Hello Eric, Thank you very much for the link. I must admit, that I had seen this before and forgot about it. I should have searched the mailing list. But the server was down, so I could not do it. I appreciate your help. Kind regards, Michael
On 5. Nov 2023, at 01:28, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Michael, As detailed here: How to update the bonding status every frame when viewing a molecular dynamic trajectory? - ChimeraX-users <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>, you can use the "perframe" and "bond" commands to recompute the bonds every trajectory frame. This will slow down interactive playback, but won't affect movie recording if that's what your ultimate aim is.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 2, 2023, at 11:31 PM, Michael Patzschke via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear colleagues,
I have a trajectory from an ab initio MD run. The output is in the form of concatenated .xyz information. I can open and visualise this in ChimeraX, but the bond topology is determined from the first step. As the simulation progresses, bonds are stretched and the broken bond in my example just gets drawn, although the distance of the involved atoms gets larger then 7 Å by the end of the simulation. Is there a way to use dynamic bonds in ChimeraX? By this I mean that the bonds are only drawn when the distance of the involved atoms is below a certain threshold.
I would appreciate any help in the matter.
Kind regards, Michael Patzschke _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/>