[Chimera-users] SSEHUnter and SSEBuilder questions

[Tom Goddard]

Hi Kristin,

   I think your approach to extract an approximate icosahedral 
asymmetric unit should work fine.  I'm guessing all the trouble comes 
from the fact that the original pif map values are negative where the 
structure is located.  Then when you use volume eraser it places zero 
values in the map where you erased and zero is a higher value than the 
density values for the structure.  That messes up the display in 
Chimera.  This is just a guess.  Let me know if it is not right.  You 
can see the range of density values in the volume dialog below the 
histogram and the current contour level density value.  The solid cube 
display can be fixed by turning off "Cap high values at box faces" at 
the bottom of the Surface and Mesh Options panel of the volume dialog.  
But I suggest you make the density values positive so you don't run into 
further problems down the line.  For example SSEHunter will probably 
fail if the density is inverted or highly shifted.

   Here's what to do about it.  If the PIF map has inverted density, 
meaning that the most negative map values are actually the most dense 
parts of your structure then you should invert the map so that the most 
positive values are the densest.  You can do that with Volume Filter 
(menu Tools / Volume Data), with Filter Type "Scale" choose the scale 
value to be -1.  Another possibility is that your map values are simply 
shifted into the negative range (not inverted).  You can use the above 
Volume Filter dialog to shift the structure density values into positive 
territory.  You could for instance shift so the mean map value is zero.  
You could find the mean using Volume Mean, SD, RMS (menu Tools / Volume 
Data).

   Here's a video that demonstrates another way to extract an 
icosahedral asymmetric subunit.

     http://plato.cgl.ucsf.edu/chimera/videodoc/IcosWedge/index.html

I don't think you should use exactly this because you need your 
subregion to extend beyond the asymmetric unit because the molecules 
will cross the asymmetric unit boundaries.  A variant of the method 
shown in the video could allow you to extract one asymmetric unit and 
its neighbors (just color the markers for each of the asymmetric units 
you want the same color).  Maybe that gives you a bigger subregion than 
you want.

     Tom


Kristin Parent wrote:
> Hello,
>
> I was hoping you could help me out. I am trying to locate secondary
> structure elements in an individual subunit of an icosahedral virus from a
> cryo-reconstruction. I have the entire virion in pif format and would like
> to use the density from a single subunit using SSEHUnter and SSEBuilder. I
> am not sure how best to get the volume data as a useable mrc input for
> this tool.
>
> I tried using the volume eraser to eliminate other areas in the map that
> are not the subunit I'd like. When I save the map and then the session,
> the subunit looks fine in the session, but if I open the subunit mrc file
> in a new session, I get what appears to be inverse density (the stuff I
> erased), and in the volume viewer, the density looks inverted. If I move
> the slide bar to the left, I end up with a solid cube. I am either doing
> something horribly wrong, or this is maybe not the best method for
> excising my subunit??? Please advise the best approach to creating a
> subunit mrc file that can be used by SSEHunter.
>
> Thanks in advance! Kristin
>
> Kristin Parent, Ph.D.
> University of California, San Diego
> Department of Chemistry and Biochemistry
> 9500 Gilman Drive, NSB 4104A, MC-0378
> La Jolla, CA, 92093-0378
> (858) 534-8038
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