.TH PDBview 1 "Feburary 1993"
.SH NAME
PDBview \- PDB Renderer, version 1.0.
.SH SYNOPSIS
.B PDBview

.SH DESCRIPTION
PDBview is a tool for rendering a PDB file (i.e. a macromolecular structure),
currently as a stick model, on any computer output device that supports X/Motif. The speed of rendering
depends on the complexity of the molecule and the hardware configuration.
Rotation and translation are controlled by horizontal scroll bars. The
best results are achieved by moving the scroll bar slowly, while only
viewing a Calpha trace. When the desired orientation is found all atoms
can be displayed. Typical uses of this tool are for quick examination
of structures prior to going to a real rendering device. PDBview can
be used to determine an orientation matrix for use by other plotting 
programs.

To view a structure of your own making youu must have a file in PDB format
containing at least ATOM, SEQRES, and END records.

.SH FEATURES
The following features are available:

.TP
.B 
.I Atom Recognition

Clicking on the structure identifies the atom and entity (amino acid or
nucleotide).

.TP
.B 
.I Mode

Mono or side-by-side stereo cam be selected.
.TP 
.B 
.I View

Calpha, main chain, or all atoms can be displayed.

.TP
.B 
.I Entities

Entities are selectable. Polypeptide chains, HET groups, DNA strands, and
water molecules are examples of entities.

.TP
.B 
.I Labels

Options are: no labels, Calphas, main chain, all atoms.

.TP
.B 
.I Postscript

Produces a Postscript file of the molecule viewing area.

.TP
.B 
.I Rotation matrix

Defines the rotation matrix relative to the orthogonal representation 
provided by the PDB file.

.TP
.B 
.I Info

Displays information from the PDB header records.

.SH FILES
.TP
.B 
.I connect
Subentity (e.g. amino acid) connectivity.

.SH "SEE ALSO"
This is a tool developed as part of a broader project at Columbia University
to: (i) develop a class library in C++ that models macromolecular structure;
(ii) make that structure persistent; (iii) develop tools that use that 
structure. PDBview is from the third category.

.SH BUGS
A subset of PDB files still cannot be read into our data structure. Attempting
to load one of these structures will cause a core dump.


.SH AUTHORS
.nf
Ilya Shindyalov, Weider Chang, Phil Bourne

Department of Biochemistry and Molecular Biophysics
Columbia University
630 W 168th St.
New York NY 10032

Contact shindyal@cuhhca.hhmi.columbia.edu

Funded by NSF Grant IRI 9116798