[AMBER] Visualizing rism3d.snglpnt output

From: Brian Radak via AMBER <amber.ambermd.org>
Date: Tue, 28 Jun 2022 14:04:11 -0400

Hopefully Tyler sees this.

I'm having a bit of a hard time visualizing grid output from
rism3d.snglpnt. Everything seems to be translated relative to the input
protein, which I realized is exactly what the manual says the default
behavior should be. I tried the (discouraged) --centering 0 option, but
this seemed to cause the densities to wrap around the grid in weird ways,
so that's probably not what I'm looking for. I don't recall having this
issue with the old OpenDx file format, but I'm more than happy with the
upgrade to .mrc otherwise.

What's the recommended way to visualize densities around a protein? Is
there a way to output the translated solute coordinates? Do I just need to
turn off centering and prepare my inputs more carefully? Something else?

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Received on Thu Aug 04 2022 - 13:33:38 PDT
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