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Hi Elaine,</p>
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Thank you very much for your prompt reply! </p>
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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.</p>
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Also, could you tell me how one enters the voxel size and other information when one imports a file, please?</p>
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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.</p>
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Here are the specs of my machine: <span style="font-family: Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont; font-size: 12pt;">Desktop computer with Windows 7 Intel Xeon CPU X5550 @ 2.67 GHz 2.66 Ghz (2 processors) 48 Gigs of Ram 64 bit OS</span></p>
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<span style="font-size: 12pt;">Graphic Card: Nvidia GeForce GTX 680 Total available graphics : 7934Mb and dedicated video memory: 4096 MB GDDR 5</span><br>
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<div style="margin-top: 0px; margin-bottom: 0px;"><font face="Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont" size="3">I can easily open and process a 10 </font><font face="Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont">gbs file and even
20 gbs with Amira without having it to crash or running too slow.</font></div>
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<div style="margin-top: 0px; margin-bottom: 0px;"><font face="Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont">I think Chimera is a really nice software and I am using it since I was particularly interested in this volume eraser tool.</font></div>
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<div style="margin-top: 0px; margin-bottom: 0px;"><font face="Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont">Best,</font></div>
<div style="margin-top: 0px; margin-bottom: 0px;"><font face="Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont">Yoland</font></div>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Tuesday, June 13, 2017 2:26:11 AM<br>
<b>To:</b> Savriama, Yoland F<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] Files generated by UCSF Chimera as .MRC format do not open with AMIRA 5.3.3</font>
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<div class="PlainText">Hi Yolanda,<br>
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?<br>
Best,<br>
Elaine<br>
----------<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
> On Jun 12, 2017, at 9:18 AM, Savriama, Yoland F <yoland.savriama@helsinki.fi> wrote:<br>
> <br>
> Greetings,<br>
> <br>
> 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:<br>
> <br>
> "No valid licence found for extension Amira Microscopy Option 5.3 Please contact us". The console also says "Access denied for 'readMRCFileStack'"<br>
> <br>
> I thought that Amira could read these standard .MRC files? Could it be there was an issue during the file export with Chimera?<br>
> <br>
> Best wishes,<br>
> Yoland Savriama, PhD<br>
> P/O Jernvall<br>
> Institute of Biotechnology<br>
> P.O. Box 56 (Viikinkaari 5)<br>
> FIN-00014 FINLAND<br>
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