[Chimera-users] Saving an EM map to open at a specific Threshold

Tom Goddard goddard at sonic.net
Fri May 30 16:17:41 PDT 2014

Hi Kevin,

  The MRC map format does not have a header value for a suggested threshold.  So Chimera guesses what threshold to use, as described in the Chimera manual (found by searching “initial threshold”): "Initial thresholds are set automatically. ...an initial threshold is set so that 1% of voxels (1% of the volume encompassed by the data region) lie above it…"


You can save a Chimera session (File / Save Session) after you open the map and set the desired threshold then whenever you load that Chimera session it will show your threshold.


On May 28, 2014, at 8:22 AM, Kevin Huynh wrote:

> Hello, 
>      I have finished processing my cryo-EM map and have set the desired volume to threshold=1 with EMAN2; however, I cannot seem to figure out how to save the map in mrc format so that I can open the map at threshold 1. I am wondering if Chimera can save the map in mrc format so that I can open it at threshold 1? If yes, how can this be done? 
> Thanks, 
> Kevin 
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