Protein Secondary Structure Analysis

Jack Breithart uscience at ix.netcom.com
Tue Sep 20 11:33:09 EST 1994

In <1994Sep13.153554.18325 at Princeton.EDU> micky at berthaw.princeton.edu (Michael West) writes: 

>Does anyone know of a program which will read a protein's pdb file, and then
>make secondary structure assignments to each amino acid?  Any suggestions or
>information would be appreciated.  Thanks.
>Michael			micky at berthaw.princeton.edu

Molecular images is a program package for searching, viewing and rendering Protein Data Bank 
files under Micosoft Windows.  PSEARCH is used to search directories of PDB files (including the 
CD-ROM) for keywords.  MOLW is a fast, interactive molecular viewing program that allows 
coloring, selecting and fitting of PDB files.  Viewing options include sticks, ball-and-stick, CPK and 
ribbons using the secondary structure information in PDB files.  Basic fitting functions allow 
mutating residues as well as rotation, translation and bond torsions.  MOLW can calculate 
distances, angles, dihedrals as well H-bonds and nearest neighbour contacts.  Several structures 
can loaded at once and least-squares superimposed.  After a view is found it can be ray-traced in 
SHOWCASE to make photo-realistic images and saved as bitmaps and as postscript for making 

Programs require Windows 3.1 and a math coprocessor for SHOWCASE only.
The academic price for the three program set is $195.00 + $10.00 shipping. Optional Stereo 
viewers are available for $59.00 . 

Available from US Science, PO Box 6689, San Diego, CA, 92106-0689, 
uscience at ix.netcom.com

To get a demo of Molw and showcase bitmaps; access the directory via anonymous ftp by ftp-ing 
to ftp.netcom.com, logging in as anonymous, and then cd-ing into pub/molw. If you are unsure 
about how anonymous ftp works, please refer to FAQ 112. Then use the get or mget command for 
file molwdemo.zip (also available is pkunzip. exe version 2.04). Download them both to a directory  
c:\molimage on your hard-drive and type pkunzip molwdemo. Run Molw.exe from your Windows 
file manager. This version will only let you load one file MOLWDEMO.PDB but is otherwise a fully 

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