Add molmap option to specify grid size

[joshua.denson@…]

Would be convenient of the molmap command could specify a grid size for making starting models for refinement that need to be cube shaped and ideally power of 2 in size. A size option would override the default padding molmap adds and it would be up to the user to specify a grid spacing that allows the molecule to fit within the grid size without being clipped.

From: Joshua Denson
Subject: [chimerax-users] Help Generating a Volume to use for 2D classification template generation
Date: February 21, 2023 at 1:14:44 PM PST
To: "chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu>
Reply-To: Joshua Denson

Hi, 
I’m trying to take an alpha fold model of my complex, generate a low resolution map of the model using molmap, and then use it for 2D template generation in CryoSparc. I am able to generate the low resolution map just fine, but the resulting map is in a rectangular volume (48x64x51) and I need it to be a cubic volume for CryoSparc to accept it. Ideally it would have dimensions of 64x64x64.
Is there a way to generate a low resolution map in a cell with specific dimensions while maintaining the protein complex dimensions? (eg. I don’t want to simply scale it into a cube)
I am using ChimeraX 1.5.
 
Best Josh
 
Joshua M. Denson
PhD Candidate (Johnson Group)
Dept. of Chemistry and Biochemistry
Utah State University