ImportError: No module named EMAN2_meta

[Madhura Paranjpe]

Hello, 

Disclaimer: total noob at linux 

I installed EMAN2.22 in my linux system (OS : Fedora, Shell : tcsh).

1) I added EMAN2 to my PATH

output of echo $PATH 

/usr/local/relion-4.0/bin:/usr/local/cuda-11.4/bin:/home/polikanov/Programs/SPAdes-3.12.0-Linux/bin:/home/polikanov/Programs/tcllib-1.20/bin:/home/cryosparc_user/.local/bin:/home/polikanov/Programs/frealign_v9.1
1/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin:/home/polikanov/Programs/ncbi-blast-2.15.0+/bin:/csb/work2/merlos/Programs/Colab_Fold/colabfold_batch/bin:/home/polikanov/Programs/pdb-extract-
v3.28/bin:/home/polikanov/Programs/autoPROC/autoPROC/bin/linux64:/home/polikanov/Programs/ccp4-7.0/etc:/home/polikanov/Programs/ccp4-7.0/bin:/home/polikanov/Programs/phenix-1.17.1-3660/build/bin:/home/polikanov/
Programs/XDS-INTEL64_Linux_x86-64_31-AUG-2024:/home/polikanov/Programs/Chimera-1.16/bin:/usr/local/relion-4.0/bin:/usr/local/cuda-11.4/bin:/home/polikanov/Programs/SPAdes-3.12.0-Linux/bin:/home/polikanov/Program
s/tcllib-1.20/bin:/home/cryosparc_user/.local/bin:/home/polikanov/Programs/frealign_v9.11/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin:/home/polikanov/Programs/ncbi-blast-2.15.0+/bin:/csb/wo
rk2/merlos/Programs/Colab_Fold/colabfold_batch/bin:/home/polikanov/Programs/pdb-extract-v3.28/bin:/home/polikanov/Programs/autoPROC/autoPROC/bin/linux64:/home/polikanov/Programs/ccp4-7.0/etc:/home/polikanov/Prog
rams/ccp4-7.0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/home/cryosparc_user/EMAN2:/home/cryosparc_user/EMAN2/bin

2) I ran echo $LD_LIBRARY_PATH, $DYLD_LIBRARY_PATH and $PYTHONPATH and the output says Undefined variable 

Does this mean that they are set to nothing? If not, then how to do so? 

3) When I run python e2version.py from the directory where an executable version of this script exists - I get the following error:

Traceback (most recent call last):
 File "/home/polikanov/Programs/EMAN2/bin/e2version.py", line 39, in <module>
   import EMAN2_meta
ImportError: No module named EMAN2_meta

4) If I do not type the word python , and instead only run e2version.py , it says command not found

Could someone please advise as to what should be done to get my EMAN2 running on the system?

Thanks in advance!

[Ludtke, Steven J.]

EMAN2.22 is _extremely_ out of date. It was released about 6 years ago. Very strongly suggest installing an up to date version.

---

Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 
Deputy Director, Advanced Technology Cores                  and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center

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[Madhura Paranjpe]

Hello Prof. Ludtke,

I installed 2.99 in my system. I am still facing the same problem. 

Command: echo $PATH

/usr/local/relion-4.0/bin:/usr/local/cuda-11.4/bin:/home/polikanov/Programs/SPAdes-3.12.0-Linux/bin:/home/polikanov/Programs/tcllib-1.20/bin:/home/paranjpe/.local/bin:/home/polikanov/Programs/frealign_v9.11/bin:

/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin:/home/polikanov/Programs/ncbi-blast-2.15.0+/bin:/csb/work2/merlos/Programs/Colab_Fold/colabfold_batch/bin:/home/polikanov/Programs/pdb-extract-v3.28/

bin:/home/polikanov/Programs/autoPROC/autoPROC/bin/linux64:/home/polikanov/Programs/ccp4-7.0/etc:/home/polikanov/Programs/ccp4-7.0/bin:/home/polikanov/Programs/phenix-1.17.1-3660/build/bin:/home/polikanov/Progra

ms/XDS-INTEL64_Linux_x86-64_31-AUG-2024:/home/polikanov/Programs/Chimera-1.16/bin:/usr/local/relion-4.0/bin:/usr/local/cuda-11.4/bin:/home/polikanov/Programs/SPAdes-3.12.0-Linux/bin:/home/polikanov/Programs/tcll

ib-1.20/bin:/home/paranjpe/.local/bin:/home/polikanov/Programs/frealign_v9.11/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin:/home/polikanov/Programs/ncbi-blast-2.15.0+/bin:/csb/work2/merlos/P

rograms/Colab_Fold/colabfold_batch/bin:/home/polikanov/Programs/pdb-extract-v3.28/bin:/home/polikanov/Programs/autoPROC/autoPROC/bin/linux64:/home/polikanov/Programs/ccp4-7.0/etc:/home/polikanov/Programs/ccp4-7.

0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/home/paranjpe/eman2-sphire-sparx:/home/paranjpe/eman2-sphire-sparx://home/paranjpe/miniconda3

Command: echo $PYTHONPATH,echo $LD_LIBRARY_PATH,echo $DYLD_LIBRARY_PATH

Undefined variable

Command: python e2version.py {In the directory that contains the executable script}

Traceback (most recent call last):

 File "e2version.py", line 36, in <module>

   import EMAN2_meta

ImportError: No module named EMAN2_meta

Command: e2version.py {In the directory that contains the executable script}

Command not found

I think for this particular version of EMAN2, I need conda, which I added to PATH (miniconda) but I am unable to access conda by using Conda init/Conda activate as the system returned the error  <conda: Command not found>.

Please advise me on what further steps I should take to be able to use EMAN2.

Thank you!

Regards, 

Madhura  N Paranjpe

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[Ludtke, Steven J.]

Did you follow the full installation instructions?  It looks like you may not have run the "conda activate EMAN2" part?

---

Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 
Deputy Director, Advanced Technology Cores                  and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CAP1b6q-e1%3DgUkbJ21dq4%2BHEhFtQ7AC8EhUzPKqnLGXu5PZ9%2BBA%40mail.gmail.com.

[Madhura Paranjpe]

Hello,

With respect to conda: I have downloaded the miniconda and added it to PATH and now when I run conda activate (or anything following conda) it says <conda: command not found>. I am unsure what else I need to do?

Please advise,

Regards,

Madhura N Paranjpe

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[Ludtke, Steven J.]

Which instructions are you following? There are several installation paths:

- last official release binary (about a year ago)

- current snapshot binary (may be out of date)

- installing binary into existing anaconda environment (may be less out of date)

- installing from source (not difficult, and gets you whatever version you like, including current development version)

When I am setting up a new machine I follow these instructions myself (even though I know what I'm doing):

https://eman2.org/Install/SourceInstall

If you follow these step by step, it should pretty much always work.

If you are following one of the other paths, please point at the specific instructions you are following and indicate at which step problems arise.

---

Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 
Deputy Director, Advanced Technology Cores                  and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CAP1b6q8zamxjpaAvM%2Bno6tiVdxhe4sp_h8wVffgHvBPxefLUYA%40mail.gmail.com.