On Jan 31, 2017, at 12:00 AM, Kenward Vaughan <kay_jay@earthlink.net> wrote:

On 01/29/2017 02:16 PM, Elaine Meng wrote:

No problem, I actually had to think about this… there's not yet a ChimeraX command to create pseudobonds, but you can list pairs of atoms in a text file, name it something.pb and then open the file.  Maybe that is still too inconvenient, however.

For example, in ChimeraX "open 1bna" and then the attached text file (if name ends in .pb).  Actually mmCIF of nucleic acids already have the base-pairing H-bonds, as you can see before opening the pb file.  You can control number of dashes with ChimeraX command “style” and color using “color” with “target p” … I don’t think there’s a command for pseudobond thickness yet, however.

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

I hope this helps,
Elaine

It certainly gives me things to gnaw on...  :-)

If a scene with H-bonds is generated in Chimera, can that be saved/exported with those bonds recorded in a way that ChimeraX will read them?


Kenward