Files generated by UCSF Chimera as .MRC format do not open with AMIRA 5.3.3
Greetings, I am a researcher working at the University of Helsinki (Finland) and I have used the software UCSF Chimera to process 3D CT-Scans data. I saved the process files as a single .MRC file. When I tried to open it with Amira 5.3.3 it displays the following error message: "No valid licence found for extension Amira Microscopy Option 5.3 Please contact us". The console also says "Access denied for 'readMRCFileStack'" I thought that Amira could read these standard .MRC files? Could it be there was an issue during the file export with Chimera? Best wishes, Yoland Savriama, PhD P/O Jernvall Institute of Biotechnology P.O. Box 56 (Viikinkaari 5) FIN-00014 FINLAND
Hi Yolanda, I’m not aware of anything special about the MRC files from Chimera. It sounds like you simply don’t have a license to use the part of Amira that reads/handles MRC files, in which case you would need to contact the Amira folks about getting such a license. Can you open any MRC files in Amira, like from sources other than Chimera? Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 12, 2017, at 9:18 AM, Savriama, Yoland F <yoland.savriama@helsinki.fi> wrote:
Greetings,
I am a researcher working at the University of Helsinki (Finland) and I have used the software UCSF Chimera to process 3D CT-Scans data. I saved the process files as a single .MRC file. When I tried to open it with Amira 5.3.3 it displays the following error message:
"No valid licence found for extension Amira Microscopy Option 5.3 Please contact us". The console also says "Access denied for 'readMRCFileStack'"
I thought that Amira could read these standard .MRC files? Could it be there was an issue during the file export with Chimera?
Best wishes, Yoland Savriama, PhD P/O Jernvall Institute of Biotechnology P.O. Box 56 (Viikinkaari 5) FIN-00014 FINLAND
Hi Elaine, Thank you very much for your prompt reply! I guess you are right although Amira suggests different file formats to open a given file including .MRC, this is why I found it strange Amira could not open it. Meanwhile I contacted Amira and I am in touch with them to solve this issue. Yes, I can open this .MRC file via Fiji, but I experience issues when I save it as a .tiff or .raw file and I tried to open it with Amira again. Amira only recognises 1 slice. It would be nice to have a save as .tiff stack or image sequence from Chimera. Also, could you tell me how one enters the voxel size and other information when one imports a file, please? Another thing I was curious about is whether or not it is possible to specify memory allocation to process volume rendering for instance. I found Chimera very slow and it often displays errors while using the volume eraser and volume rendering at a number of 2, even if I process the volume at 16 it is still really slow. Here are the specs of my machine: Desktop computer with Windows 7 Intel Xeon CPU X5550 @ 2.67 GHz 2.66 Ghz (2 processors) 48 Gigs of Ram 64 bit OS Graphic Card: Nvidia GeForce GTX 680 Total available graphics : 7934Mb and dedicated video memory: 4096 MB GDDR 5 I can easily open and process a 10 gbs file and even 20 gbs with Amira without having it to crash or running too slow. I think Chimera is a really nice software and I am using it since I was particularly interested in this volume eraser tool. Best, Yoland ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, June 13, 2017 2:26:11 AM To: Savriama, Yoland F Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Files generated by UCSF Chimera as .MRC format do not open with AMIRA 5.3.3 Hi Yolanda, I’m not aware of anything special about the MRC files from Chimera. It sounds like you simply don’t have a license to use the part of Amira that reads/handles MRC files, in which case you would need to contact the Amira folks about getting such a license. Can you open any MRC files in Amira, like from sources other than Chimera? Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 12, 2017, at 9:18 AM, Savriama, Yoland F <yoland.savriama@helsinki.fi> wrote:
Greetings,
I am a researcher working at the University of Helsinki (Finland) and I have used the software UCSF Chimera to process 3D CT-Scans data. I saved the process files as a single .MRC file. When I tried to open it with Amira 5.3.3 it displays the following error message:
"No valid licence found for extension Amira Microscopy Option 5.3 Please contact us". The console also says "Access denied for 'readMRCFileStack'"
I thought that Amira could read these standard .MRC files? Could it be there was an issue during the file export with Chimera?
Best wishes, Yoland Savriama, PhD P/O Jernvall Institute of Biotechnology P.O. Box 56 (Viikinkaari 5) FIN-00014 FINLAND
Hi Yoland, (sorry for getting your name wrong before!) Maybe others can comment on the rest, but I'll address this point:
On Jun 13, 2017, at 1:35 AM, Savriama, Yoland F <yoland.savriama@helsinki.fi> wrote:
Also, could you tell me how one enters the voxel size and other information when one imports a file, please?
In the Volume Viewer menu, choose Features… Coordinates. Then there will be entry fields where you can change voxel size etc.: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
If you get errors or crashes you should report a bug (Chimera will often ask after an error if you want to report it, or use menu Help / Report a Bug…) — describe exactly what you were doing before the error. There is a volume data cache size — see the Chimera volume command documentation to learn how to use it. I don’t know if that will speed up your operation because you did not explain exactly what operations are slow. With a 10 or 20 Gb map everything is likely to be slow. Tom
On Jun 13, 2017, at 1:35 AM, Savriama, Yoland F <yoland.savriama@helsinki.fi> wrote:
Hi Elaine,
Thank you very much for your prompt reply!
I guess you are right although Amira suggests different file formats to open a given file including .MRC, this is why I found it strange Amira could not open it. Meanwhile I contacted Amira and I am in touch with them to solve this issue. Yes, I can open this .MRC file via Fiji, but I experience issues when I save it as a .tiff or .raw file and I tried to open it with Amira again. Amira only recognises 1 slice. It would be nice to have a save as .tiff stack or image sequence from Chimera.
Also, could you tell me how one enters the voxel size and other information when one imports a file, please?
Another thing I was curious about is whether or not it is possible to specify memory allocation to process volume rendering for instance. I found Chimera very slow and it often displays errors while using the volume eraser and volume rendering at a number of 2, even if I process the volume at 16 it is still really slow.
Here are the specs of my machine: Desktop computer with Windows 7 Intel Xeon CPU X5550 @ 2.67 GHz 2.66 Ghz (2 processors) 48 Gigs of Ram 64 bit OS Graphic Card: Nvidia GeForce GTX 680 Total available graphics : 7934Mb and dedicated video memory: 4096 MB GDDR 5
I can easily open and process a 10 gbs file and even 20 gbs with Amira without having it to crash or running too slow.
I think Chimera is a really nice software and I am using it since I was particularly interested in this volume eraser tool.
Best, Yoland
From: Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> Sent: Tuesday, June 13, 2017 2:26:11 AM To: Savriama, Yoland F Cc: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Files generated by UCSF Chimera as .MRC format do not open with AMIRA 5.3.3
Hi Yolanda, I’m not aware of anything special about the MRC files from Chimera. It sounds like you simply don’t have a license to use the part of Amira that reads/handles MRC files, in which case you would need to contact the Amira folks about getting such a license. Can you open any MRC files in Amira, like from sources other than Chimera? Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 12, 2017, at 9:18 AM, Savriama, Yoland F <yoland.savriama@helsinki.fi <mailto:yoland.savriama@helsinki.fi>> wrote:
Greetings,
I am a researcher working at the University of Helsinki (Finland) and I have used the software UCSF Chimera to process 3D CT-Scans data. I saved the process files as a single .MRC file. When I tried to open it with Amira 5.3.3 it displays the following error message:
"No valid licence found for extension Amira Microscopy Option 5.3 Please contact us". The console also says "Access denied for 'readMRCFileStack'"
I thought that Amira could read these standard .MRC files? Could it be there was an issue during the file export with Chimera?
Best wishes, Yoland Savriama, PhD P/O Jernvall Institute of Biotechnology P.O. Box 56 (Viikinkaari 5) FIN-00014 FINLAND
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participants (3)
-
Elaine Meng -
Savriama, Yoland F -
Tom Goddard