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
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://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume> ) 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@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
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@cgl.ucsf.edu on behalf of meng@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> ) 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@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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://secure-web.cisco.com/1niVHy2nRN-giYgBrfC6y6iY1aA4FUL5GMI6ZuVbqAYxX8n... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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@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@cgl.ucsf.edu <mailto:chimera-users-bounces@cgl.ucsf.edu> on behalf of meng@cgl.ucsf.edu <mailto:meng@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_hHO1zGFYtl3CJ8P56TeOIxzPvNxSRxXYTiTTS... <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@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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participants (4)
-
Elaine Meng -
Hunkeler, Moritz -
Smith Lee -
Tom Goddard