Hi Józef, We certainly do plan to bring the more extensive MD analysis capabilities that Chimera had to ChimeraX. But it competes against other re-implementation priorities (e.g. energy minimization) and completely new capabilities (e.g. Phenix integration) that we also need to accomplished. Nonetheless, I have bumped up its priority some on my personal to-do list so maybe I'll find time to work on it in the not ridiculously far future! I guess I was secretly hoping that the MD capabilities would show up in a magical bundle some Good Samaritan submitted to the toolshed. ;-) --Eric Eric Pettersen UCSF Computer Graphics Lab

On May 10, 2023, at 12:39 PM, Lewandowski, Jozef via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Thank you, Elaine. That should do it. Distance monitors are indeed useful when looking through a trajectory and I often use the just in this way. However, if you try to output the trajectory as a movie, the numbers are often changing too quickly to be of any use and they become more of a distraction than a useful feature. In this context it would be better to have a look at a distance trace in Plot Distance function in Chimera (is there a plan to bring such features to ChimeraX? - this is one of the few features that make me go back to Chimera, for most other stuff I typically prefer the solutions in ChimeraX). That said your suggestion does exactly what I need. I agree with Tom that having a command to make a pseudobond rather than have to load a file would be a useful feature.

Thanks, Regards, Józef

-----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, May 10, 2023 4:56 PM To: Lewandowski, Jozef <J.R.Lewandowski@warwick.ac.uk> Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Hiding distance labels during trajectory playback

Hi Józef, Well, the whole purpose of the distance monitors is to show distances, so even if you delete the label from the current frame they will reappear for other frames.

Instead: if you just wanted to draw a bunch of pseudobonds without labels, the way to do it is to create a pseudobond file in a text editor (rows just specify the pairs of atoms you want to draw lines between). E.g. containing lines something like:

/A:5@sd /A:1@he1

The file format is described here in more detail, including how to specify the initial color, radius, and number of dashes (which you could also change with other methods after the fact):

<https://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>

You could just close or delete the distances, or just hide them if you want to have them for later analysis.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On May 10, 2023, at 7:00 AM, Lewandowski, Jozef via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

Is there an easy way to hide distance labels during the playback of an MD trajectory? Even if I delete or hide the labels in one frame they get generated when next frame is loaded. I tried to include hiding/deleting the labels command in perframe but they flash on before they are removed. Ultimately, I would like to record a movie where only the pseudobonds are shown but not the labels.

Thank you, Józef

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