Dale, something you are going to want to investigate is the JVXL format.
http://chemapps.stolaf.edu/jmol/docs/misc/JVXL-format.pdf
This format is designed for exactly your purpose. You have a specific map
with a specific cutoff, trimmed to a specific subset of the protein. You
would use the Jmol application (not web applet) to create it. I recommend:
load =8tln;
isosurface ID DenMap sigma -1 within 7.0 {26:E} color blue "=8tln" mesh
nofill
write "8tlnDenMap.jvxl"
Actually, even better would be:
load =8tln;
isosurface ID DenMap sigma -1 within 7.0 {26:E} color blue "=8tln" mesh
nofill
isosurface cache
# adjust to your viewing preference.
write PNGJ "8tlnDenMap.png"
The cool thing there is that you now have a self-contained compressed file
(187K in this case) that contains the image, the structure, a highly
compressed version of the map, and the view you want. Should load instantly
using
script 8tlnDenMap.png
Bob
On Tue, Mar 18, 2014 at 2:16 PM, Dale Tronrud <de...@daletronrud.com> wrote:
> Hi,
>
> In my continuing quest to display a bit of protein with an electron
> density map I am still having problems. In my html page I have the
> following three buttons.
>
> <br>
> <a href='javascript:Jmol.script(jmolApplet0,"isosurface ID DenMap sigma
> -1 within 7.0 {26:E} color blue \"=8tln\" mesh nofill")'>Load Map from
> EDS</a>
> <br>
> <a href='javascript:Jmol.script(jmolApplet0,"isosurface ID DenMap sigma
> 1 within 7.0 {26:E} color blue data/2fo-fc_6.map mesh nofill")'>Load
> CCP4 format Map from Disk</a>
> <br>
> <a href='javascript:Jmol.script(jmolApplet0,"isosurface ID DenMap sigma
> 1 within 7.0 {26:E} color blue data/8tln.omap mesh nofill")'>Load O
> format Map from Disk</a>
>
> The first loads a map from the EDS server. This map file is in O's
> DSN6 format and the filename ends in .omap. When I press this button
> a bit of time passes but nothing is displayed.
>
> The second reads a CCP4 format map from my server. I created this map
> file with software of my own construction and the density map loads up
> just fine.
>
> I used wget to grab the omap file from the EDS server and placed it on
> my server. When I press the third button a little time passes but no
> map is displayed. When I replace this file with a DSN6 format file,
> produced by the same software I used to create the CCP4 format map, I
> still get nothing.
>
> How do I get jsmol to read DSN6 format maps?
>
> Thanks,
> Dale Tronrud
>
>
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--
Robert M. Hanson
Larson-Anderson 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
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"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
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