AMBER Archive (2006)

Subject: RE: AMBER: Grid command of ptraj

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Mon Oct 23 2006 - 11:24:20 CDT

> > trajin md.crd 1 1 1
> > trajout snap pdb
> > center :1
> > image
> > strip :2-99999999
> > translate x 0.25 y 0.25 z 0.25
> > (the grid runs from -49 to 50 so the coordinates need to be shifted by
> +1/2 grid spacing or 0.25).
>
> Now I could display in chimera! Thanks.
> But I can't understand the reason that the coordinates need to be shifted by
> translate command. Why do the coordinates need to be shifted toward positive
> ?
>
> Coud you please give me more details ?

As mentioned in the e-mail, the "grid" runs on integers from -49 to +50.
I could not figure out how to get the XPLOR density to instead be centered
correctly (i.e. run from -49.5 to +49.5) so instead the grid is
effectively shifted in the positive direction by 1/2 grid spacing.

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