[Chimera-users] Smoothing and binning volume data

Tom Goddard goddard at sonic.net
Thu Mar 16 12:08:32 PDT 2017


Set "step 1” above the histogram in the Volume Viewer window to display the full resolution of the data.  If step is 2 that means only every other density map grid point is shown along each axis.  The step gets set automatically to values greater than 1 when the map is large to avoid slowing down the graphics (rotating, zooming…).  The initial step it chooses is controlled by the volume viewer menu Features / Data Display Options… , “Adjust step to show at most [N] Mvoxels”.

	Tom

> On Mar 16, 2017, at 11:41 AM, Andrea Fera <andrea.fera at gmail.com> wrote:
> 
> Hi Tom!
> 
> Tank you for your information. 
> Let me try to explain better what I asked.
> 
> What I seem to have revised is that the virtual sections of my maps have a much higher resolution than  the rendered images by Chimera. 
> This should be because, evidently, I didn't understand yet how to control the default smoothing and/or binning in the volume viewer, of which I used until now the default value. 
> Can you tell me how to do, or what to vary?
> 
> Thank you for the tip about using two colors in the rendering. Going to try immediately.
> Thanks,
> Andrea
> 
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> 
> --
> Andrea Fera, PhD – [Senior Research Scientist]
> Advanced Molecular Imaging ; DUNS 824-XXX-XXX
> U​nit for Cytoskeletal Dynamics , NICHD, National Institute of Health
> ​Email: andrea.fera at gmail.com <mailto:andrea.fera at gmail.com> 
> 
> 
> On 16 March 2017 at 14:28, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
> Not sure what you are asking.  You can do Gaussian filtering to smooth a map, or binning to average 2x2x2 voxels together producing a smaller smoother map using the Volume Filter tool.
> 
> To color “solid” style map rendering different colors at different data values click the nodes on the yellow line on the volume viewer histogram and then click the color button below the histogram to change the colors.
> 
> 	Tom
> 
> 
>> On Mar 15, 2017, at 7:49 PM, Andrea Fera wrote:
>> 
>> Dear Tom,
>> 
>> How are you?
>> I am using Chimera more and more recently, and I have come to the point where I need to be able to control the amount of smoothing and/or binning that it inserts passing from the virtual sections to the rendering.
>> 
>> Could you please send me some information on where I could look for this information?
>> 
>> Another, related, thing. Is there a way that I can color in red or brighter color the part of the rendering including voxels below (or above)  a certain threshold value?
>> 
>> I hope that I am not asking anything too strange.
>> Especially the first thing would help me greatly.
>> 
>> Thank you,
>> Andrea
>> 
>> --
>> Andrea Fera, PhD – [Senior Research Scientist]
>> Advanced Molecular Imaging ; DUNS 824-XXX-XXX
>> U​nit for Cytoskeletal Dynamics , NICHD, National Institute of Health

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