[DI] Secondary structure from PDB for MolScript

"JohnMichaelSauder"sauder at castor.rm.fccc.edu "JohnMichaelSauder"sauder at castor.rm.fccc.edu
Fri Oct 6 11:42:59 EST 1995


	I can't remember who the original poster was, or if this was even
the correct newsgroup, but if you want to define the secondary structure 
in MolScript, and the PDB file doesn't give you that information, I'd highly
recommend RasMol.  RasMol is free and will run on a Mac, PC, or UNIX system 
(like Silicon Graphics).  It will read in a PDB and calculate secondary 
structure based on the hydrogen-bonding.  You can then create a MolScript 
input file with the molecule in the correct orientation and all of the 
secondary structure defined.  From the RasMol command line, just type:

	write molscript file.in

The MolScript input file (file.in) usually needs some editing.  There's usually
a lot of extra 'turns' defined in between helical units or beta strands.  Just
delete all the 'turn' commands, then replace all the 'coil' commands with 
'turn's.  (I recommend using 'turn' instead of 'coil', since coil does a LOT
of averaging of the alpha carbon positions and you don't get a very good feel
for what the structure actually looks like.  The 'turn' command draws the 
ribbon through all of the alpha carbon positions without any averaging.)

	RasMol is written by Roger Sayle and is available via anonymous ftp
from:  ftp.dcs.ed.ac.uk:/pub/rasmol
	If you have any trouble getting a copy of it, I could probably email
it to you uuencoded...
-- 

                                                  Mike S. (M_Sauder at fccc.edu)



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