Dear Elaine, Thank you for your answer. I will take a look back at Chimera. Best regards. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse@cea.fr <color: purple;> W eb: http://biodev.cea.fr/rasmot3d/ <color: purple;> ----------------------------------------------- Le 14/09/2023 17:53, « Elaine Meng » <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> a écrit : Hi Philippe, For now you would need to use our older program Chimera for plotting and writing out distances and angles along a trajectory. See the Chimera MD Movie tool for trajectory playback and analysis, and specifically the section on plotting. The "Dump Values" button on the bottom of the resulting plots can be used to write out the values. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie....> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#...> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#plotting>> We would like to have similar tools in ChimeraX in the future, but they are not yet implemented. Although you could theoretically do it in ChimeraX by writing a lot of python code, it is not feasible for most users (including myself). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 14, 2023, at 3:01 AM, CUNIASSE Philippe via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear all,
I am wondering if there is a mean in ChimeraX to monitor distances, angles and torsion angles along a MD trajectory. The ideal would be to export a vector containing the frame id (a number) and the value measured for the distance or torsion angle. At the moment I can only built a distance histogram (which is already very usefull) after having created a pseudobond. But doing this, you lose the time evolution along the trajectory. Thanks in advance for your help. Best regards. Philippe.