[chimerax-users] Pseudobond in Metalloproteins

[Elaine Meng]

Hi Rachael!
Welcome to ChimeraX  :-)

You can change the display of pseudobonds without needing to make them into covalent bonds.  You can change pseudobond coloring to halfbond mode with command:

color halfbond true

...or if there are other pseudobonds and you only want to change the ones in HEM residues:

color :hem halfbond true

The "color" commands above will also change bonds to halfbond true, but normally they're already in that mode anyway. (color halfbond option ignores the color "target" option currently)
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple>

Since the metal-ion is shown as sphere by default, the change in coloring doesn't really look like half of the bond, but you can change the ion sphere radius (e.g. command: size ions atomradius 0.4) to  change its style to stick  (e.g. command: style ions stick) to make it smaller.

If you don't want dashes but instead a single solid stick to represent a pseudobond, then command:

style dashes 0
- or -
style :hem dashes 0

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/style.html>

In version 1.3 recent daily builds, you can also use the Selection Inspector to change "halfbond" mode of pseudobonds only (not bonds):

(1) Ctrl-click the pseudobond to select it, and then if you want to change all of the coordination pseudobonds, press keyboard up-arrow to promote the selection to all of them.
(2) Next click the green magnifying-glass icon in the Home tab of the toolbar (or use menu: Actions... Inspect) to open the Selection Inspector.
(3) In the Selection Inspector, inspect: Pseudobond, check the box to turn on "Halfbond mode"

Selection Inspector (can also use to change atom sphere radii, etc.):
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html>

Pseudobonds in general:
<https://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html>

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

> On May 17, 2021, at 2:44 PM, Rachael Coleman <rec287 at cornell.edu> wrote:
> 
> Hello!
> I have recently switched over to using ChimeraX from PyMol and I'm really enjoying it a lot! My one question that I haven't been able to figure out is how to deal with pseudobonds in a heme-containing protein. I want ChimeraX to treat the bond between the porphyrin N atoms and the Fe atoms like a bond and not a pseudobond (so I want it to be half blue and half orange to correspond to the colors of those atoms). 
> 
> Is there an easy way to tell the program that a pseudobond is a bond? 
> Best,
> Rachael Coleman