April 2024 - ChimeraX-users - RBVI Mailing Lists

question about pb file
by Renee Garza 02 Apr '24

02 Apr '24

Hi there! I've been saving pb files and see that the colors are of varying shades and transparency. I have looked at the link regarding the color key however some colors in the pb files are not in the list. I'm wondering if there's a place to look at the degree of confidence based on color somewhere or a way to have the output with the general color like red, blue, orange, yellow, etc. instead of very specific shades. Thanks, Renee

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Range selection dose not work.
by 洪冉 02 Apr '24

02 Apr '24

Dear Users and Developers of ChimeraX, I am attempting to make a selection of a range of atoms by their numbers in ChimeraX. However, the command I have used does not seem to work in my case. The command in question is sel #1:@1-3. Could anyone assist me with this issue? For screenshots, please see below. Many thanks in advance! Ran

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Can α-carbon trace and bond be adjust for PBC?
by qz.chen＠tamu.edu 02 Apr '24

02 Apr '24

Hi, I want to use ChimeraX to visualize the protein slab simulation in the condensed phase as the link below. Unlike typical protein simulations, simulations of the condensed phase slab often need to keep the atoms inside the box for more accurate visualization. This means that particles between proteins may be jumping, leading to unreasonable lines appearing in the visualization. I have not found a way to adjust this in ChimeraX. https://www.biorxiv.org/content/10.1101/2020.08.05.237008v1.full Is there a way to limit the maximum distance between carbon and bond among particles? Thanks!

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Define axis along z?
by Oliver Clarke 01 Apr '24

01 Apr '24

Hi, For symmetric EM volumes, it would be useful to be able to easily create an axis corresponding to the molecular symmetry axis - generally coincident with a vector parallel to the Z-axis of the box, directly through the center. Is there an easy way to create such an axis in ChimeraX for an arbitrary map? It would be useful to have such an axis in order to rotate a volume around the molecular symmetry axis, even in the absence of a model (this is fairly easy to do if a model is present using define axis). This might be a useful generic extension to "define axis", if there isn't already an easy way to do so. Cheers Oli

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Difficulty with Z-translation - bug?
by Oliver Clarke 01 Apr '24

01 Apr '24

Hi, I can't seem to get the mousemode "Z-translate selected models" to work properly. I have "translate selected" set to Alt+left-drag, so per the docs ("assigned button + Ctrl (in that order) switches to Z-translation instead"), Alt+Ctrl+left-drag should translate the selected model in Z. It does not, or at least in any reproducible manner. Watch the selected yellow marker in the side view here on the right hand side: https://www.dropbox.com/scl/fi/vds0cwu0zizclg64vlxqc/z_translate_bug.mov?rl… 1. Initially I translate in x-y using Alt-drag - works fine. 2. I try to translate in z using alt-ctrl-drag - nothing happens 3. I keep trying translate in z, and eventually it "works" - but if you look closely you will see that the movement of the marker is not synced up with the direction/speed of the mouse cursor. Is this a bug? I remember testing this when it was initially implemented and I thought it worked fine so I suspect so...? Cheers Oli

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