[Chimera-users] on chimera mask

Hunkeler, Moritz Moritz_Hunkeler at DFCI.HARVARD.EDU
Mon Feb 22 08:57:15 PST 2021


I could be wrong, but I am not sure whether the other program (Relion?) refers to the Gaussian cube format. Rather, I think it is literally just saying that the generated mask is not a cube-shaped grid (X^3) but a non-cube (XxYxZ). I think Relion for example complains about that. One solution could be to resample the newly generated mask onto your initial grid, e.g. 'vop resample #1 onGrid #0', which will place your mask onto the cube-shaped grid of #0.


On 2/22/21, 11:21, "Chimera-users on behalf of Elaine Meng" <chimera-users-bounces at cgl.ucsf.edu on behalf of meng at cgl.ucsf.edu> wrote:

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    Hi Smith,
    We are not experts in other programs, so I can only guess:  maybe the other program does not want MRC format.  There is some other map format called "cube" that Chimera can read (Gaussian cube format in this list: <https://secure-web.cisco.com/17Qgqo7DM_hHO1zGFYtl3CJ8P56TeOIxzPvNxSRxXYTiTTSqQAOlbP7lFUc7NJDjjYsX5ui0bIVFjn5IST0rCUw5-80tFI39LokTva_Zl7iSBrZ-G28aiKIWo-_-6lSbQqMzoZ_-GRh7TA9a6eimvvIGtZ3ZQh158tdkSnRvr5E_OKgQb4US-yzLzF9KIlZyNZb6T8tLMrBVVY3zD1wnnHa6T7D_AWpBDmZ8tuv-0sF4ybJ_Xd91ceC3-z9j7QLEIoRbjwyIlmGFQLKz-IECmYg/https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ffiletypes.html%23volume> ) but Chimera cannot write that format, sorry.  You will need to find some other program to convert from mrc to cube, and even so, I don't know if it is the same cube format that the other program wants.
    I hope this helps,
    Elaine C. Meng, Ph.D.                       
    UCSF Chimera(X) team
    Department of Pharmaceutical Chemistry
    University of California, San Francisco

    > On Feb 21, 2021, at 9:49 PM, Smith Lee <smith_lee123 at yahoo.com> wrote:
    > Dear All,
    > When I use command "mask ones #0" to get the mask for #0 image and use the mask.mrc for further processing by other program, it says the mask.mrc got was not in the "cube volume" format.
    > Will you please explain what is the "cube volume" format mrc, and is any way to convert the above mentioned 'non-cube volume" format mask.mrc to "cube volume" format mask.mrc?
    > Best wishes,
    > Smith

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