[Chimera-users] CHIMERA help - coloring density maps

Thomas Goddard goddard at cgl.ucsf.edu
Fri Apr 23 13:43:23 PDT 2004

Hi Padma,

  There is a Chimera command called "longbond" described in the Chimera
User's Guide / Basic Functions / Commands / longbond


that removes long bonds.

  There is currently no radial masking tool.  But using the Isosurface
Colorizer extension from EMAN you can set the color to transparent black
outside or inside a certain radius.  That will make it invisible.  For
example you can make the color blue at radius 10 nm, and transparent
black at 10.01 nm.  You will also want to turn on the Volume Viewer /
Options / Dim transparent surface mesh switch to get rid of the specular
highlights on the transparent black part of the surface.  This trick
for masking does not "cap" the isosurface at the radius where it is cut.
So you see the inside of the isosurface.  Turning off two sided lighting
in Volume Viewer / Options will make the interior of the surface dark.
To cut and cap the isosurface at a specific radius you really want to
the display to act as if the volume data were zero outside a specified
radius.  I don't have any way to do that, although it probably would
not be too hard to hack something into surface.py that copied the 3-d
matrix and made it zero outside a specified radius.

  By the way, the modification I described to Chimera surface.py to make
the Isosurface Colorizer from EMAN work is not needed in Chimera 1917.
That change was included in Chimera 1917.

  I you are looking at models of virus particles you might be interested
in the Chimera Multiscale extension.  Here are some example images:


The images at the bottom of that page show the RNA in satellite tobacco
mosaic virus.


> From: Padmaja Natarajan <nataraja at scripps.edu>
> Subject: Re: [Chimera-users] CHIMERA help - coloring density maps
> Date: Fri, 23 Apr 2004 13:08:02 -0700
> To: Thomas Goddard <goddard at cgl.ucsf.edu>
> Hi Tom,
> Thank you very much for the details you had given me earlier in
> making the radial coloring work for surfaces.
> I , with the help of my colleague Jeff  who made the changes in the 
> chimera (version 1917) script, am
> able to produce radial coloring for my density map!
> Can ask more questions??
> 1) I have coordinates for an icosahedron, but when I read it into 
> chimera,
> several un-wanted connections are made (probably because of the way the
> PDB file is written - for use in the graphics program O). I do not see 
> any distance cut off
> criterion  command that would help (probably) remove some of those 
> connections!
> 2) density map: I would like a radial masking tool, that can be used to 
> choose
>    minimum and maximum values for radius and be able to see the map only 
> within this
> radius range. For example, this helps in looking at the inner (RNA) 
> density in a  virus structure.
> thanks again!
> regards
> Padma
> ______________________________
> Padmaja Natarajan, Ph.D
> The Scripps Research Institute
> La Jolla, California, USA.

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