Hi James, I'm not sure what you mean by "duplicate," but I will try to answer. (A) If you mean showing a single plane or thin slab, you could do it by dragging the plane interactively to where you want in these two steps: (1) use "volume planes" with desired axis (and thickness if more than one plane), e.g. volume planes z,10,10,1,3 for Z-slab 3 layers thick initially positioned at 10th plane, or for single Z-plane volume planes z see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#planes> (2) ....and then move it manually to intersect the atom, e.g. use mouse mode to drag plane interactively ( in the Right Mouse tab of the toolbar and then use right mouse drag) <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> (B) Another idea is to show the whole map but then use clipping planes centered on the atom, e.g. if it is selected, view sel; zoom 0.5 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#initial> ...which would use near/far planes (not rotatable), or to instead use front/back clip planes that can be rotated relative to the viewer, for example: clip front -1 back 1 position sel <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clip.html> You can use different offset values from the -1 and 1 in my example to give a different thickness. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Dec 3, 2024, at 10:17 AM, Vitali James via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Chimera users

I have to make a slice of a map on the selected atom. Is it possible to duplicate this map view? in chimeraX

James

Hi Oli, Why yes, we have a "measure weight" command. However, it will only include the atoms that are present as coordinates (does not use sequence information), e.g. no missing segments or even hydrogens, unless you've added them. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#weight> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Dec 3, 2024, at 12:55 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

Is there a ChimeraX command to calculate the molecular weight of the selection? It would be convenient for calculating how much ordered mass is present (especially for e.g. nucleic acid protein complexes).

Cheers Oli

Dear James, Yes, it is best to explain your situation with as much detail as possible when asking a question so that we can try to give a useful answer. If you mean you just want to combine sessions, see "open" command to open the session .cxs file, with option "combine true": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#composite> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#combine> 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 Dec 4, 2024, at 1:26 PM, Vitali James via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Elaine, Many thanks and it's really very helpful.

Actually I have made a view of Fo-Fc map by using the map eraser tool. I just keep the region of interest and show it as a mesh. I wanted to overlay the same map view and show it as a surface and make a blend of the mesh lines and a transparent surface. If I saved it a chimeraX session and make a second copy of the same and open the second session into the first session, it does not work. How It can be achieved.

best James

On Tue, Dec 3, 2024 at 9:51 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi James, I'm not sure what you mean by "duplicate," but I will try to answer.

(A) If you mean showing a single plane or thin slab, you could do it by dragging the plane interactively to where you want in these two steps:

(1) use "volume planes" with desired axis (and thickness if more than one plane), e.g.

volume planes z,10,10,1,3

for Z-slab 3 layers thick initially positioned at 10th plane, or for single Z-plane

volume planes z

see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#planes> (2) ....and then move it manually to intersect the atom, e.g. use mouse mode to drag plane interactively ( in the Right Mouse tab of the toolbar and then use right mouse drag)

<https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode>

(B) Another idea is to show the whole map but then use clipping planes centered on the atom, e.g. if it is selected,

view sel; zoom 0.5

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#initial>

...which would use near/far planes (not rotatable), or to instead use front/back clip planes that can be rotated relative to the viewer, for example:

clip front -1 back 1 position sel

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clip.html>

You can use different offset values from the -1 and 1 in my example to give a different thickness.

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

...

On Dec 3, 2024, at 10:17 AM, Vitali James via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Chimera users

I have to make a slice of a map on the selected atom. Is it possible to duplicate this map view? in chimeraX

James

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