[3dem] Compiling RELION3 for TIFF files

[Dominique Gutierrez]

Hello,


I installed libtiff devel with yum install libtiff-devel. During make the message "Found TIFF: /usr/lib64/libtiff.so (found version “4.0.3”)" showed up. Sorry the Ghostscript message was because I accidentally used my relion2 and not relion3 bashrc file. Now that I have the right environment and run



`which relion_run_motioncorr` --i Import/job001/movies.star --o MotionCorr/job026/ --first_frame_sum 1 --last_frame_sum 0 --use_own  --j 1 --bin_factor 1 --bfactor 150 --angpix 1.1 --v

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



I get the message below:



in: /usr/local/relion-3.0_beta/src/image.h, line 205
=== Backtrace  ===
/usr/local/relion-3/bin/relion_run_motioncorr(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x42fd51]
/usr/local/relion-3/bin/relion_run_motioncorr(_ZN13fImageHandler8openFileERK8FileNamei+0x90b) [0x44c5bb]
/usr/local/relion-3/bin/relion_run_motioncorr(_ZN10Micrograph8setMovieE8FileNameS0_d+0x338) [0x4a3188]
/usr/local/relion-3/bin/relion_run_motioncorr(_ZN10MicrographC2E8FileNameS0_d+0x282) [0x4a3dc2]
/usr/local/relion-3/bin/relion_run_motioncorr(_ZN16MotioncorrRunner3runEv+0x1d9) [0x44b549]
/usr/local/relion-3/bin/relion_run_motioncorr(main+0x3d) [0x41582d]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x7f639189db35]
/usr/local/relion-3/bin/relion_run_motioncorr() [0x415e0f]
==================
ERROR:
TIFF support was not enabled during compilation

Is there something else I should be doing for libtiff to work?

Best Regards,
Dominique Gutierrez

________________________________
From: Takanori Nakane <tnakane at mrc-lmb.cam.ac.uk>
Sent: Tuesday, September 11, 2018 12:58:27 PM
To: Dominique Gutierrez
Cc: 3dem at ncmir.ucsd.edu
Subject: Re: [3dem] Compiling RELION3 for TIFF files

Hi,

It looks like MotionCor2 failed to run.
Did you specify the correct path to MotionCor2 binary?

Best regards,

Takanori Nakane

P.S.
Please paste error messages as texts and avoid attaching screen shots.
Images are large and cannot be searched.

> Hello,
>
> Thanks very much! Installing the library and recompiling relion3 looked
> like relion found the library but I now get the ghostscript error
> attached. Could this be because it is not linked correctly? How exactly
> would I need to link it? The system is a linux version
> 3.10.0-514.21.2.el7.x86_64.
>
>
> Best Regards,
>
> Dominique Gutierrez
>
> ________________________________
> From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Takanori Nakane
> <tnakane at mrc-lmb.cam.ac.uk>
> Sent: Monday, September 10, 2018 4:28:08 PM
> To: 3dem at ncmir.ucsd.edu
> Subject: Re: [3dem] Compiling RELION3 for TIFF files
>
> Hi,
>
> It depends on your system, but usually you can install as
> packages like libtiff-dev, libtiff-devel, etc.
> (You need 'developer' packages that includes header files,
> not just dynamic link libraries)
>
> Best regards,
>
> Takanori Nakane
>
> On 2018/09/10 21:08, Dominique  Gutierrez wrote:
>> Hello,
>>
>>
>> I am trying to run motioncorr2 via relion3 on TIFF files. I get the
>> error message attached TIFF support not being enabled during
>> compilation. How should relion3 be compiled to run with tiff files? Any
>> help would be much appreciated!
>>
>>
>> Best,
>>
>> Dominique Gutierrez
>>
>>
>>
>> _______________________________________________
>> 3dem mailing list
>> 3dem at ncmir.ucsd.edu
>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
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