Hi Padma, There is a Chimera command called "longbond" described in the Chimera User's Guide / Basic Functions / Commands / longbond http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/longbond.html 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: http://www.cgl.ucsf.edu/home/goddard/viper/ The images at the bottom of that page show the RNA in satellite tobacco mosaic virus. Tom

From: Padmaja Natarajan <nataraja@scripps.edu> Subject: Re: [Chimera-users] CHIMERA help - coloring density maps Date: Fri, 23 Apr 2004 13:08:02 -0700 To: Thomas Goddard <goddard@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.