[chimera-dev] Volume Eraser: Recentering the eraser

[Tom Goddard]

Hi Mohan,

  Here are a few more details about how to erase the density inside the capsid of a virus density map.  The trick as you’ve seen is getting the sphere centered at the center of the virus and having the correct radius.  Here’s how I do this.  First I adjust the volume eraser sphere radius so it visually looks about the same radius as the outside of the virus map.  Then I move the sphere with the mouse to try to center it on the virus.  I rotate to look at it from different view angles and center with the mouse at each view direction.  It helps if the radius of the sphere is set so that just a little bit of the density pokes through so you can visually see whether the same amount of density is poking through on all sides.  Now I have the right centering and I try to get the radius I want.  For this it helps to clip the map and sphere using menu Favorites / Side View and move the left vertical yellow line to the right to clip the models.  I move the clip plane to cut through near the center of the virus, then adjust the sphere radius.  In this view you can see the sphere size relative to the concentric layers of density.  It helps here to make the sphere not transparent by clicking the color square in the Volume Eraser dialog and setting the A (opacity) channel to 1.  I’ve attached a pickture.

  To do this in a more precise way I create a sphere and mask using it with commands

shape sphere radius 240 center 0,0,0 coordinateSystem #0 color blue
mask #0 #2 invert true

This requires that the origin of the map is set to the center of the virus capsid.  You can choose this center grid point using Volume Viewer menu Features / Coordinates setting the Origin Index.

	Tom



> On Jan 7, 2016, at 9:38 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hello Mohan,
> If you read the Help for Volume Eraser (press the Help button on the dialog to see it), it explains how to move and resize the eraser sphere.  Or, you can see this information on our website:
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html>
> 
> Basically you can set which mouse button will be used to move the sphere, and then use the mouse to move it to where you want, including with Shift to move in Z (toward or away from you). There isn’t a feature to automatically put it at the center of the capsid.
> 
> For user questions, the better address is chimera-users at cgl.ucsf.edu (not this address chimera-dev, which is more for programming questions).
> 
> 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 Jan 6, 2016, at 9:01 AM, Mohan Sudabattula <mk.sudabattula at gmail.com> wrote:
>> 
>> Hello,
>> 
>> My name is Mohan Sudabattula, I am fairly new at using Chimera so please excuse my lack of understanding the program.
>> 
>> I am currently utilizing the Volume Eraser tool and am trying to employ it erase the internal structure of a viral capsid. Upon opening the Volume Eraser it always seems to orient itself to the "frontmost face of the current display region". This is problematic because it is now only partially erasing what I am needing to be erased.
>> 
>> Instead I am looking to have it oriented so that it is in the center of my virus. Is there any way to reorient the eraser so that this may be the case?
>> 
>> ​Thank you!​
>> Mohan Sudabattula
>> 
> 
> 
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> Chimera-dev at cgl.ucsf.edu
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> 

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