Re: [chimerax-users] Test files for bug report [ChimeraX] #5467: AmiraMesh
Hi Roden,
These 3 Amira files are vertex/edge/point data, not 3D lattices. The ChimeraX reader only handles 3D lattices Amira files. It does not look like our ChimeraX documentation explains this. I'll try to get this on our docs (3d lattice volume data, float, unsigned 16-bit, uncompressed only).
Tom
On Oct 25, 2021, at 12:20 PM, Roden Deng Luo deng.luo@kaust.edu.sa wrote:
Dear Tom and Andrea,
Thanks for the quick responses. Upon the kind approval from Andrea, I attached the .am file I received from Andrea (in the format of 2.0), as well as the other two that are exported from this file (in the format of 3.0, one is in ascii as revealed by the name).
Best regards, Roden
Hi Tom,
Many thanks. I am very new to both ChimeraX and Amira. As shown in the screenshot on the right, it looks to me the data is a segmentation map. I initiated the original post because I wanted to use the functionality "Fit in map" in ChimeraX. Will there be a workaround that I can achieve this? As a first step, I would like to fit only a very small fragment of the segmentation map.
Best, Roden
On Mon, Oct 25, 2021 at 10:29 PM Tom Goddard goddard@sonic.net wrote:
Hi Roden,
These 3 Amira files are vertex/edge/point data, not 3D lattices. The ChimeraX reader only handles 3D lattices Amira files. It does not look like our ChimeraX documentation explains this. I'll try to get this on our docs (3d lattice volume data, float, unsigned 16-bit, uncompressed only).
TomOn Oct 25, 2021, at 12:20 PM, Roden Deng Luo deng.luo@kaust.edu.sa
wrote:
Dear Tom and Andrea,
Thanks for the quick responses. Upon the kind approval from Andrea, I
attached the .am file I received from Andrea (in the format of 2.0), as well as the other two that are exported from this file (in the format of 3.0, one is in ascii as revealed by the name).
Best regards, Roden
Hi Roden,
ChimeraX fitting works on volume data, also called "maps", 3d rectangular arrays of intensity values. The Amira SpatialGraph formats are I think vertices, edges and points and won't be of use for fitting in ChimeraX. File formats like an MRC map or Amira lattice data are the only kind that ChimeraX would do fitting in.
Tom
On Oct 25, 2021, at 12:49 PM, Roden Deng Luo via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Tom,
Many thanks. I am very new to both ChimeraX and Amira. As shown in the screenshot on the right, it looks to me the data is a segmentation map. I initiated the original post because I wanted to use the functionality "Fit in map" in ChimeraX. Will there be a workaround that I can achieve this? As a first step, I would like to fit only a very small fragment of the segmentation map.
Best, Roden
On Mon, Oct 25, 2021 at 10:29 PM Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: Hi Roden,
These 3 Amira files are vertex/edge/point data, not 3D lattices. The ChimeraX reader only handles 3D lattices Amira files. It does not look like our ChimeraX documentation explains this. I'll try to get this on our docs (3d lattice volume data, float, unsigned 16-bit, uncompressed only).
TomOn Oct 25, 2021, at 12:20 PM, Roden Deng Luo <deng.luo@kaust.edu.sa mailto:deng.luo@kaust.edu.sa> wrote:
Dear Tom and Andrea,
Thanks for the quick responses. Upon the kind approval from Andrea, I attached the .am file I received from Andrea (in the format of 2.0), as well as the other two that are exported from this file (in the format of 3.0, one is in ascii as revealed by the name).
Best regards, Roden
This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email._______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Dear Tom,
Thanks very much! I will rethink the whole workflow and see if we can leverage all the data we have and the functionalities of all ChimeraX. Probably somehow convert the Amira SpatialGraph into a volume.
Best, Roden
On Tue, Oct 26, 2021 at 12:20 AM Tom Goddard goddard@sonic.net wrote:
Hi Roden,
ChimeraX fitting works on volume data, also called "maps", 3d rectangular arrays of intensity values. The Amira SpatialGraph formats are I think vertices, edges and points and won't be of use for fitting in ChimeraX. File formats like an MRC map or Amira lattice data are the only kind that ChimeraX would do fitting in.
Tom
On Oct 25, 2021, at 12:49 PM, Roden Deng Luo via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom,
Many thanks. I am very new to both ChimeraX and Amira. As shown in the screenshot on the right, it looks to me the data is a segmentation map. I initiated the original post because I wanted to use the functionality "Fit in map" in ChimeraX. Will there be a workaround that I can achieve this? As a first step, I would like to fit only a very small fragment of the segmentation map.
Best, Roden
On Mon, Oct 25, 2021 at 10:29 PM Tom Goddard goddard@sonic.net wrote:
Hi Roden,
These 3 Amira files are vertex/edge/point data, not 3D lattices. The ChimeraX reader only handles 3D lattices Amira files. It does not look like our ChimeraX documentation explains this. I'll try to get this on our docs (3d lattice volume data, float, unsigned 16-bit, uncompressed only).
TomOn Oct 25, 2021, at 12:20 PM, Roden Deng Luo deng.luo@kaust.edu.sa
wrote:
Dear Tom and Andrea,
Thanks for the quick responses. Upon the kind approval from Andrea, I
attached the .am file I received from Andrea (in the format of 2.0), as well as the other two that are exported from this file (in the format of 3.0, one is in ascii as revealed by the name).
Best regards, Roden
This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email._______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users__;!!Nmw4Hv0!kCTAH1Tz6cRPrO41k0nOO9RhBcmGzIFXOBraShh_VjxAH2dqJnc8jOWFSsuSLsNdudY$
participants (2)
-
Roden Deng Luo -
Tom Goddard