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Kinemage

DAVID F. BISHOP BISHOP at MSVAX.MSSM.EDU
Mon Feb 22 20:10:51 EST 1993


From:	MSVAX::BISHOP       "DAVID F. BISHOP" 20-FEB-1993 20:15:23.32
To:	IN%"bio-soft at net.bio.net"
CC:	BISHOP
Subj:	Kinemage


Kinemage is a program which runs on PC's and Mac's to view protein
structures derived from the Protein Data Bank.  It was written by 
Jane and David Richardson.

I finally figured out how to get Kinemage in a form I could run on my
Mac II.  Since I suspect there are others wanting to do this and since 
it is a little harder than transfering a text file, I'm sharing what
worked for me in our VAX environment.
   First, type:
ftp orion.oac.uci.edu
   to hook up to one of the sites (Office of Academic Computing, University
   of California, Irvine) where this program can be found (thanks to Cornelius
   Krasel for this info)
   Then change directories to protein/Kinemage/macMAGE and type:
binary
   to set the file transfer type to binary so crucial information is not lost.
   Then type:
get MAGE_all.sea
   and wait till the 229K file is transfered.

   To transfer the program to my Mac from the VAX over a modem line reqired
   using Kermit in binary mode.  I don't have a direct network connection yet.

   On the VAX side type (depending on what flavor of Kermit you have):
set file type binary
   I also changed the default block check type:
set Block_check_type 3
   (=CRC)
   On the Mac side, in VersaTerm Pro, I changed the settings to MacBinary, CRC
   and then sent the file to my Mac.

What you shoud end up with is a self extracting application named MAGE_all.sea

Double click on this and it will unstuff into the programs and demo files.

This is a very nice program.  It displays backbone views with sidechains
optionally visable depending on how the file was created.  A program is
included to allow you to convert PDB files into Kinemage.kin files for
viewing.  This looks like it will take some practice.  The demo files
that are supplied include such things as a leucine zipper and an active
site region with substrate.  The image can be viewed in stereo in either
wide-eyed or cross-eyed format and residue identity and distances between
residues obtained by pointing and clicking.  It is in full color on a black
background.  Rotation is immediate upon clicking and dragging.

Now we'll need an FTP site to deposit our PDB.kin creations for sharing
with each other.  Isn't the Internet wonderful!

Cheers,

David Bishop                             | EMail:Internet:Bishop at msvax.mssm.edu
Div. of Medical and Molecular Genetics   |         Bitnet:Bishop at msrcvax
Mount Sinai School of Medicine, Box 1203 | Phone: (212) 241-6946
Fifth Avenue and 100th Street            | FAX:   (212) 360-1809
New York, NY 10029                       | 




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