[Chimera-users] volume eraser and imod isosurface

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 6 09:07:20 PST 2016


Dear Wouter,
The issue is that an IMOD file makes surfaces in Chimera, not a volume model (map or density grid with associated values at each grid point).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#object>

Volume Eraser only works with volume models, formats listed here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume>

Maybe your original data was or could be written in one of those formats?

Also, Hide Dust only hides small surface bits; it does not delete any data.

I hope this makes it clearer,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. appears to be a duplicate question, I’ll just answer this one

On Jan 6, 2016, at 6:39 AM, Wouter Van Putte <wouter.vanputte at gmail.com> wrote:

> Dear,
> 
> I would like to use chimera for removing some densities manually of an isosurface generated with imod. I've loaded the map/model (.mod) and already used the function 'hide dust' to remove most of the noise. I now would like to use 'volume eraser' to remove the other noise manually. This however doesn't work, probably due to the file format (.mod). I thought saving in another file format would help, but it gave me errors when opening the file. How should I proceed?
> 
> best wishes,
> 
> Wouter




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