[Jmol-users] Re: new Jmol- and Rasmol-oriented resource

[Dan B. <dm...@mr...>]

On Thu, 21 Oct 2004, timothy driscoll wrote:

>hello,
>
>I have created a new resource for Jmol, Rasmol, and Chime developers
>called Color Gradients.  you can use it to create script commands that
>apply a gradient color scheme to your molecule of choice.  this is
>similar to the 'color group' command already present in Rasmol, but with
>some improvements:
>
>1. choose from among four different gradient styles (rainbow,
>blue-white-red, black-white, or white-black).
>
>2. create gradients that apply to a single chain, span multiple chains,
>or apply separately to each chain of a multi-chain structure.  up to
>four chains are supported at this time.
>
>
>Color Gradients is comptible with Jmol, Rasmol, and Chime, and is
>available here:
>
><http://www.molvisions.com/resources/color_gradients/>
>
>
>(you can also access it under the Resources menu at my home page,
><http://www.molvisions.com/>.)  it will run in any Web browser; not even
>javascript is required.  ;-)
>
>to use Color Gradients, you will need to enter the chain designators,
>and the starting and ending residue numbers for each chain.  the output
>is a simple html file containing your script commands, from which you
>can select all, copy, and paste into your spt file (or an empty text
>file).
>
>plans for the future include allowing a pdb file to be uploaded
>directly, to read chains and residues from the file itself, and other
>output and command formatting options.
>
>
>if anyone has any suggestions for improving this resource, or if it
>doesn't work as expected, please feel free to send me email (offlist, if
>you prefer).

This looks really great. One thing I expected was that the gradient would
be 'squashed' to fit the length of the selection, so I would always see
one blue, one white and one red even if I only selected three
residues. Selecting around 40 residues I only see (a very nice:) gradient
from white to red.

One other thing I spotted using the grayscale was the following color
"color [255,-0,0]", which rasmol doesn't like.

I was attempting to build something vaguely similar (in concept) with the
'pdbHighlight' project, basically a resource for visually annotating PDB
files. Although I haven't found time to make my perl scripts into a CGI
page yet.

http://bioinformatics.org/pdbHighlight/ 

This has been a work in progress for a couple of years ;)

One thing I would love to see is if you could 'serve' your scripts as a
web service with an API, then rasmol / jmol / chime could be configured to
lookup the results of that web service on a certain command (i.e. based on
a config file which would expand the language syntax). The only practical
difference with this approach is that it avoids the need to copy / paste
from one platform to another, but it also opens up the possibility of
sending all kinds of cool commands to peoples molecular viewers on
request.

Cheers,
Dan.

>
>
>regards,
>
>tim
>