Re: [Jmol-users] dots documentation additon

[Bob H. <ha...@st...>]

Except I don't quite think that does what you say. You mean

set dotSurface on/off

set dotSurface ON  # (the default)

creates for the selected atoms only that part of the overall molecular 
"dot surface" that is associated with that atom.

set dotSurface OFF

creates full, possibly overlapping, spheres of dots around each selected 
atom.

What

set dotsSelectedOnly ON

does is to tell Jmol to ignore all atoms not selected when any future 
"dots on" command is given. This allows, for example, dots to fully 
encase a ligand even though it is in contact with a protein. Otherwise, 
with (the default)

set dotsSelectedOnly OFF

Jmol creates for each selected atom only the dots that would be 
attributed to that atom on the overall molecular "dot surface."

The setting of dotsSelectedOnly ON or OFF only has an effect when 
dotSurface is set ON.


Frieda Reichsman wrote:

> Information on 'set dotsSelectedOnly' is missing form the 
> documentation, except for a brief statement under the command 
> 'calculate'. 
>
> Under 'dots', it could say something like,
>
> set dotsSelectedOnly on
> creates dots on subsets of bonded atoms, so that each atom is a 
> finished sphere of dots.
>
> set dotsSelectedOnly off 
> (which is the default state)
> creates dots only where the surface of the atoms is sovlent-accessible.
>
> Apologies if this is not an accurate description; at least its a 
> starting point...
>
> Frieda
>
> ///////////////////////////////////////////
>
>
> Frieda Reichsman
>
> Molecules in Motion
>
> Interactive Molecular Structures
>
> http://www.moleculesinmotion.com
>
>
> ///////////////////////////////////////////
>
>
>
>------------------------------------------------------------------------
>
>-------------------------------------------------------------------------
>This SF.net email is sponsored by: Splunk Inc.
>Still grepping through log files to find problems?  Stop.
>Now Search log events and configuration files using AJAX and a browser.
>Download your FREE copy of Splunk now >>  http://get.splunk.com/
>
>------------------------------------------------------------------------
>
>_______________________________________________
>Jmol-users mailing list
>Jmo...@li...
>https://lists.sourceforge.net/lists/listinfo/jmol-users
>  
>


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get. 

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900