\name{chime3D}
\alias{chime3D}

\title{Produce web graph of 3D graph that can be viewed using Chime web browser plug-in from a pdb file}
\description{
\code{chime3D} produces a html web page with a 3D graph of a pdb file that can be rotated and manipulated in a web browser that 
supports the chime plug-in. 
}
\usage{
chime3D(pdbfilename, classvec = NULL, title = NULL, filename = "output.html", point.size=40,cols=NULL,  ...)
}

\arguments{
  \item{pdbfilename}{Input pdb filename, this is an output file from \code{html3D}.}
  \item{classvec}{Factor or vector which describes classes in the df. Default is NULL. If specified each group 
   will be coloured in contrasting colours}
  \item{title}{Character, the title (header) of the web page saved if writehtml is TRUE. The default is NULL.}
  \item{filename}{Character. The filename of the html to be saved. The default is 
   "output.html".}
  \item{point.size}{Numeric, size of the points in plot. Default is 40}
 \item{cols}{Vector, of colours to be used.  The length of the vector must equal the length levels(classvec), that is the number of classes or groups of samples. The default is NULL, colours will be choosen using getcol.} 
  \item{\dots}{ further arguments passed to or from other methods }
}
\details{
 Produces a html file, of a 3D graph which can be rotated using the FREEWARE chime (win, MacOS). 
 Will colour samples by classvec if given one, and will produce chime script to highlight groups, spin on/off, 
and include button for restore for example see \url{http://bioinf.ucd.ie/research/microarrays/}.
}
\value{
chime3D output is a html file that can be viewed in any web browser that supports the Chime plug-in.
}

\author{Aedin Culhane  }
\note{ 
Note chime is only available on windows or Mac OS currently. Using the chime plug-in on Linux 
is slightly complicated but is available if the CrossOver Plug-in is installed. Instructions on installing this and chime on Linux 
are available at  \url{http://mirrors.rcsb.org/SMS/STINGm/help/chime_linux.html}.


If you wish to view a 3D graph in Rasmol, you will need to execute a Rasmol script similar to 
\preformatted{

load pdbfilename.pdb; 
set axes on; 
select off; 
connect;
set ambient 40; 
rotate x 180; 
select *;  
spacefill 40
}

}


\seealso{ }
\examples{

}
\keyword{internal}% at least one, from doc/KEYWORDS