[Chimera-users] writing MRC maps

Elaine Meng meng at cgl.ucsf.edu
Wed Aug 11 11:24:05 PDT 2010

Hi Matt,
The real expert Tom G is away, but after some experimentation, I think you can do what you want with the "mask" command.

It will create a new dataset with smaller bounds that enclose a specified surface, optionally with padding.  After color zone and split, I used mask on one of the resulting datasets with its own isosurface, for example:

mask #3 #3 pad 2.5


This will alter the data, however, in that values outside the isosurface will be set to zero in the new, masked dataset.  If you did not want that to happen, alternatives are specifying a subregion or zone in Volume Viewer, then saving only that part, for example with the "volume" command save options:

Specifying the subregion could be inconvenient since you'd either need to know the indices, or draw a box manually.  With the zone approach, you could possibly skip the splitting step (you'd just use the same zones as used to color), but it would be tedious because you'd have to do them one by one.

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

On Aug 10, 2010, at 9:32 PM, Dougherty, Matthew T wrote:

> I have an MRC map that is 800^3.  I do a color zone and split the map, generating eight maps, each 800^3.
> The first of the split maps I throw away, the volume of interest of the other seven maps is 50^3 each.
> How do I save the seven maps not at 800^3, but reduce their size to 50^3?
> thanks, Matt

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