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

Mohan Pradhan mohan.pradhan at ymail.com
Thu Sep 10 09:20:17 PDT 2015

Dear Tom and Elaine,
                  Thank you both for your response. I think I was not very clear with my question. Let me rephrase my query here again in more detail.

I have done Molcular Dynamics simulation of my protein in explicit solvent. Following which I calculated the water density from the trajectory using grid-based approach with grid cells of size 0.5 X 0.5 X 0.5 Å. A sample of the grid-based density output file is attached here for your reference.

We then used Chimera to visualize the map using the volume viewer menu. We are attaching two image files here at two different isocountor threshold cutoff. One which was set to the isovalue at which we observe the maximum value of the historgram at an isovalue of 37. (image-1)

Second we set it to 2.5 times that isovalue 2.5 X 37 ~ 93) (Image-2).

The issue we wanted to clarify was what do these histogram actually depict with regard to the input grid file?

What is the histogram depicting at an iso-value of zero?

Why is there a sinusodial curve for the histogram towards the lower isovlaue?

     On Wednesday, September 9, 2015 4:07 AM, Tom Goddard <goddard at sonic.net> wrote:

 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 2.5Is 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.
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