From: Axel Kohlmeyer (
Date: Sat Sep 12 2009 - 13:01:35 CDT

On Sat, 2009-09-12 at 17:05 +0000, Andres Morales N wrote:
> Dear all

dear andres,

> I want to get a matrix that contains coordinates of alpha carbon atoms
> of a structure, it mean a matrix like the adjoint picture.

there is no picture. ...and regardless of that, a matrix is no intrinsic
data type in Tcl, all you have are strings, ints, floats, and lists. so
how a matrix would look like, depends on how you implement it, e.g. as
an associative array or a list of lists. which is the better way depends
on the individual application.

> I want to put in each row the coordinates (x y z) of all alpha carbon
> of a frame of dcd file. I have a dcd file with 100 frames, protein I
> am using has 50 resids, then I need to get a 100 x 150 matrix. First I
> aligned ths strtures.
> Are there any script for that? Or does somebody have any idea to do
> that?

this is very elementary Tcl scripting task and easy to do. you get
the coordinates of the alpha carbons by creating a selection with
"name CA", which according to the usual conventions for biomolecules
should only match alpha carbons. the "get {x y z}" subcommand to
the generated selection function. for details, see the user's guide
and other script example/tutorials.

as stated above, it all depends on what you want to do with the data
once you have reformatted it. you will have to explain the next step,
if you need more detailed help.


ps.: the same holds in
> Thanks for your suggestions.
> Andres
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Dr. Axel Kohlmeyer 
Research Associate Professor
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.