Re: AMBER: (no subject)

From: M. L. Dodson <>
Date: Wed, 30 May 2007 12:54:04 -0500

Catein Catherine wrote:
> Dear All,
> I tried to find the correlation movement for various domain of a
> protein, I do the correlation with ptraj module and got the
> correlation.dat file. However, I have difficult to view the 800 x 800
> matrix table. Could anyone kindly help what should I do to visualize
> the dat files?
> I noted some paper report a 800x800 boxes with red representing +ve and
> blue represent -ve correlations, can I do the same for the dat file? If
> yes, could anyone tell me how to do so?
> Many thanks!
> Cat

OK, this is so unpolished I hesitate to send it in, but here is a perl
driver script I use to generate "heatmap"-style correlation plots from
ptraj correlation matrices using the plot program gri. I'm sending this
in as completely unsupported (DO NOT ask me how to use it, etc.) If you
cannot figure it out yourself, then do not use it.

The only reason I am sending it to the list is that several similar
requests have been posted over the years. The example encapsulated
PostScript file was generated from the (ptraj) trajectory correlation
matrix of C-alpha positions of the protein component of a DNA-protein
simulation I recently did. There was not much movement (the protein is
evidently a "brick"), so it is not a very good "advertisement" for the

I am releasing this code to the public domain. Do anything you want
with it, but if your cat dies or your house burns down because you run
it, don't blame me. (In other words, I will not be held responsible for
any consequences arising from the use of the code.)

You will need perl and gri to use the script. The last system command
converts the PostScript to encapsulated PostScript using ps2epsi.
ps2eps will work, but gets the bounding box wrong for reasons I have not
followed up. Comment out the last system command if you do not have

If anyone has a better procedure, please post it.

Bud Dodson
M. L. Dodson
Email:	mldodson-at-houston-dot-rr-dot-com
Phone:	eight_three_two-56_three-386_one

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Received on Sun Jun 03 2007 - 06:07:13 PDT
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