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…"

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volume...

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.

Tom

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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users