Hi Kristin, Here are some commands to take a wedge out of a virus. I'll use example EMDB 1408 which is a small 63^3 map. volume #0 region 0,0,0,31,31,62 This shows a 90 degree wedge of the map, grid points with x and y indices from 0 to 31 (region argument is imin,jmin,kmin,imax,jmax,kmax). If I wanted to see the complement of this wedge (the remaining 3/4 of the virus) one trick would be to open the map 4 times, or one time and use the volume dialog File / Duplicate 3 times. Then create the 4 wedges: volume #0 region 0,0,0,31,31,62 volume #1 region 31,0,0,62,31,62 volume #2 region 0,31,0,31,62,62 volume #3 region 31,31,0,62,62,62 then just show 3 of the maps. You can also use the vop octant command to get a similar effect. Normally that command removes just one octant (1/8 of the virus) and you asked for 1/4. But it can be tricked into removing 1/4 by specifying a center vop #0 octant center 31,31,0 shows the quadrant (indices 31 <= i <= 62, 31 <= j <= 62) while vop #0 ~octant center 31,31,0 shows the complement. This is different from the volume region command in that it makes a new map and sets some of the grid values to zero. The volume region command simply restricts display of the original map to a sub-box. This creates a different appearance where the volume region result gives flat surface faces where the map was clipped (due to volume cap high values at box faces option), while the vop octant version gives curved surfaces at the cut because it is just making a contour surface between the high map density values and the zero values at the next grid point. To produce flatter surface appearance at the cut value with the vop octant command you can fill the masked out grid points with a large negative number instead of 0. vop #0 octant center 31,31,0 fill -1000 Use commands "help vop" and "help volume" to show the Chimera documentation for more details. None of these commands are working in the Chimera 1.4 daily builds from the past 2 weeks because of a bug introduced in command parsing. So use the Chimera 1.3 production release. The bug should be fixed in the daily builds by Thursday. Tom -------- Original Message -------- Subject: [Chimera-users] erase octant question From: Kristin Parent <kparent@ucsd.edu> To: chimera-users@cgl.ucsf.edu Date: 8/17/09 11:23 AM
Hello,
I was wondering if you could help me. I am trying to visualize a 3D density map from a cryo-TEM reconstruction of a virus (ccp4 format). I would like to use the "erase octant" function (link below), but actually erase a full quarter of the map to see inside the interior. I would like to do it accurately, and not by dragging the subregions box by hand. Can you help me understand how to set the command line function in order to do this? Thanks in advance. Kristin
http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#octant
Kristin Parent, Ph.D. University of California, San Diego Department of Chemistry and Biochemistry 9500 Gilman Drive, NSB 4104A, MC-0378 La Jolla, CA, 92093-0378 (858) 534-8038 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
