Re: [AMBER] autoimage for grid analysis with cpptraj

From: Daniel Roe <>
Date: Tue, 22 Sep 2020 09:38:08 -0400


The 'familiar' option turns on some extra code in the imaging routines
that ensures each object being imaged is not only in the primary unit
cell, but as close as possible to the specified center point. For unit
cells with alpha=beta-gamma angles of 109.47 deg., the effect is to
make the general triclinic rhombohedron more "spherical" and you end
up with the "familiar" truncated octohedron shape. For other unit cell
types, if the cell is already somewhat "spherical" I could see there
being no discernible effect.

If you're interested, the code is in ImageRoutines.cpp in one of the
Image::Nonortho() functions.

Hope this helps,


On Tue, Sep 22, 2020 at 6:06 AM Gustaf Olsson <> wrote:
> I am trying to perform a grid analysis with a small peptide and a number of other molecules. I think managed to work out most of the details though one question remains.
> I was recommended to use the “familiar” option with autoimage.
> autoimage :1-11 origin familiar
> rms rms_1-11_ds_of :1-11 out rms_1-11_out_of.dat first
> average avg1-11_of.pdb :1-11
> grid out_1-11_AAC_of.xplor 60 0.5 60 0.5 60 0.5 :AAC
> However, I have run the same analysis without the “familiar” option and I cannot detect any difference at all. Is this familiar recommendation based on the old “image” methodology and can ignored now or should it indeed remain. Are there any benefits for using the familiar truncated-octahedral shape? The original cell is not a truncated octahedron.
> Best regards
> // Gustaf
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Received on Tue Sep 22 2020 - 07:00:03 PDT
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