Dear B, If it's just the visual that you want, you can use "clip" to clip a slab. Although the more common clipping is just near/far (always perpendicular to line of sight) there are also front/back planes that can be oriented in any angle. Example commands: open emdb:60539 ... you can rotate with the mouse/trackpad and see that it is a long section of fibril view orient ... to reset it so that Z is front/back, to prepare for the following clip command: clip front -20 back 20 axis z ... you can rotate again to see it is a shorter section of fibril I'm not sure what offset distance values you would need in your case, and you may need to give a fancier axis specification if the data are not already aligned on Z. See the "clip" help for the description of options: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clip.html#model> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Jul 3, 2024, at 4:24 PM, Binh Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear all,

Is there a way to display say 10% on the Z-axis of a fibril density map? Or maybe save 1 or 2 layers of the map?

<image.png>

I know 2 ways to do it but they both take a long time, and I wonder if we have an easier way to do it. • Use volume eraser with a big diameter sphere • Build a rough backbone carbon model in 1 layer, and do zone selection.

Thanks,

B

UT Southwestern Medical Center The future of medicine, today. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

Dear Elaine and Tom, Thank you so much. Both works. Elaine 's method can visualize 2-3 layers quickly with the right mouse click and drag. [cid:e7230686-e66b-49a6-8f87-e0ac5f8ddc6b] Tom's method re-define the unit cell. So one can turn on the Outline box for a precise visualisation while choosing the Z value. [cid:3acbfbdd-9122-4edb-a588-8fc7195014c8] Thank you so much. Best, B _____________________________________________ Binh A. Nguyen, Ph.D. Instructor @ Saelices's Lab Center for Alzheimer’s and Neurodegenerative Diseases Peter O’Donnell Jr. Brain Institute UT Southwestern Medical Center ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Wednesday, July 3, 2024 8:01 PM To: Binh Nguyen <AnBinh.Nguyen@UTSouthwestern.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] show 5% or 10% Z-axis of a fibril density EXTERNAL MAIL Hi Binh, You can show only a limited set of z planes of the map using the volume command region option volume #1 region 0,0,50,255,255,70 The 6 numbers are the grid indices imin,jmin,kmin,imax,jmax,kmax where i,j,k are gride indices along the x,y,z axes. So the example shows just z planes 50 - 70. And you can save just that part of the map if you want save map_z50_z70.mrc model #1 You can also use the Crop mouse mode (Right Mouse Toolbar) and simply drag the z-faces of your volume to crop it to a smaller size in z. It might help to show the map outline box (Map Toolbar / Outline Box button) when using the mouse mode so you can easily see where the map box bounds are. When you use the mouse mode it will put in the log the volume command with the region option to do the cropping so you can see the exact grid indices used. But it looks to me that your layers in the filament are in planes that are not perpendicular to z so showing a slab in z is going to include partial tilted layers. To cleanly get just 2 layers you would fit an atomic model to those two layers and use the "volume zone" command. There is no magic simpler way to define the tilted, probably not even planar layers you want to extract. Tom On Jul 3, 2024, at 4:24 PM, Binh Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Dear all, Is there a way to display say 10% on the Z-axis of a fibril density map? Or maybe save 1 or 2 layers of the map? <image.png> I know 2 ways to do it but they both take a long time, and I wonder if we have an easier way to do it. 1. Use volume eraser with a big diameter sphere 2. Build a rough backbone carbon model in 1 layer, and do zone selection. Thanks, B ________________________________ UT Southwestern Medical Center The future of medicine, today. _______________________________________________ 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://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/__;!!MznTZTSvDXGV0Co!CAHKsOyy2PfnnruLBhsl40cBrpPKRLK_JYU17uCXXtuliub83Tduz9yGS_kH4sYGGGH6Vxk1DenzTWcyKznWCNddmL8$> CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.