[Chimera-users] Screen shots from coot

John Rose rose at bcl4.bmb.uga.edu
Tue Mar 1 07:43:10 PST 2016


Sorry, Raster3D is what I meant.  I know about the Volume Viewer and I have used it to produce some very nice ED figures.  

The COOT save/RasMol import does not require all the fiddling with the Volume Viewer settings it is essentially what you see in COOT is what you get in pyMol but with better defination.



John Rose Ph.D.
Associate Professor
B204B, The Fred C. Davison Life Sciences Complex
120 Green Street
Department of Biochemistry and Molecular Biology
University of Georgia
Athens, GA 30602-7229
Phone:     706-542-1750
Fax:        706-542-3077

> On Feb 29, 2016, at 6:22 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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 <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/features.html#density>>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/density.html <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 <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
> <image2.png>
>> On Feb 29, 2016, at 7:22 AM, John Rose <rose at bcl4.bmb.uga.edu <mailto: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

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