[Chimera-users] 3D movies for projects

Eric Pettersen pett at cgl.ucsf.edu
Thu Feb 2 11:28:17 PST 2017

> On Jan 31, 2017, at 12:00 AM, Kenward Vaughan <kay_jay at 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 at ND1” in Chimera X would be “/A:11 at 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 Pettersen
	UCSF Computer Graphics Lab

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