Subject: Re: CCL:Cluster according to internal coordinates

From: [email-masked] (Peter Shenkin)
Date: Thu, 14 Sep 95 12:37:15 -0400

> From: Zhang Hongyu <[email-masked]>
> Subject: CCL:Cluster according to internal coordinates

> 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 ? 

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. *************