[Chimera-users] erase octant question

Tom Goddard goddard at cgl.ucsf.edu
Tue Aug 18 14:04:28 PDT 2009

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 

    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.


-------- Original Message --------
Subject: [Chimera-users] erase octant question
From: Kristin Parent <kparent at ucsd.edu>
To: chimera-users at 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 at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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