[Chimera-users] Surface vertex density

[Tom Goddard]

For a density map you can control the number of surface triangles and vertices by choosing the subsampling “step” size in the Volume Viewer dialog.  Step 2 will use every other grid point along x,y,z axes and result in a coarser mesh.  For molecular surfaces computed from atoms, change the vertex density as described here

	http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005889.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005889.html>

  Tom


> On Jul 31, 2018, at 5:53 AM, ⁨עמיחי הולצר⁩ wrote:
> 
> And another question - there is "Surface and Mesh options" under the "Features" tab, so one can control the smoothing of the surface, thickness, etc. How can I control the number of nodes of the surface? I mean, I want the mesh not to be so dense. Is it possible?
> 
> Thanks again!
> 
> 2018-07-31 13:38 GMT+03:00 עמיחי הולצר :
> When I save it as OBJ file, how can I watch it in chimera again as a molecule with "atoms" and "bonds" (like CONECT line in pdb file)?
> I see that OBJ file look like a xml file, and contains coordinates and edges, but does it reflect the mesh?
> 
> Thanks,
> Amichai
> 
> 2018-07-30 19:37 GMT+03:00 Tom Goddard :
> Hi Amichai,
> 
>   Chimera computes density map isosurfaces using the marching cubes algorithm.  It can be saved in various file formats for example OBJ, others are described with the export command
> 
> 	https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html>
> 
>   Tom
> 
> 
>> On Jul 29, 2018, at 3:06 AM, ⁨עמיחי הולצר⁩wrote:
>> 
>> Hi Chimera support,
>> 
>> I have 2 questions:
>> 
>> 1. How does Chimera calculate the mesh from the density map?
>> 
>> 2. How can I save the mesh as a file?
>> 
>> Thanks a lot,
>> Amichai Holzer
>> Huji
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> 
> 

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