Subject: Re: CCL:visualizing normal modes?

From: Philippe Youkharibache <[email-masked]>
Date: Wed, 19 Nov 1997 18:09:44 -0800

Dan Strahs wrote:
> 
> I'm trying to visualize some the normal mode eigenvectors for systems I've
> been working with.
> 
> I have a number of options, but none really satisfy me.
> 
> a) I can use Insight/Biosym/MSI to draw arrows attached to the atom
> positions; but this is an extraordinarily crude approach. It also requires
> me to iteratively read in and delete the objects associated with the
> particular mode I want to consider.
> 
 ....
> Is there some package (preferably free) which will:
> 
>         1) Display atoms and eigenvectors in a 3-D, rotatable reference
> frame;
>         2) Allow me to import the entire calculated set of normal modes
> and visualize them individually without progressive reloads;
> 
>         3) Generate some form of output (i.e. Postscript)
> 
> Thanks for any help that can be offered in this regard.

Dan,

First of all, for a repetitive task in InsightII you can use BCL
MACROS.  There
should be one available and floating around to precisely visualize
normal modes.
As you said though it is not a viable solution if you have hundreds of
vectors and
if you want to animate them.

I don't know if you know about DeCipher which is completely integrated
to InsightII
There are ways of doing that - with the latest release that is about to
ship (version 97).  
This is essentially a version of the MSDA-DeCipher software version 4.1
that we developed for Bristol-Myers-Squibb early 1995 while I was still
at Biosym :-(.  What you could do is the following (on top of my head
after two years of not even touching the software - so give a +/-), and
this is BTW a general back-door to all types of external data import. 

Since DeCipher is a toolkit you'll have a few definition steps and then
it should be a brise.
You will not have to know anything else than to use a spreadsheet (a
minimum) and define
mathematical functions (no programming, no looping at all).

1/ Read in a text file containing your vectors on an atom basis - in a
spreadsheet -.
 You could read in any set of scalars, vectors and even tensors on an
atom basis (row)
-AND- frame basis if you have an animation (note that there is a
transpose command
if needed).

2/ define a muldidimensional numerical function "normal_modes" (numeric)
of type "vector" (first row of spreadsheet atom1.xyz, atom2.xyz ...,
then optionally
one row per frame if you read-in a trajectory, which would have to be in
a supported format).
What a numerical function does is to attach a number or set of numbers 
(vectors, tensors) to each atom (or residue or molecule as a matter of
fact (use option).
Use the option Map_To_Molecule (the fact is that you can map
on any point in space).  Normally (if there are no bugs !) they should
then rotate with the molecule. 

For normal modes it is just a matter of considering each mode associated
to a
frame. For that the only issue is to read in a synthetic trajectory of
3N-6
frames that can be all identical to the equilibrium (or not) structure
you 
used for the calculation, as DeCipher does not know specifically of
normal
modes.  The other way around, more satisfactory if you have just a few
modes
is to define a function per mode, you can then display them one at a
time
or simultaneously (see hereafter) on the same structure.

3/ Create a multi-dimensional vector object
(or an object in the Insight sense with atom based vector components
representing
normal modes. you define a geometrical object (called geometrics in
DeCipher)
 in your case a "Vector" with the From_Function option, specifying the
"normal_mode" 
function you've just defined. You end up with ONE object representing an
atom-based 
vector function, this object is dynamic so if the molecule is animated
AND normal 
modes have been read, you can browse through normal modes.

Warning: you should check if functions and geometrics are saved with say
a .psv file.

Note also that you can change the numbers in the spreadsheet, the
function will update and
so will the vector ... this is a dynamic information system.  Properties
can be expressed
formally as functions of atomic variables and are recomputed (or
re-looked up) dynamically.
Also if you define functions of these normal modes, they'll be updated
dynamically in a
table or on the molecule.

4/ Printing 
Well the good news is that it should now print as anything else in
Insight (I hope it's true).

I know it might sound esoteric to those of you who have been using
DeCipher in previously
released version, which sadly really dates 1993.  I am the first one
to be sorry that this software has not been released before, although I
made it available
to a small group thanks to the generosity of Bristol-Myers-Squibb early
1995.  I just hope 
you can put your hands on it soon, and I have been told that it is
shipping now.

Good Luck.

Philippe Youkharibache

-- 
=======================================================================
  Philippe Youkharibache, Ph.D.
  InPharmatics Corp.                    e-mail: [email-masked]
  11440 W. Bernardo Court, Suite 300    tel:    (619) 530 8550
  San Diego, CA 92127                   fax:    (619) 530 8555         
=======================================================================

---

From: "Robert Fraczkiewicz" <[email-masked]>
Date: Thu, 20 Nov 1997 11:09:08 -0600

Dan,

> I have a number of options, but none really satisfy me.

You don't have to draw eigenvectors by hand. Program DT2 in the RAMVIB package
produces an output in the XYZ format that contains entire set of normal modes
with the ACTUAL (i.e., as they come from NCA calculations) eigenvectors. This
output is directly readable by, e.g., free molecular graphics program XMol
1.3.1 from Minnesota Suprcomputing Center. Just make sure that the option
"Display-Vectors" is set.

RAMVIB is available free of charge from CCL archives:
ftp://www.ccl.net/pub/chemistry/software/SGI/ramvib/

> 					Dan Strahs, Chemistry Dept., NYU

XMol can do all of this. In addition, program ANIM from RAMVIB uses DT2 output
to generate normal mode animations (30 frames) in XYZ format also readable by
XMol. Use option "Extras-Animate" to display the movie.

Hope that helps,
Robert Fraczkiewicz
University of Texas Medical Branch
Galveston, TX 77555