RIBOSOME V1.0

RIBOSOME - PROGRAM TO BUILD COORDINATES FOR PEPTIDES FROM SEQUENCE

Raj Srinivasan

Johns Hopkins University

Jenkins Department of Biophysics

Baltimore, MD 21218.

Table of Contents

1. Introduction
2. Command Reference
3. Files & Things
4. Examples
5. Download

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..

Ribosome is a program to construct coordinates for a peptide/ protein from the sequence. The program is written in SGI Fortran and includes the common do , enddo extension and the getarg() unix function. It should compile without any modification on most unix machines.

The program can be downloaded.

To run the program type

ribosome "filename.com" "output_filename" res.zmat

All options to the program are passed through a command file. Each command must be given on a separate line. Keywords are case insensitive . All whitespace and tab characters are ignored. All blank lines and lines beginning with a "#" character are ignored.

The commands/keywords currently recognised by RIBOSOME are given below.

Title

Default

AllH

Residue

Syntax: title "string"

The RIBOSOME title command permits the input of a title for the molecule. The title may contain white spaces,tabs etc. Only the first 70 characters of the title, including spaces and tabs is printed. This is an optional command.

example: title my peptide sequence

sets the title to "my peptide sequence"

Syntax: default "options"

The RIBOSOME default command is used to specify the default conformation for the residues. Valid options are:
helix to set the conformation to alpha-helix
sheet to set the conformation to beta-sheet
extended to set the conformation to the extended form
"angref" value
where angref is one of phi,psi,omega,chi1,chi2,chi3,chi4,chi5 and value is the dihedral angle value.

examples:

default helix
default phi -90 psi -45

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

command is used to specify the sequence. Each residue should be on a separate line. This command can also be used to specify the conformation of the residue. For e.g. the command
residue phe phi -60 psi 120 chi1 -60 chi2 90
specifies the residue as phenyl alanine, and sets the phi, psi, chi1 and chi2 values to those indicated.

RIBOSOME uses a file calles res.zmat ( or any other name that you prefer ) to read in residue decsriptions. The file contains a z-matrix dexcription for each residue. The file is free-format and can be edited as desired. Additional residue descriptions may be added to the file.

The first line for each residue contains the name and number of atoms in the residue. Thus

name ala numatm 6
specifies the residue name as ala with 6 atoms in the residue. The residue name may be no longer than 4 characters. The program is currently dimensioned for a maximum of 50 residue types, with a maximum of 100 atoms per residue type.

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:

o 1.231 120.800 139.000 3 2 1
This line describes the atom with name "o" and specifies the distance between this atom and atom number 3 ( column 5) as 1.231 angstroms( column 2), the angle between this atom, atom number 3 and atom number 2 (column 6) as 120.8 degrees (column 3) and the dihedral between the atoms "o" , 3, 2 and 1 (column 7) as 139.0 degrees (column 4). A negative value in any of the columns 5, 6, or 7 specifies an atom from a previous residue.

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