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

[Roden Deng Luo]

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 at 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 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> 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>
>> 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
>>
>>
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