[Chimera-users] Question about missing segments/pseudobonds

[Elaine Meng]

Hello Olman,
The "missing segments" dashed lines show where the protein is really connected even though the structure did not contain XYZ coordinates for the atoms.  Sometimes a loop is too flexible or disordered for crystallography to solve the atom positions, for example.  So even though the residues between those two parts are in the "real" molecule that was used in the crystallography experiment, there are no atomic positions available.  The missing segment line is shown so that you know there is one continuous chain even though there is a break in the ribbon.

If you don't want to see them, just use command:

  ~longbond

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/longbond.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 Jul 18, 2020, at 11:56 PM, OLMAN JOSE GOMEZ ESPINOZA <o.gomez01 at ufromail.cl> wrote:
> 
> Dear colleagues, hope your fine well. I have a question about the pseudobonds/missing segments, what those missing segments really mean?. After I performed some docking analysis (using auto dock vina), I used ViewDock to evaluate the results, but I noticed some dotted lines between some atoms in the molecule, so I went to PseudoBond Panel and realized that this dotted lines are missing segments. So I did not understand if this missing segments are a truly chemical bond, or what are they? What would be its importance or relevance for my structure?
> 
> Thanks in advance for your help
> Olman Gomez E.