[Chimera-users] After fitting a PDB into a cryo-EM density, is it possible to color the PDB atoms by the local EM density in the cryo-EM map?

Eric Pettersen pett at cgl.ucsf.edu
Tue May 27 16:09:16 PDT 2014

…and if you need to compare two fittings you could fit the PDB into one map, make an attribute, fit it in a second map and make a second (different) attribute and then use the Attribute Calculator tool to make a third attribute that is the difference of the first two attributes and then use Render By Attribute on that.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

On May 27, 2014, at 3:06 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Jonathan,
> Sure, you can use the "Values at Atom Positions" tool (in menu under Tools… Volume) to evaluate densities at atom positions and assign them as an atom attribute, then easily map attribute values to colors with "Render by Attribute" and/or the "rangecolor" command.
> Values at Atom Positions:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html>
> Clicking the Histogram button on that tool will open the "Render by Attribute" tool.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>
> It's basically the same as coloring by bfactor, hydrophobicity, sequence conservation etc.
> 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 May 27, 2014, at 2:53 PM, "Lai, Jonathan" <jlai7 at illinois.edu> wrote:
>> Dear Chimera-users,
>> I have several cryo-EM maps of an assembly process and a PDB of the final product; what I want to do is to have a visual depiction of how the local EM density around structural elements in the final product changes over time.   After fitting the PDB into the cryo-EM density, I am wondering if it is possible to color the PDB atoms by a reference EM density at each point.  For example, I want to color every residue that intersects isosurface == 0 blue, every residue that intersects isosurface == 1 red, and have a continuous color scheme for all intermediate values from (0 to 1).  I already have fitted the PDBs into the cryo-EM maps.  Is there any easy way to do this?
>> Cheers,
>> Jonathan Lai
>> University of Illinois at Urbana-Champaign
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