[Chimera-users] setting solvent density threshold at 2.5 times of the bulk solvent density

Tom Goddard goddard at sonic.net
Tue Sep 8 13:07:17 PDT 2015

Hi Mohan,

  What you suggest is not correct.  I don't know if your map is from x-ray crystallography or electron microscopy but in both cases the map values are not literally "density" (ie mass per unit volume).  The processing of the maps often introduces negative values, and often puts the most common map value (peak histogram) at zero or even a negative value.  As Elaine, suggested you would need to ask someone expert in the processing of maps.  Chimera only uses the numeric values in the map file, it knows nothing about how those values relate to physical properties.  I have never seen an attempt to quantify mass density with x-ray or EM of biological samples.  X-ray researchers instead usually look at a iso-contour 1 or 1.5 or 2 standard deviations above the mean map value.


> On Sep 8, 2015, at 1:52 AM, Mohan Pradhan wrote:
> Dear Chimera users,
> I am using the Volume Viewer application in Chimera to visualize the solvent density around protein at a threshold value of 2.5 times of the bulk solvent density.
> My understanding is that the iso value corresponding to the bulk solvent density is marked by the peak in the plot of the volume viewer. I am then multiplying the iso value of the peak by 2.5
> Is this the right way of identifying regions in protein that have a solvent density of 2.5 times of the bulk solvent density?
> Kindly suggest.
> Thanks,
> Mohan
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20150908/b415a6f6/attachment.html>

More information about the Chimera-users mailing list