Re: [AMBER] autoimage for grid analysis with cpptraj

From: Gustaf Olsson <>
Date: Wed, 23 Sep 2020 06:54:44 +0000

Hi Dan and thank you for getting in touch.

The way I interpret this would be that including “familiar” should then almost be done by default, unless there is a good reason to exclude it. Assuming that it can potentially produce more accurate results?

Thank you for the tip as well, I’ll put checking on the code onto my todo list.

Best regards
// Gustaf

> On 22 Sep 2020, at 15:38, Daniel Roe <> wrote:
> Hi,
> 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,
> -Dan
> 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 Wed Sep 23 2020 - 00:00:03 PDT
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