroms, nanometers, or something else. I hope this helps, Elaine On Sep 7, 2006, at 6:11 PM, Masako Terada wrote:

Hi. I have a VRML file, which was created with different softwares. Is there anyway I can use Chimera to measure length of this tube-like structure?

Thanks, in advance! ---------------------------------------------------- Masako Terada

National Center for Microscopy and Imaging Research Center for Research in Biological Systems University of California, San Diego (858)534-7968 mterada@ncmir.ucsd.edu ----------------------------------------------------

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

Hi Masako, Chimera reads VRML files but does not support all of the VRML format. If Chimera correctly displays your VRML model you can measure a length. You can't directly measure the VRML. You would have to trace a new path using the VRML as a guide and measure that path in Chimera. You would use the Volume Path Tracer tool which allows you to place a chain of markers. The path tracer dialog is shown with menu entry Tools / Volume Data / Volume Path Tracer You'll need to turn on the "Drop markers on empty space" option and the "Move markers with mouse" option. Then you can place a marker with the mouse and drag it to the location you want. The path tracer tool only knows how to automatically position markers in the z-direction (perpendicular to the screen) for volume data, not for VRML models. So you will have to do that positioning by hand with the mouse. Holding down the Shift key while dragging the marker will move it in the z direction. When you have placed markers on the VRML model to define the path you would like to measure you can select the path (ie the links connecting the markers) and use the keyboard shortcut "pl" to measure the lengths. You'll need to turn on keyboard shortcuts using menu entry Tools / General Controls / Accelerators On To select the path you want to measure use ctrl-left-mouse-button to drag a box around the selected markers. The markers and links will be outlined in green. Another approach is to ctrl-click on one of the markers and use the "sc" keyboard shortcut to extend the selection to all the connected links and markers. The sc shortcut is in Chimera version 1.2255 in the snapshots section of the Chimera download page but not in 1.2199 production release version. I talked to Maryann Martone at the BioImage meeting about measuring neural spine lengths. If that is what you are looking at here are a few additional ideas. If you have 3-D microscopy data it would be easier to place markers and trace paths directly on that data in Chimera. Chimera reads about a dozen volume map formats -- probably MRC is the most commonly used. If you use a format Chimera cannot read I can look into adding it. Another idea is that if you have already traced the spines in other software (maybe that is where the VRML came from?) then a text list of xyz marker positions could be read into Chimera, avoiding the need to retrace the structure in Chimera. The format for importing the markers into Chimera is described in the Chimera manual http://www.cgl.ucsf.edu/chimera/1.2199/docs/ContributedSoftware/volumepathtr... and is a text file using XML syntax. Let me know if you have further questions. Tom