Subject: Summary: clustering according to internal coordinates,

From: Zhang Hongyu <[email-masked]>
Date: Fri, 6 Oct 1995 20:10:04 -0700 (PDT)

Dear CCL'ers,

Two weeks ago, I posted a question on clustering according to internal
coordinates, although there's no many responses, I'd still like to give a
summary. BTW, I am sorry for an address error in last post, this time it 
is definately right. More infomation is welcome, especially for free code. 

Henry

----------------------------------------------------------------------
Henry Hongyu Zhang, Ph.D. student |  email: [email-masked]
Molecular Design Laboratory       |  	    [email-masked]
Institute of Physical Chemistry   |  Tel: 8610-2501490
Peking University                 |  Fax: 8610-2501725
Peking 100871 , China		  |  URL: http://www.ipc.pku.edu.cn/moldsgn/
				  |       zhy/hom.htm

-----------
               Too hard, to be broken
                   Too soft, to be worthless 
                      			------------ Old Chinese Saying
========================================================================

My original post,

> I've got from a simulated annealing process a group of conformations of a
> penta-ptide with 3D coordinates, and want to cluster them according to
> internal coordinates, i.e. value of Phi and Psi angle, but I haven't found
> the relative function in SYBYL or QUANTA.  Can anyone tell me where to find
> suitable softwares ? 
>
> BTW, I also want to get the standard of dividing Ramanchandra graph
> (explicit value), i.e., if I got a pair of Phi-Psi value, how can I tell
> whether it fall into A,D,or D*? 

-------- From: [email-masked] (Peter Shenkin)

Our program, XCluster, is designed to do exactly this.  It's included
with MacroModel, which isn't free, but is very cheap to academics.

For further info, "finger [email-masked]".  If
you visit our WWW home page and work your way down to a description
of the XCluster program, you'll see some images that show what 
clusters of conformations look like if the ensemble indeed exhbits
strong clustering.  Our home page is:

       http://www.cc.columbia.edu/~chempub/mmod/mmod.html

XCluster can work in either torsional space or in Cartesian space;
the user decides at run-time.  You can read more about XCluster in:
Shenkin & McDonald, J. Comput. Chem., v.15, pp.899-916, 1994.

Also, the latest version of MacroModel, Version 5.0, includes
converters that translate from SYBYL Mol2 format to MacroModel
format (and vice versa) -- so if you've been using SYBYL, it ought 
to be easy to get your conformations into a format that MacroModel 
can understand.

> BTW, I also want to get the standard of dividing Ramanchandra graph
> (explicit value), i.e., if I got a pair of Phi-Psi value, how can I tell
> whether it fall into A,D,or D*? 

XCluster doesn't do this for you;  sorry.  But the way I'd do this
is to print out the Phi-Psi values (MacroModel can do this for you).
Then calculate the distance of each pair to the "generic" pair value
for the  A, D and D* regions, taking the periodicity of angle space
into account.  The "generic" pair value a given Phi-Psi pair is
closest to defines which region it belongs to.

	-P.

******** When somebody says, "It's a matter of principle,"... ********
*Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,*
*NY, NY  10027;  [email-masked];  (212)854-5143;  FAX: 678-9039*
************ ...it's a sure sign he wants the whole pie. *************

------------ From [email-masked]  Fri Sep 15 15:25:19 1995

Dear Henry,
 
> I've got from a simulated annealing process a group of conformations of a
> penta-ptide with 3D coordinates, and want to cluster them according to
> internal coordinates, i.e. value of Phi and Psi angle, but I haven't found
> the relative function in SYBYL or QUANTA.  Can anyone tell me where to find
> suitable softwares ? 

Along with software, it might be useful to inspekt a certain selection of
conformers by eye ! Often, the best is to first cluster on hydrogen bonding
(using any criteria for HB), and then look at only backbone dihedrals to
subdivide groups with same hydrogen bonds.
  
> BTW, I also want to get the standard of dividing Ramanchandra graph
> (explicit value), i.e., if I got a pair of Phi-Psi value, how can I tell
> whether it fall into A,D,or D*? 

You should find this in Zimmerman, S.S. & Scheraga, H.A. Biopolymers 1977,
v. 16, 811-843.

Regards,

Frank Eisenmenger
 
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------ From: "FOUNTAIN, KEN" <[email-masked]>

Hi Henry,
     I'd be very interested in whatever you find out about this.
Could you please post to the list any answers you get.

     BTW, my son, Daniel Fountain, is at Peking  Language university
 in the Friendship Dormatory.  If you get over that way please look
 him up and introduce yourself.  He is a graduated chemical engineer
>from Georgia Tech, who is studying Chinese language and culture for two
years in your country.  I'm sure he would like to see someone who is
talking to his father.
Sincerely,  Ken Fountain Professor of Chemistry
Truman/Northeast Miussouri State University

---------------- From: Mrigank <[email-masked]>
To: [email-masked]

I have written a program which can find phi, psi, omega and chis from PDB
or MoMoS format files and output in a cpmpact tabular or a GNUPLOT script that
also markout the Ramachandran allowed regions. It is in Fortran. 

If interested i can send it .

Mrigank
----
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