[Chimera-users] Files generated by UCSF Chimera as .MRC format do not open with AMIRA 5.3.3

[Tom Goddard]

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 at 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 at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>>
> Sent: Tuesday, June 13, 2017 2:26:11 AM
> To: Savriama, Yoland F
> Cc: chimera-users at cgl.ucsf.edu <mailto:chimera-users at 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 at helsinki.fi <mailto:yoland.savriama at 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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