[Chimera-users] Inverse volume-erasing

Kai Zhang kzhang at mrc-lmb.cam.ac.uk
Wed Feb 25 16:53:51 PST 2015


Hi Tom,

Many thanks for your detailed explanation! This is really helpful. 

Best,
Kai

On Wed, 2015-02-25 at 12:39 -0800, Tom Goddard wrote:

> Hi Kai,
> 
> 
> 
>   The Chimera volume eraser can erase everything outside the sphere
> using keyboard shortcut “eo” as described in the documentation — if
> you press the Help button on the Volume Eraser dialog you will see
> this.  You have to enable keyboard shortcuts with menu Tools / General
> Controls / Keyboard Shortcuts or Chimera command “ac” also enables
> them.  But this probably isn’t what you want. because it does not add
> what is shown each time you move the sphere and use “eo” it just keeps
> erasing everything outside the sphere.
> 
> 
>   So it isn’t clear how you would use the uneraser sphere since how
> would you be able to see what you are trying to unerase, especially
> when you start with everything erased.  But here’s a tricky idea.
>  Open two copies of your map and erase one copy which will show the
> other copy underneath.  Keep erasing the one copy until you exposed
> all the parts of the underneath map.  Then subtract the full map minus
> the erased map (Chimera command: vop subtract #4 #5)  to get just the
> part you exposed by erasing.  Here’s a screen capture of my test.
> 
> 
>   A few important things to make this work: the volume erase dialog
> acts on the map that is highlighted in the volume viewer dialog (shown
> with its name in blue in the attached image) — click on the map name
> you are erasing in the volume viewer dialog to choose the right copy.
>  If two copies of a map have the same threshold they are exactly on
> top of each other and one or parts of both may appear.  You might want
> to raise the contour level of one copy so it is hidden by the lower
> contour level copy.
> 
> 
> Tom
> 
> 
> 
> 
> 
> 
> 
> > On Feb 25, 2015, at 9:44 AM,  wrote:
> > 
> > 
> > 
> > Dear Chimera users,
> > 
> > 
> > Dose anyone know how to do inverse volume-erasing? Normally we use
> > the
> > eraser to erase density we don't want to keep. However, what shall I
> > do if
> > I want to keep the density within the eraser while getting rid of
> > other
> > parts?
> > 
> > Many thanks
> > Kai
> > 
> > 
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> > 
> > 
> 
> 
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20150226/6475e235/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: unerase.png
Type: image/png
Size: 317420 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20150226/6475e235/attachment-0001.png>


More information about the Chimera-users mailing list