[Chimera-users] erase octant question

Tom Goddard goddard at cgl.ucsf.edu
Tue Aug 18 15:14:39 PDT 2009

Hi Kristin,

  The "vop octant" command examples in my previous email should have 
used the "icenter" option instead of "center".  The "icenter" option 
specifies the center in grid index units, while the "center" option 
specifies it in physical units (usually Angstroms).  For the map I 
tested on the grid plane spacing was reported as 1 Angstrom so it didn't 
make any difference.


-------- Original Message --------
Subject: Re: [Chimera-users] erase octant question
From: Tom Goddard
To: Kristin Parent
Date: 8/18/09 2:04 PM
> 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
> 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

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