raj@www.roselab.jhu.edu
The information supplied in this document is believed to be true but no liability is assumed for its use or for the infringements of the rights of the others resulting from its use.
This package is distributed without any conditions. It may be lent, re-sold, hired out or otherwise circulated without the supplier's prior consent, in any form of packaging or cover. Any part of this manual or accompanying software may be reproduced, stored in a retrieval system on optical or magnetic disk, tape or any other medium, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording or otherwise for any purpose..
The program can be downloaded.
To run the program type
The commands/keywords currently recognised by RIBOSOME are given below.
Syntax: title "string"
example: title my peptide sequence
sets the title to "my peptide sequence"
Syntax: default "options"
examples:
Syntax: allh
The RIBOSOME allh command is used to specify that all hydrogens (polar & non-polar) should be written. By default, only hydrogens on hetroatoms are written.
Syntax: residue [option]
The RIBOSOME residue
The first line for each residue contains the name and number of atoms in the residue. Thus
Following the residue name line, there should be a line for each atom describing it's name, it's zmatrix parameters and indicators as to whether it is a default atom, and a pointer to any torsional angle that it may point to. The default decsriptor is either a '+' or a '-' symbol, and is used to determine whether the coordinates for the atom are written to the output file. The file supplied has all hydrogens connected to carbons flagged with a '-' symbol. Thus, by default coordinates for these hydrogens are not written. Each line should begin with the atom name which should be four characters or less in length.
The z-matrix decsription of an atom, specifies it's positon in internal coordinates with respect to three other atoms, usuall called parent, grand-parent and great grandparent. Consider the following description:
Example # 1
# sample command file. this builds the peptide as a helix
title RIBOSOME EXAMPLE NUMBER 1
default helix
res ace
res ala
res arg
res asn
res asp
res cys
res gly
res gln
res glu
res his
res ile
res leu
res lys
res met
res phe
res pro
res ser
res thr
res trp
res tyr
res val
res nme
# sample command file. this builds the peptide as a helix
# except for the glycine which has a phi of 90.0 and psi of 0.0
RIBOSOME EXAMPLE 2
default helix
res ace
res ala
res arg
res asn
res asp
res cys
res gly phi 90 psi 0
res gln
res glu
res his
res ile
res leu
res lys
res met
res phe
res pro
res ser
res thr
res trp
res tyr
res val
res nme
# sample command file. this builds the peptide as a helix
# with the chi1 of all residues set to -60
title RIBOSOME EXAMPLE 3
default helix
res ace
res ala
res arg chi -60
res asn chi -60
res asp chi -60
res cys chi -60
res gly
res gln chi -60
res glu chi -60
res his chi -60
res ile chi -60
res leu chi -60
res lys chi -60
res met chi -60
res phe chi -60
res pro
res ser chi -60
res thr chi -60
res trp chi -60
res tyr chi -60
res val chi -60
res nme
# sample command file. this builds the peptide as a helix with
# phe set to have a phi of -60 and psi of 130 and the phe-pro
# peptide bond is also set to be cis
title RIBOSOME EXAMPLE 4
default helix
res ace
res ala
res arg
res asn
res asp
res cys
res gly
res gln
res glu
res his
res ile
res leu
res lys
res met
res phe phi -60 psi 130
res pro omega 0
res ser
res thr
res trp
res tyr
res val
res nme
# sample command file. this builds the peptide as a sheet
#except for proline which has a phi of -70
title RIBOSOME EXAMPLE 5
default sheet
res ace
res ala
res arg
res asn
res asp
res cys
res gly
res gln
res glu
res his
res ile
res leu
res lys
res met
res phe
res pro phi -70
res ser
res thr
res trp
res tyr
res val
res nme
# sample command file. this builds the peptide in a
#extended conformation
title RIBOSOME EXAMPLE 6
default extended
res ace
res ala
res arg
res asn
res asp
res cys
res gly
res gln
res glu
res his
res ile
res leu
res lys
res met
res phe
res pro phi -70
res ser
res thr
res trp
res tyr
res val
res nme
# sample command file. this builds the peptide in a
# left handed helix conformation except for proline
title RIBOSOME EXAMPLE 7
default phi 60 psi 40
res ace
res ala
res arg
res asn
res asp
res cys
res gly
res gln
res glu
res his
res ile
res leu
res lys
res met
res phe
res pro phi -70 psi 120
res ser
res thr
res trp
res tyr
res val
res nme
# sample command file. this builds the peptide in a
# extended conformation with chi1 values set to -60.0
# and a type II beta turn between his and ile
title RIBOSOME EXAMPLE 8
default extended
default chi1 -60
res ace
res ala
res arg
res asn
res asp
res cys
res gly
res gln
res glu
res his phi -60 psi 120
res ile phi 80 psi 0
res leu
res lys
res met
res phe
res pro
res ser
res thr
res trp
res tyr
res val
res nme