[Chimera-users] Depicting entropy and mobility in pdb files

[Elaine Meng]

Hi George,
Yes, you can can color by B-factor (i.e. whatever values are  in the B-factor column) or show “worms” with thickness scaled by the per-residue average of those values.

B-factor is just one example of an “attribute” or property with values per atom or per residue.  Other examples are residue hydrophobicity or conservation in an associated sequence alignment.

You can color by any atom or residue attribute value, or “worm” by any residue attribute value with the Render by Attribute tool (in menu under Tools… Depiction):
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render>

... or color by attribute with the “rangecolor” command:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>
…for example:
rangecolor bfactor min medium blue mid red max yellow

(You could also give specific values instead of “min” “mid” “max” and use whatever colors you want.  The min/mid/max would include ligand, ion, and solvent values, if any, so you might not see the max color on the ribbon.  Render by Attribute GUI is easier for seeing the range of values because it shows a histogram.)

There is no command for worms, only the Render by Attribute GUI.  In that tool, you can color atoms by by the bfactor attribute of atoms, or change to attributes of residues (instead of atoms) in order to color ribbons and/or show worms.  The average bfactor (over the atoms of each residue) is automatically listed as a residue attribute choice when you have a structure with bfactors open.

This tutorial has coloring by B-factor of the surface using Render by Attribute, but coloring by atoms is the same, just don’t show surface. It also includes showing a color key.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html>

This tutorial includes coloring ribbons and showing worms by the residue attribute of sequence conservation, but you can do it similarly for the residue attribute of average B-factor, which is automatically listed in the Render by Attribute menu of residue attributes:
<http://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/outline.html>

Also, attributes can be loaded in from a separate file, so you don’t have to smush them into the B-factor column, although it’s OK if you want to do it that way.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attribdef>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

2gbp color and worms by residue average B-factor:

> On Aug 27, 2018, at 9:13 AM, George Tzotzos <gtzotzos at me.com> wrote:
> 
> Hi everybody,
> 
> I’ve generated two pdb files which are of identical coordinates. Their only difference is that the b-factor column has been replaced with data indicating residue conservation (structure 1) and residue intrinsic mobility from normal mode analysis (structure 2).
> 
> Below are indicative atomic coordinates.
> 
> Structure 1
> ATOM     24  NH1 ARG A   5       5.258 -15.260 -22.393  1.00  2.87           N
> ATOM     25  NH2 ARG A   5       6.717 -16.030 -20.793  1.00  2.87           N
> ATOM     26  N   ARG A   6        3.934 -11.168 -16.245  1.00  2.84           N
> ATOM     27  CA  ARG A   6       5.160 -10.666 -15.652  1.00  2.84           C
> 
> Structure 2
> ATOM     24  NH1 ARG A   5       5.258 -15.260 -22.393  1.00  1.35           N
> ATOM     25  NH2 ARG A   5       6.717 -16.030 -20.793  1.00  1.35           N
> ATOM     26  N    ARG A   6       3.934 -11.168 -16.245  1.00  1.73           N
> ATOM     27  CA  ARG A   6       5.160 -10.666 -15.652  1.00  1.73           C
> 
> Is there a way to visualise these differences (e.g. by different thickness of ribbons or any other means e.g. colour of spheres).
> 
> Thank in advance for any suggestions
> 
> George
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