Hi Tristan,

Thanks a lot for the reply and the helpful command options. The primary reason for preferring the secondary structure steps over the single amino acid steps is the time it takes to go systematically through large models (>10 000 residues). I also find it sometimes easier to see more residues in context rather than focusing on a single one – the distance argument you mentioned is helpful there.

In case there is a chance for reviving the secondary structure steps I would be happy to hear about it 😊

Best wishes,

Matthias

From: Tristan Croll <tcroll@altoslabs.com>
Date: Tuesday, November 26, 2024 at 10:43
To: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at>
Cc: ChimeraX-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Stepping through model in secondary structure element steps (ISOLDE)

Hi Matthias,

I'm afraid I retired the "per-secondary-structure-element" stepping mode some time back - it was always just a bit too flaky for my liking. I guess it wouldn't be too difficult to add a command with the equivalent functionality... but could you expand on what you dislike about the new mode? There are a couple of options to the "isolde step" command that might help you tweak it more to your liking: "interpolateFrames {integer}" will set the number of frames used in the "sliding" animation - the default is 15; I often set it to 5 when working through a big model; 1 will cause it to simply jump instantly to the next residue. "viewDistance {float}" will set the distance in Angstroms between residue and camera (default is 10). For both of these it will remember the last value you set.

Best,

Tristan

On Sun, Nov 24, 2024 at 12:54 PM Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear all, 

I seem to remember that it was possible to step through a model in Isolde one secondary structure element at a time, however I don't find that option anymore. Is this possible at all? I prefer this to the isolde step option that goes through the model one residue at a time. 

Many thanks in advance, 

Matthias 

Sent from Outlook for Android

---

Matthias Kopano Vorländer
Postdoc
matthias.vorlaender@imp.ac.at

Plaschka Lab
IMP – Research Institute of Molecular Pathology - imp.ac.at

Part of Vienna BioCenter.
www.viennabiocenter.org

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