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Hello,</p>
<p style="color: rgb(0, 0, 0); font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 12pt; margin-top: 0px; margin-bottom: 0px;">
<br>
</p>
<p style="margin-top: 0px; margin-bottom: 0px;"><span style="font-size: 12pt;">I installed libtiff devel with yum install </span><span style="font-size: 12pt;">libtiff-devel. During make the message "</span><span style="font-size: 12pt;">Found TIFF: /usr/lib64/libtiff.so
(found version “4.0.3”)" showed up. Sorry the Ghostscript message was because I </span>
accidentally<span style="font-size: 12pt;"> used my relion2 and not relion3 bashrc file. Now that I have the right environment and run </span></p>
<p style="color: rgb(0, 0, 0); font: 11px Menlo; margin: 0px; background-color: rgb(255, 255, 255);">
<br>
</p>
<p style="color: rgb(0, 0, 0); font: 11px Menlo; margin: 0px; background-color: rgb(255, 255, 255);">
<span style="font-variant-ligatures: no-common-ligatures;"><br>
</span></p>
<p style="color: rgb(0, 0, 0); font: 11px Menlo; margin: 0px; background-color: rgb(255, 255, 255);">
<span style="font-variant-ligatures: no-common-ligatures;">`which relion_run_motioncorr` --i Import/job001/movies.star --o MotionCorr/job026/ --first_frame_sum 1 --last_frame_sum 0 --use_own<span class="Apple-converted-space">
</span>--j 1 --bin_factor 1 --bfactor 150 --angpix 1.1 --v</span></p>
<p style="color: rgb(0, 0, 0); font: 11px Menlo; margin: 0px; background-color: rgb(255, 255, 255);">
<span style="font-variant-ligatures: no-common-ligatures;">oltage 300 --dose_per_frame 1.34 --preexposure 0 --patch_x 1 --patch_y 1 --gainref 17apr04c_04103608_01_3838x3710_norm_0_mod.mrc --gain_rot 0 --gain_flip 0 --dose_weighting<span class="Apple-converted-space"> </span></span></p>
<p style="color: rgb(0, 0, 0); font: 11px Menlo; margin: 0px; background-color: rgb(255, 255, 255);">
<br>
</p>
<p style="color: rgb(0, 0, 0); font: 11px Menlo; margin: 0px; background-color: rgb(255, 255, 255);">
<span style="font-variant-ligatures: no-common-ligatures;"><span class="Apple-converted-space" style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;"><br>
</span></span></p>
<p style="color: rgb(0, 0, 0); font: 11px Menlo; margin: 0px; background-color: rgb(255, 255, 255);">
<span style="font-variant-ligatures: no-common-ligatures;"><span class="Apple-converted-space" style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;">I get the message below: </span></span></p>
<p></p>
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<br>
</p>
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<br>
</p>
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</p>
<div><span style="font-size: 9pt;">in: /usr/local/relion-3.0_beta/src/image.h, line 205</span></div>
<div><span style="font-size: 9pt;">=== Backtrace ===</span></div>
<div><span style="font-size: 9pt;">/usr/local/relion-3/bin/relion_run_motioncorr(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x42fd51]</span></div>
<div><span style="font-size: 9pt;">/usr/local/relion-3/bin/relion_run_motioncorr(_ZN13fImageHandler8openFileERK8FileNamei+0x90b) [0x44c5bb]</span></div>
<div><span style="font-size: 9pt;">/usr/local/relion-3/bin/relion_run_motioncorr(_ZN10Micrograph8setMovieE8FileNameS0_d+0x338) [0x4a3188]</span></div>
<div><span style="font-size: 9pt;">/usr/local/relion-3/bin/relion_run_motioncorr(_ZN10MicrographC2E8FileNameS0_d+0x282) [0x4a3dc2]</span></div>
<div><span style="font-size: 9pt;">/usr/local/relion-3/bin/relion_run_motioncorr(_ZN16MotioncorrRunner3runEv+0x1d9) [0x44b549]</span></div>
<div><span style="font-size: 9pt;">/usr/local/relion-3/bin/relion_run_motioncorr(main+0x3d) [0x41582d]</span></div>
<div><span style="font-size: 9pt;">/lib64/libc.so.6(__libc_start_main+0xf5) [0x7f639189db35]</span></div>
<div><span style="font-size: 9pt;">/usr/local/relion-3/bin/relion_run_motioncorr() [0x415e0f]</span></div>
<div><span style="font-size: 9pt;">==================</span></div>
<div><span style="font-size: 9pt;">ERROR: </span></div>
<div><span style="font-size: 9pt;">TIFF support was not enabled during compilation</span></div>
<div><br>
</div>
<div>Is there something else I should be doing for libtiff to work?</div>
<div><br>
</div>
<div>Best Regards,</div>
<div>Dominique Gutierrez</div>
<p></p>
</div>
<hr style="display:inline-block; width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Takanori Nakane <tnakane@mrc-lmb.cam.ac.uk><br>
<b>Sent:</b> Tuesday, September 11, 2018 12:58:27 PM<br>
<b>To:</b> Dominique Gutierrez<br>
<b>Cc:</b> 3dem@ncmir.ucsd.edu<br>
<b>Subject:</b> Re: [3dem] Compiling RELION3 for TIFF files</font>
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<div class="BodyFragment"><font size="2"><span style="font-size:11pt">
<div class="PlainText">Hi,<br>
<br>
It looks like MotionCor2 failed to run.<br>
Did you specify the correct path to MotionCor2 binary?<br>
<br>
Best regards,<br>
<br>
Takanori Nakane<br>
<br>
P.S.<br>
Please paste error messages as texts and avoid attaching screen shots.<br>
Images are large and cannot be searched.<br>
<br>
> Hello,<br>
><br>
> Thanks very much! Installing the library and recompiling relion3 looked<br>
> like relion found the library but I now get the ghostscript error<br>
> attached. Could this be because it is not linked correctly? How exactly<br>
> would I need to link it? The system is a linux version<br>
> 3.10.0-514.21.2.el7.x86_64.<br>
><br>
><br>
> Best Regards,<br>
><br>
> Dominique Gutierrez<br>
><br>
> ________________________________<br>
> From: 3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of Takanori Nakane<br>
> <tnakane@mrc-lmb.cam.ac.uk><br>
> Sent: Monday, September 10, 2018 4:28:08 PM<br>
> To: 3dem@ncmir.ucsd.edu<br>
> Subject: Re: [3dem] Compiling RELION3 for TIFF files<br>
><br>
> Hi,<br>
><br>
> It depends on your system, but usually you can install as<br>
> packages like libtiff-dev, libtiff-devel, etc.<br>
> (You need 'developer' packages that includes header files,<br>
> not just dynamic link libraries)<br>
><br>
> Best regards,<br>
><br>
> Takanori Nakane<br>
><br>
> On 2018/09/10 21:08, Dominique Gutierrez wrote:<br>
>> Hello,<br>
>><br>
>><br>
>> I am trying to run motioncorr2 via relion3 on TIFF files. I get the<br>
>> error message attached TIFF support not being enabled during<br>
>> compilation. How should relion3 be compiled to run with tiff files? Any<br>
>> help would be much appreciated!<br>
>><br>
>><br>
>> Best,<br>
>><br>
>> Dominique Gutierrez<br>
>><br>
>><br>
>><br>
>> _______________________________________________<br>
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