[Chimera-users] Screen shots from coot

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 29 15:22:38 PST 2016


Hi John,
I don’t know anything about Rasmol format from Coot, but I see it can write a Raster3D file.   Chimera does not read rasmol or raster3D files, but it can certainly read density maps in many formats:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume>

…and has many options for density map display.  Just open the density map with File… Open and then adjust the contour level interactively in the Volume Viewer, which will automatically appear when you open the map.  You can show isosurfaces as mesh or transparent surfaces, color them however you like, control mesh linewidth, show only the density near some selected atoms,  etc. 

Example images, tutorial:
<http://www.rbvi.ucsf.edu/chimera/features.html#density>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/density.html>

Further, you can change the background color and turn on shadows, for example, commands:
set bgColor white
set shadows

If you want the mesh to look like solid sticks, try command “meshmol”
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html>

Those are just a few options of many.  I attached an example of meshmol with shadows below.  I didn’t spend time optimizing appearance, but it gives you a rough idea.
I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On Feb 29, 2016, at 7:22 AM, John Rose <rose at bcl4.bmb.uga.edu> wrote:
> 
> Hi,
> I colleague of mine just showed me that pyMOL can display great looking ED images from COOT which were saved in RASMOL format.  Is there a way for CHIMERA to do this.
> John Rose
>  

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20160229/495e1049/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image2.png
Type: image/png
Size: 317266 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20160229/495e1049/attachment-0001.png>


More information about the Chimera-users mailing list