# [Chimera-users] icosahedral reconstruction volume color

Tom Goddard goddard at sonic.net
Mon Sep 24 14:25:25 PDT 2012

```Hi Reggie,

The following video shows how to place markers on your icosahedral
map, replicate them using symmetry, then use the Color Zone tool to
color part of the map near chosen markers.

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

The video is trying to solve a different problem from what you want but
the same techniques will do the job.

Tom

-------- Original Message --------
Subject: Re: [Chimera-users] icosahedral reconstruction volume color
From: Elaine Meng
To: Reginald McNulty
Date: 9/20/12 10:37 AM
> Hi Reggie,
> I can't think of a way to do that directly, but here are some related ideas:
>
> (a) for visualizing the 5-fold and 6-fold vertices,  the command "hkcage" can be used to create an icosahedral mesh of hexagons and pentagons - you specify radius, h and k values (where virus T number = h^2 + hk +k^2).  It makes a wire model which could be converted to sticks with command "meshmol".  The difficulty would probably be in getting the orientation and placement of the cage to match that of your reconstruction.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html>
>
> (b) "Color Zone" colors surfaces to match nearby atoms or pseudoatomic "markers" -- theoretically you could use "Volume Tracer" to place a red marker at each 5-fold vertex and then use Color Zone to color those regions of the surface red, and then undisplay the atoms or markers.  (These tools are in the menu under Tools... Volume Data.) However, the difficulty I see is in placing the markers exactly symmetrically so each vertex would get the same amount of coloring.  If you knew coordinates for the vertices (again the hard part) you could just create a PDB file with those fake atoms, color them red, ...
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>
>
> (c) there is a "Cage Builder" (menu under Tools... Higher-Order Structure) that lets you interactively construct a cage of hexagons and pentagons.  This is an additional method of generating markers.  The "Create Mesh...." option would generate single edges and vertices from the initially generated doubled set (you'd have to look at the figure in the docs to understand that part) and in the result, you could color the 5-fold vertices red and proceed as above with Color Zone.  The difficulty may be in building/scaling/positioning the cage to coincide correctly with your reconstruction.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/cagebuilder/cagebuilder.html>
>
> Sorry I haven't come up with simpler solutions,
> Elaine
>
> On Sep 20, 2012, at 10:04 AM, Reginald McNulty wrote:
>
>> Hi Elaine,
>> I'm wondering if I can color just the five-fold vertices of my icosahedral surface red, without coloring the entire surface red.
>> Reggie
>> ______________
>> From: Elaine Meng [meng at cgl.ucsf.edu]
>> Sent: Thursday, September 20, 2012 9:22 AM
>> To: Reginald McNulty
>> Cc: chimera-users at cgl.ucsf.edu
>> Subject: Re: [Chimera-users] icosahedral reconstruction volume color
>>
>> Dear Reggie,
>> I'm not sure what you mean by coloring according to symmetry... radial coloring perhaps? Our expert in this area is away this week, so I will try to answer, but please bear with me.
>>
>> You can open and display the vol file in Chimera, assuming it is the SPIDER format:
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume>
>>
>> You can then adjust the isosurface level in the "Volume Viewer" dialog and apply various kinds of coloring to the isosurface with "Surface Color" (in menu under Tools... Volume Data) or command "scolor".
>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html>
>>
>> These support coloring by
>> (a) map value or gradient norm
>> (b) distance from a point, axis or plane
>>
>> radial coloring = coloring by distance from a point, where the point is the center of symmetry
>>
>> I hope this helps,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>> On Sep 20, 2012, at 8:00 AM, Reginald McNulty wrote:
>>
>>> Dear Users,
>>> I've done a symmetric reconstruction utilizing Viper (I1) icosahedral symmetry with XMIPP. Is there a way to color my recon.vol file surface according to symmetry?
>>> Kind regards,
>>> Reggie
>
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```