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PDB to VRML Converter


Manual

The PDB to VRML converter has the following general syntax:

pdb2vrml OPTIONS FILE

The OPTIONS are listed in the table below. FILE can be a regular file name or '-' which means stdout. The different options can be repeated several times. This feature can be used to load more than one structure or to change the representation of the molecular model several times. The order of the options given on the command line is of importance, because options changing the representation of a model will only affect files loaded afterwards.

Examples

pdb2vrml -pdb foo.pdb -

Converts the PDB file foo.pdb into a VRML model (wireframe) and prints the result on stdout.

pdb2vrml -cpk -pdb foo1.pdb -stick -pdb foo2.pdb foo.wrl

Converts the PDB file foo1.pdb in a CPK model and the PDB file foo2.pdb in a ball-and-stick model. The output is written into foo.wrl. Remember to give -cpk and -stick before you read the corresponding PDB files.

pdb2vrml -solid -ribbon -pdb foo.pdb foo.wrl

Converts the PDB file foo.pdb in a ribbon model with a solid representation. Ribbon models are only created for protein structures.


Comand-Line Options

Molecular Structures
-pdb FILE Reads a PDB file. The value of FILE may be '-'. In this case the structure is read from stdin.
-mol2 FILE Reads a SYBYL molecular structure file. The value of FILE may be '-'. In this case the structure is read from stdin.
-hyd Adds the hydrogen atoms to the model, if available. (default)
-nohyd Ignores the hydrogen atoms in the structure.
-side Adds the side chains of the amino acid residues. (default)
-noside Ignores the side chains of the amino acid residues. This option works only if the structure is a regular protein and all residues are known by the program.
-wire Turns on wireframe mode. The following structures are represented by a wireframe model. (default)
-capped Turns on capped-sticks mode. The following structures are represented by a capped-sticks model.
-stick Turns on ball-and-stick mode. The following structures are represented by a ball-and-stick model.
-cpk Turns on CPK mode. The following structures are represented by a CPK model.
-ribbon Turns on ribbon mode. The following structures are represented by a ribbon model. The default display style is dots. You can change to a solid representation with -solid.
-ribbonParam WIDTH HEIGHT INTERPOL Controls the layout of the ribbons. WIDTH is the width in A (0.4 A default). HEIGHT is the height in A (1.5 A default). INTERPOL is the number of interpolation points between to peptide bonds (3 default).
Molecular Surfaces
-surface FILE Reads a molecular surface file. The value of FILE may be '-'. In this case the structure is read from stdin. The format of the surface files is the one used by MOLCAD and SYBYL.
-dot Turns on dot mode. The following surfaces are represented by dots. (default)
-line Turns on line mode. The following surfaces are represented by a network of lines.
-solid Turns on solid mode. The following surfaces are represented by a solid model.
Miscellaneous Options
-color COLOR Changes the actual color. Possible values for COLOR are: byatom, yellow, blue, red, white, green, pink, brown
-quality COMPLEXITY Changes the tessellation of the spheres and the cylinders. The value for COMPLEXITY ranges from 0 to 1. Higher values mean more triangles. This option generates Complexity nodes which are only regonized by WebSpace, because they are not a part of the VRML 1.0 specification.
-vrml The results will be written in VRML V1.0 format. (default)
-iv The results will be written in OpenInventor V2.0 format. This reduces the sizes of the files. If you are using a OpenInventor based viewer, the objects will be rendered a bit faster.


This page was obtained from the pdb2vrml webpage and modified by P. Fleming


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Last Modified: Thursday, 19-Oct-2000 11:18:53 EDT by P. Fleming