[chimerax-users] Test files for bug report [ChimeraX] #5467: AmiraMesh

[Tom Goddard]

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 at 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 at sonic.net <mailto:goddard at 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).
> 
>         Tom
> 
> 
> > On Oct 25, 2021, at 12:20 PM, Roden Deng Luo <deng.luo at kaust.edu.sa <mailto:deng.luo at 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 at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20211025/443a80ab/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: amira_export_segmentation.png
Type: image/png
Size: 2053710 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20211025/443a80ab/attachment-0001.png>