AMBER Archive (2006)

Subject: RE: AMBER: Grid command of ptraj

From: Atsutoshi Okabe (okabe_at_cherry.bio.titech.ac.jp)
Date: Tue Oct 17 2006 - 23:19:13 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 ?

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Thomas Cheatham
Sent: Wednesday, October 18, 2006 12:40 AM
To: amber_at_scripps.edu
Subject: RE: AMBER: Grid command of ptraj

> And could you please give me one more suggestion?
>
> In my figure which I attached in previous mail, there is no solute
Molecule
> (residue 1) . How can I also display the solute molecule in my Solvent
> distribution figure at once ?

The grid ONLY contains the density for the atoms you selected. If you
want to display something else, you will have to load that up.

> > trajin md.crd
> > center :1
> > image
> > rms first mass out rms :1
> > grid wat.xplor 100 0.5 100 0.5 100 0.5 :WAT

To get a PDB file of residue one in the same reference frame:

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).

Then, load up the PDB file "snap.1" and then load up the grid in
chimera...

Likely you will want an average structure (unless :1 is rigid) that you
can load up and RMS fit to the "snap.1".

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