[chimerax-users] How can I use command crosslinks with bonds?

[Elaine Meng]

Hi Junha,
If the links are all longer than reasonable “normal” covalent bonds, it might work to simply save your marker/link model as PDB and then read it back in.  The CONECT records for long connections will automatically be interpreted as pseudobonds.

To answer your broader question, it was mainly just a historical series of events, that some IHM (integrative hybrid model) files include chemical crosslinking constraints that are read into ChimeraX as pseudobonds, and the crosslink command was written to allow analysis of these constraints and how well they fit the structural models.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.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 Mar 2, 2019, at 7:20 AM, Jun Ha Song <junhasong at berkeley.edu> wrote:
> 
> Dear RBVI,
> 
> I want to use few command lines that are exclusively available for pseudobonds. The problem is that my model is consisted of markers and links, and there seems like no possible way for me to simply transfer bonds into pseudobonds.
> 
> What commands like crosslinks histogram provide seems way to good for it to be limited for pseudobonds only. Is there a technical reason why such command is only applicable with pseudobonds? Can commands in Chimera/ChimeraX that work with pseudobonds easily be adapted to work with bonds, or is that too much of technical difficulty?
> 
> If it is not feasible, is there a way to turn bonds into pseudobonds?
> 
> Best,
> Junha Song.