Inspect xyz-axis chimerax?

3D Refinement
1

Hi, is there a way to show xyz axis and zero point in chimerax

AI’s answer seems to be not working.

i’m trying to verify the symmetry axis after C2-refine

2

and when do C2-refine, will symmetry always be Z-axis?:saluting_face:

3

hi, you may have better luck posting on the chimerax forums than here. however, easy way to check is to go to the medical image tab in the banner toolbar, click “outline box”, and then click “orient” – the little image on the toolbar shows xy direction and z is in/out of monitor plane

1 Like
4

you can also choose “markers”, then “surface”, and then right click on various parts of the box. the log on the right will show you x,y,z of where you clicked.

5

Can use the build command to put at atom at start or desired location

build start atom “Calcium” position 0,0,0 resname Ca select true
help build

1 Like
6

thanks a lot :kissing_face_with_closed_eyes::kissing_face_with_closed_eyes::kissing_face_with_closed_eyes::kissing_face_with_closed_eyes::kissing_face_with_closed_eyes::kissing_face_with_closed_eyes::kissing_face_with_closed_eyes::kissing_face_with_closed_eyes:

7

just find some useful answear by deepseak
hope this can help someone who has the same problem.

Based on official CryoSPARC documentation and user community discussions, when symmetry alignment goes wrong and you need to inspect or adjust the C2 symmetry axis, you can approach this from two levels: visual verification and in-software correction.

1. Visually Checking Symmetry Axis Orientation

CryoSPARC follows a fixed coordinate axis convention for different point groups:

  • C symmetry (e.g., C2): The symmetry axis is the Z-axis.

  • D symmetry (e.g., D1, D7): The principal symmetry axis is the Z-axis, and the two-fold axes lie on the Y-axis.

You can visualize the coordinate axes in ChimeraX and compare them against your density map to check whether the Z-axis indeed corresponds to the C2 symmetry axis:

  • Display axes using a command: Type cofr show true in the ChimeraX command line. This will show a small RGB axis indicator in the corner of the screen (X red, Y green, Z blue).

  • Import a BILD file: Create a simple BILD format file to display 3D arrows. As a basic example, create a text file (e.g., axes.bild) with the following content:

    text

.color red
.arrow 0 0 0 50 0 0
.color green
.arrow 0 0 0 0 50 0
.color blue
.arrow 0 0 0 0 0 50

  • Then open this file in ChimeraX. It will display arrows pointing from the origin along the positive X, Y, and Z axes.

  • Advanced inspection: For more complex checks, the CryoSPARC developers have provided a script that generates a BILD file containing indices for all symmetry operators, making it easy to visualize the rotation axis corresponding to each symmetry copy in ChimeraX.

2. In-Software Correction Methods

If you find that the symmetry axis is not correctly aligned, the issue typically occurred during the C2 Refinement step. You can try the following correction strategies:

  • Method 1: Manually adjust and re-run symmetry refinement

    1. Manually align in external software: In Chimera or ChimeraX, use the move or turn commands to manually rotate the density map obtained from your C1 reconstruction so that its C2 symmetry axis aligns with the Z-axis. Then save the aligned density map as a new file.

    2. Import as initial model: In CryoSPARC, import this manually aligned map as the initial reference (Initial Volume).

    3. Disable automatic symmetry axis alignment: When running a new C2 Refinement (such as Non-uniform Refinement), uncheck the “Align symmetry” parameter, but keep “Enforce symmetry” checked (selecting C2). This forces the refinement job to use the pre-aligned orientation you provided as the initial direction, without attempting to automatically search for the symmetry axis.

  • Method 2: Use “Volume Alignment Tools” for automatic alignment
    CryoSPARC provides a dedicated utility for this purpose.

    1. Run Volume Alignment Tools, and input your C1 density map.

    2. In the parameters, set the Symmetry group to the symmetry you need (e.g., C2), and enable the symmetry axis alignment function.

    3. This utility will automatically rotate your density map so that its symmetry axis aligns with CryoSPARC’s internal coordinate axis convention (i.e., the Z-axis).

    4. Use the aligned map output by this utility as the initial model for subsequent C2 Refinement jobs.

  • An advanced workflow combining Symmetry Expansion
    If your goal is not only to obtain a symmetrized structure but also to analyze potential symmetry-breaking features (asymmetry), the correct workflow is crucial:

    1. Ensure that your particles have passed through a refinement job that enforced symmetry (C2), so that the particle poses are aligned with the symmetry axis.

    2. Run a Symmetry Expansion job, selecting C2 symmetry. This will duplicate your particles based on the symmetry operations, preparing them for subsequent localized analysis.

    3. When performing subsequent analyses, such as Local Refinement or 3D Variability Analysis (3DVA), you must set the symmetry to C1. This is because the symmetry has already been “encoded” through particle expansion—applying C2 symmetry again at this stage would actually introduce errors.

In summary, if you find the C2 symmetry axis is wrong, the most direct diagnostic approach is to check your density map against the Z-axis in ChimeraX. The core idea of correction is: first obtain an initial model that is correctly aligned with the Z-axis, then disable the automatic symmetry axis search function during refinement.

8

.translate 172 172 172
.color red
.arrow 0 0 0 50 0 0 1.5
.color green
.arrow 0 0 0 0 50 0 1.5
.color blue
.arrow 0 0 0 0 0 50 1.5

this is a better one, 172 172 172 is the center of my volume, which is determined by sufrce color-center

1.5 is the radius of arror

9

This is wrong - it’s right in the middle of whatever objects you have visible, on the centre of rotation.

10

:open_mouth:

maybe try the .bild:
.translate 172 172 172
.color red
.arrow 0 0 0 50 0 0 1.5
.color green
.arrow 0 0 0 0 50 0 1.5
.color blue
.arrow 0 0 0 0 0 50 1.5
I think this works