[Chimera-users] on chimera mask

[Tom Goddard]

Another way to get an N by N by N map starting from map that is not a cube would be the volume command region option to crop to a cube subvolume.

   https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#dimensions <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#dimensions>

  Tom


> On Feb 22, 2021, at 8:57 AM, Hunkeler, Moritz <Moritz_Hunkeler at DFCI.HARVARD.EDU> wrote:
> 
> Hello,
> 
> 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.
> 
> Best,
> Moritz
> 
> 
> On 2/22/21, 11:21, "Chimera-users on behalf of Elaine Meng" <chimera-users-bounces at cgl.ucsf.edu <mailto:chimera-users-bounces at cgl.ucsf.edu> on behalf of meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>> wrote:
> 
>            External Email - Use Caution        
> 
>    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 <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
>    -----
>    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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