MolAuto v1.1

Introduction
Changes in version 1.1
How to use MolAuto
Command-line options
Known bugs
Caveat for version 1.1

Introduction

MolAuto is a program for producing good first-approximation MolScript input files (scripts) from a coordinate file. The program locates secondary structure in the protein 3D structure by one of several different criteria and outputs the appropriate schematic object commands. It also finds ligand residues present in the coordinate file and outputs commands to render these. There are some command-line options that fine-tune the type and appearance of the different objects.

The MolAuto program does not find transformations to produce good views of a molecule. This must be done manually by the user, most easily using the interactive OpenGL mode of MolScript.

Changes in version 1.1

The default secondary structure is now that given in the PDB file. Previously, the DSSP-like algorithm in MolAuto (option -ss_hb) was the default.
Double-quote characters in the string for the title command now use the character escape mechanism added to MolScript v2.1.
A bug involving single amino-acid residues among ligand residues has been fixed. The bug caused a coil of length 1 to be output, which is invalid in MolScript. The PDB data set 1HIV was an example of a coordinate data set which had this problem.

How to use MolAuto

MolAuto is invoked with the coordinate file (in PDB format) as the single required argument on the command line. The program reads the coordinate file, analyses it, and outputs the MolScript input file to stdout (standard output):



% molauto pdb1rbp.ent > 1rbp.in

MolAuto can be part of a UNIX pipe with MolScript, for example when producing a quick display of a PDB structure using the OpenGL implementation in MolScript:



% molauto pdb1rbp.ent | molscript -opengl

A VRML 2.0 representation of a protein may be produced easily:



% molauto pdb1rbp.ent | molscript -vrml

Command-line options

Any combination of command-line options may be used, except for a few pathological combinations which may generate an error. If conflicting options are used, then the last one on the line determines the result.

command-line option action

-notitle Do not produce a title item at the top of the MolScript input file. By default, a title item is produced if there is a COMPND record in the PDB file.

-nocentre Do not produce a transformation command that centres the molecule in the coordinate system. The molecule is kept in its original position. By default, such a centering command is produced.

-cylinder Use the cylinder command to render helices, instead of the helix command (which is the default).

-turns Produce turn commands when turns are specified in the secondary structure definitions in the PDB file (TURN records). The default is to convert all such turns into coil commands.

-nice Nice rendering: The schematic protein and nucleotide representations are coloured along the sequence on a residue-per-residue basis by a rainbow colour ramp. Also, more segments are used.

-thin Use thin variants (zero thickness) of the schematic representations; strand arrows are rendered as flat surfaces and coils as lines.

-noligand Do not produce commands that render ligands, i.e. residues that are not amino-acid residues or waters. By default, such residues are rendered.

-bonds Render ligands using the bonds command. This is the default.

-stick Render ligands using the ball-and-stick command.

-cpk Render ligands using the cpk command.

-nocolour Do not use colours for schematic representations. By default, the schematic residue graphics objects are given colours in a rainbow ramp on an object-by-object basis.

-ss_pdb Use the secondary structure given in the PDB file for the schematic representation. This is the default.

-ss_hb Use a DSSP-like algorithm (Kabsch & Sander 1983) based on hydrogen-bonding patterns to determine the secondary structure used for the schematic representation.

-ss_ca Use an algorithm based on CA-CA distance patterns to determine the secondary structure used for the schematic representation. This is less accurate than the DSSP-like algorithm, but requires only CA atoms coordinates.

-h Output a listing of the available command-line options to stderr (standard error output). No other output is produced.

command-line option	action
`-notitle`	Do not produce a title item at the top of the MolScript input file. By default, a title item is produced if there is a `COMPND` record in the PDB file.
`-nocentre`	Do not produce a transformation command that centres the molecule in the coordinate system. The molecule is kept in its original position. By default, such a centering command is produced.
`-cylinder`	Use the cylinder command to render helices, instead of the helix command (which is the default).
`-turns`	Produce turn commands when turns are specified in the secondary structure definitions in the PDB file (`TURN` records). The default is to convert all such turns into coil commands.
`-nice`	Nice rendering: The schematic protein and nucleotide representations are coloured along the sequence on a residue-per-residue basis by a rainbow colour ramp. Also, more segments are used.
`-thin`	Use thin variants (zero thickness) of the schematic representations; strand arrows are rendered as flat surfaces and coils as lines.
`-noligand`	Do not produce commands that render ligands, i.e. residues that are not amino-acid residues or waters. By default, such residues are rendered.
`-bonds`	Render ligands using the bonds command. This is the default.
`-stick`	Render ligands using the ball-and-stick command.
`-cpk`	Render ligands using the cpk command.
`-nocolour`	Do not use colours for schematic representations. By default, the schematic residue graphics objects are given colours in a rainbow ramp on an object-by-object basis.
`-ss_pdb`	Use the secondary structure given in the PDB file for the schematic representation. This is the default.
`-ss_hb`	Use a DSSP-like algorithm (Kabsch & Sander 1983) based on hydrogen-bonding patterns to determine the secondary structure used for the schematic representation.
`-ss_ca`	Use an algorithm based on CA-CA distance patterns to determine the secondary structure used for the schematic representation. This is less accurate than the DSSP-like algorithm, but requires only CA atoms coordinates.
`-h`	Output a listing of the available command-line options to `stderr` (standard error output). No other output is produced.

Known bugs

The option -nice should really be two separate, functionally orthogonal options.
PDB files containing MODEL records (i.e. structures derived from NMR data) are not handled sensibly. Only the first coordinate set is analysed, and the output MolScript file contains commands that do not deal with the multiple coordinate sets in any way.
The DSSP-like algorithm used for the -ss_hb command-line option hasn't been validated as well as it should be. It may contain bugs.

Caveat for version 1.1

The command-line options in MolAuto v1.1 are not set in stone. It is conceivable that future versions of MolAuto may change the meaning of some options, or that some options may disappear. Experience with the program may prompt modifications.

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