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/style.html>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.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
Hi Kenward, Strictly speaking, the answer is no. Atom specs in Chimera and ChimeraX differ. For instance, the Chimera atom spec “:11.A@ND1” in Chimera X would be “/A:11@ND1”. As you generate H-bonds in Chimera, there’s an option to save them to a file. You would then have to edit that file and swizzle things around to get the info into the atom-pair format that ChimeraX can read as pseudobonds. —Eric Eric Pettersen UCSF Computer Graphics Lab