<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">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.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jun 13, 2017, at 1:35 AM, Savriama, Yoland F <<a href="mailto:yoland.savriama@helsinki.fi" class="">yoland.savriama@helsinki.fi</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class=""><div dir="ltr" class=""><div id="x_divtagdefaultwrapper" dir="ltr" class=""><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 12pt;" class=""><br class="Apple-interchange-newline">Hi Elaine,</div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 12pt;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 12pt;" class="">Thank you very much for your prompt reply! </div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 12pt;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 12pt;" class="">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.</div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 12pt;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 12pt;" class="">Also, could you tell me how one enters the voxel size and other information when one imports a file, please?</div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 12pt;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 12pt;" class="">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.</div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 12pt;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols; font-size: 12pt;" class="">Here are the specs of my machine: <span style="font-family: Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont; font-size: 12pt;" class="">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></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont; font-size: 12pt; margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 12pt;" class="">Graphic Card: Nvidia GeForce GTX 680 Total available graphics : 7934Mb and dedicated video memory: 4096 MB GDDR 5</span><br class=""></div><div style="font-family: Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont; font-size: 12pt; margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 12pt;" class=""><br class=""></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><font face="Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont" size="3" class="">I can easily open and process a 10 </font><font face="Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont" class="">gbs file and even 20 gbs with Amira without having it to crash or running too slow.</font></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><font face="Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont" class=""><br class=""></font></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><font face="Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont" class="">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><div style="margin-top: 0px; margin-bottom: 0px;" class=""><font face="Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont" class=""><br class=""></font></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><font face="Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont" class="">Best,</font></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><font face="Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont" class="">Yoland</font></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><font face="Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont" class=""><br class=""></font></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><font face="Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont" class=""><br class=""></font></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><font face="Calibri, Arial, Helvetica, sans-serif, serif, EmojiFont" class=""><br class=""></font></div></div><hr tabindex="-1" style="display: inline-block; width: 1197.546875px;" class=""><div id="x_divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Tuesday, June 13, 2017 2:26:11 AM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Savriama, Yoland F<br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] Files generated by UCSF Chimera as .MRC format do not open with AMIRA 5.3.3</font><div class=""> </div></div></div><font size="2" class=""><span style="font-size: 10pt;" class=""><div class="PlainText">Hi Yolanda,<br class="">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 class="">Best,<br class="">Elaine<br class="">----------<br class="">Elaine C. Meng, Ph.D.<span class="Apple-converted-space"> </span><br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><br class="">> On Jun 12, 2017, at 9:18 AM, Savriama, Yoland F <<a href="mailto:yoland.savriama@helsinki.fi" class="">yoland.savriama@helsinki.fi</a>> wrote:<br class="">><span class="Apple-converted-space"> </span><br class="">> Greetings,<br class="">> <span class="Apple-converted-space"> </span><br class="">> 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 class="">> <span class="Apple-converted-space"> </span><br class="">> "No valid licence found for extension Amira Microscopy Option 5.3 Please contact us". The console also says "Access denied for 'readMRCFileStack'"<br class="">> <span class="Apple-converted-space"> </span><br class="">> I thought that Amira could read these standard .MRC files? Could it be there was an issue during the file export with Chimera?<br class="">> <span class="Apple-converted-space"> </span><br class="">> Best wishes,<br class="">> Yoland Savriama, PhD<br class="">> P/O Jernvall<br class="">> Institute of Biotechnology<br class="">> P.O. Box 56 (Viikinkaari 5)<br class="">> FIN-00014 FINLAND<br class=""><br class=""></div></span></font></div><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Chimera-users mailing list:<span class="Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">Chimera-users@cgl.ucsf.edu</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Manage subscription:<span class="Apple-converted-space"> </span></span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br class=""></div></body></html>