SUMMARY: Displaying the output of GCG FOLD Program on the VAX

Ashok Aiyar axa12 at po.CWRU.Edu
Thu Oct 10 07:06:47 EST 1991

I thank all those who answered my query on displaying RNA strcutures
from the GCG FOLD program.

Several others asked me to forward suggestions to them or post a 
summary to this group.

That is what this is:

A)  There are several commercially available communication packages
	which provide excellent VT240 emulation.  Once source for
	such a package is:
	465 Science Drive
	UW Research Park
	Madison Wisconsin 53711
	Domestic TEL: 608-273-6000  European TEL: 49 89 361-6310
	Fax 089/361 7094

     Other packages include Relay Gold for DOS and the KEATerm
	family of products (which can also handle TCP/IP)

B)  One solution is download the *.connect file from the VAX
	and view it on the PC using J. Thompson's program
	Molecule.  Molecule is available at several FTP sites.
	This solution works really good, and the resultant
	display (particularly is you have an EGA and up monitor)
	is excellent.  The negative aspect is that you have to
	run the analysis on the VAX, then view it on the PC,
	before going back to the VAX to redo the analysis with
	different parameters.  If you are going to do this, then
	the *.connect file has to edited in the following manner.

FOLD of: Hivmal.Vi Check: 7986 from: 1 to: 350

Length: 350  Energy: -106.6
    1 G       0    2    0    1
    2 G       1    3    0    2
    3 U       2    4  348    3

350  Energy: -106.6
    1 G       0    2    0    1
    2 G       1    3    0    2
    3 U       2    4  348    3

This method works fine with files upto 1000 bases in length.  In my 
personal opinion, since Molecule is interactive and you can change
the display (as well as see all the bases on the screen), this method
is xcelent.

C)  I have gotten in toch with Prof. Joe Doupnik (author of Kermit).
	Prof. Doupnik has generously agreed to help me by examining
	the problems that TEK emulation in Kermit ver 3.11 has in
	displaying these files which the Tek program (in GCG) has been
	run to redirect the output of the file GCGPLOT.PLT such that
	it can be displayed on a Tektronics 4014.  Dr. Doupnik will
	perhaps write a patch for the TEK emulation of Kermit 3.11.
	Kermit ver 3.11 will work in TCP/IP and Serial communications.

Ashok Aiyar
Department of Biochemistry
CWRU-Medical School
  Ashok A. Aiyar   Department of Biochemistry   CWRU Med. School
   		       axa12 at
		   aiyar at
                Visit the IBM-PC Sig on Freenet

More information about the Methods mailing list