[chimerax-users] ChimeraX cross links

[Elaine Meng]

> On Jun 4, 2020, at 1:25 AM, Dina Schneidman <duhovka at gmail.com> wrote:
> 
> Hi,
> We are getting addicted to the ChimeraX graphics, amazing!
> I couldn't find how to add cross-links on top of the structure. What would be the best way to do this?
> Also, is there a way to color different cross-link types in distinct colors?
> Thanks and stay safe!
> Dina

Hi Dina,
Glad you like it, and I certainly hope you and your family are staying safe too!  

As I understand it there are two ways for atomic structures with crosslinks to be shown in ChimeraX:

(1) some integrative modeling structures include such crosslinks.  If you download the "cif" from the PDB IHM site <https://pdb-dev.wwpdb.org/> and then change its filename suffix to "ihm" instead, then you can open it in ChimeraX.  If the IHM model has crosslinks, they should show up somewhere in the model hierarchy of that data, which you can explore in the Models panel.  An example of one with crosslinks is the BBSome:
<https://pdb-dev.wwpdb.org/entry.html?PDBDEV_00000018>

(2) or if you just have any atomic structure already in ChimeraX and you want to add crosslinks, you can read in pseudobond file (filename.pb), which is just a series of atom-pair specifications in plain text.  You can also include color, radius, number of dashes.  The file description is the bottom section of this page:
<http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html>

Also, you can change colors, number of dashes, and radius of any pseudobonds already in the structure or previously added, just using the commands "color" "style" and "size"; see the links in the top section of the pseudobonds page.

There is a chimerax mailing list CC-d here for questions (unless they contain private data).  I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco