Dear Florian,
you are certainly using the correct command and got the right arguments.
However, it appears that you have an old Coot version that cannot do the
solid map surfaces (something pre 0.6.2). So, please update.
And since Coot is a GUI oriented program you dont even need to use the
Scripting window as you can change the map display style using the
Display Manager->(Map) Properties. The second box in the pop-up dialog
will allow you to change the map style, select opacity etc.
Hope this help,
B
Jason Vertrees, now in charge of PyMOL, implemented a very nice feature
to display volumetric informations, like electron density (see
here:http://pymol.org/volume).
It is much richer/informative than isocontours and is very helpful for
model building.
I asked Paul if something similar could be done in Coot, and replied
promptly that the "multi-chicken" command
(Extensions>Maps>Multi-chicken) can be used to make something visually
very similar (http://data.imagup.com/10/1131391136.png)
I understand that the function "set-draw-solid-density-surface" must be
used to display a transparent isosurface instead of a mesh.
I'm not familiar at all with scheme scripting, but according to the
manual, the function has two arguments, "imol", which I guess is the map
number as it appears in the display manager, and "state", which is an
integer, and I guess, should be either 0 or 1 (off or on)?
But when I type: (set-draw-solid-density-surface 3 1)
I get
##
coot> (set-draw-solid-density-surface 3 1)
Backtrace:
In current input:
4: 0* (set-draw-solid-density-surface 3 1)
<unnamed port>:4:1: In expression (set-draw-solid-density-surface 3 1):
<unnamed port>:4:1: Unbound variable: set-draw-solid-density-surface
ABORT: (unbound-variable)
##
That is probably a stupid syntax error, but I could not get it right?
BTW, Coot is so much GUI oriented that I never had to use the scheme
functions to date. And it took me more than half an hour and research
using google (!) to figure out that functions must be typed in the
"Calculate>scripting>Scheme" window (!). The user manual was unhelpful
to find this key information because the corresponding paragraph is
entitled "scripting", which did not catch my attention when looking for
informations on how to directly run commands. May be it should be
renamed something like "Running commands and scripts".
Cheers!
Florian.
--
***************************************************
Dr. Bernhard Lohkamp
Assistant Professor
Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB)
Karolinska Institutet
S-17177 Stockholm
Sweden
phone: (+46) 08-52487651
fax: (+46) 08-327626
email: [email protected]
