Hi Sam,

  The initial volume threshold level is set to make the surface enclose 1% of the grid points.  That seems like a high threshold.  It encloses along a line about 1 in 5 grid points  (1/100 ** 1/3) which usually is an ok starting point for cryoEM and x-ray maps.  It doesn't use standard deviation or root-mean-square thresholds (although those can be used with the sdLevel and rmsLevel options of the volume command after the volume is open) because cryoEM often has very large padding around the actual structure so those statistics based levels are skewed to very low levels (unlike in X-ray where the structure extends to the edge of the volume data).  ChimeraX will use grayscale display of a single plane for large data (>= 256 million grid points) and it uses a linear ramp of the gray levels from the threshold where 90% of grid values are higher up to the threshold where 1% of the grid values are higher (ie from threshold rank 10% to rank 99%).

  These 1% and 90% default threshold parameters are currently not settable using a command.  I could allow setting those defaults, although I think only you would use that and am reluctant to tamper with the code (and introduce new bugs) for a feature only used by one person.

Tom


On Sep 12, 2023, at 2:38 AM, Samuel Haysom via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,
 
Is it possible to change the default step and level that ChimeraX uses when it opens maps? My data (cryoEM) mostly opens at step 2 with the level set too low for useful viewing, necessitating adjusting these settings for every map I open. Is there a global setting that I can change (for instance by specifying it in a startup script) to change this behaviour so my maps always open at step 1 and at a specified level (say rmsLevel 8)?
 
KR,
Sam 
Samuel Haysom
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