Hi, I have a .rec density map 2000x2000x1000 (xyz) but when i open it in Chimera it only shows the first image of the series (i.e. the dimensions are 2000x2000x1). do i need to convert it to a different format? thanks Matt ***************************** Matthew D. Shawkey, Ph.D. Assistant Professor Department of Biology Integrated Bioscience Program University of Akron Akron, OH 44325-3908 (office) +1 330-972-8192 (lab) +1 330-526-3225 http://gozips.uakron.edu/~shawkey
Hi Matt, That is normal Chimera behavior. If you open a large volume file it shows just one plane and there is a slider in the volume dialog to flip through planes. This is to allow fast initial display. If you want to display all planes press the "All" button below the Planes slider. The volume size at which only a single plane is shown is controlled by the volume dialog setting under "data display options" called "show plane when data larger than X voxels". I think the default is 256 million voxels (grid points). You can change that and save the default volume dialog settings (menu entry at bottom of Features menu). With a 4 Gvoxel map (2000x2000x1000) Chimera is going to of course subsample the data, i.e. volume step size is going to be greater than 1 if you try to show the full data. Tom
Hi Matt, There is a Volume Viewer setting that just shows 1 plane at first if the dataset is bigger than some cutoff. In the Volume Viewer "Features" menu, - choose "Planes" to put plane options in the dialog, then click All to show all planes - to control initial display, choose "Data display options" to put those options in the dialog, then turn the "show plane..." option off or change the cutoff size <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volume...
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volume...
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volume...
I hope this helps, ELaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 24, 2010, at 3:00 PM, Shawkey,Matthew D wrote:
Hi, I have a .rec density map 2000x2000x1000 (xyz) but when i open it in Chimera it only shows the first image of the series (i.e. the dimensions are 2000x2000x1). do i need to convert it to a different format? thanks Matt
participants (3)
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Elaine Meng -
Shawkey,Matthew D -
Tom Goddard