[Chimera-users] shape factor

Tom Goddard goddard at sonic.net
Fri May 13 12:09:05 PDT 2011

Hi Maria,

If you mean you want to create a map that is all ones inside a surface, 
for example inside an icosahedron, I just today made the Chimera "mask" 
command able to do that.

     shape icosahedron radius 160
     mask ones #0 spacing 3.5 border 20

You would need to get tonight's Chimera daily build to use the "mask 
ones" capability.


>       The video has been useful for me, thank you.
>       Other question: the "meshmol" command creates a molecule model from a surface, there are a command to create a map from a surface?
>       Thank, María.

-------- Original Message --------
Subject: Re: [Chimera-users] shape factor
From: Tom Goddard
Date: 5/12/11 9:31 AM
> I don't understand what you want to do. Here is an example of using the
> hkcage command
> http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#icoscage
> You will want to add a radius option (e.g. radius 330 for 330 Angstrom
> radius cage) to that example and you will need to figure out the h and k
> lattice parameters.  Chimera cannot figure out the h,k values you need.
> I usually try a few values by hand and visually determine the correct
> values.  When you say "shape factor" I guess you probably mean "sphere
> factor", the Chimera term for the radial interpolation factor (0 to 1)
> between a flat faced icosahedron and a sphere.  Chimera has no way to
> automatically determine that value.  I sometimes judge that by eye using
> the Icosahedron Surface dialog, menu entry
>       Tools / Higher-Order Structure / Icosahedron Surface
> That dialog has sliders to adjust the radius of the icosahedron and the
> "sphere factor" so you can interactively try different values.
>     It would be nice if Chimera could automatically determine the
> icosahedral coordinate system, outer radius, and best sphere factor, but
> currently that is only done by eye.
>       Tom
>>       Hello,
>>       We are using Chimera to classify viruses. We use pdb files from viper.
>>       We want a way to obtain exactly shape factor and/or compare with an icosahedron. We have problem do it. We open pdb file, draw icosahedron using "hkcage" (all models actives) and try to compare that two figures using "fit in map", or similar but doesn't work. What is the best and exactly way to do it?
>>       Thank you.
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