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
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@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Kai Zhang -
kzhang＠mrc-lmb.cam.ac.uk
-
Tom Goddard