problem updating EMAN2

[吴思彧]

Hi, Steve.

I just updated my EMAN2.07 to EMAN2.11.linux64 followed the instruction on the following page
http://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstall.
I don't understand how to do the part "add eman2.bashrc to your login script ". I've been using EMAN on that computer for a while but I'm still a totally noob for linux system.

Right now the version seems updated, but there's an error:
bash: /home/chengde/EMAN2-2.07/EMAN2/eman2.bashrc: No such file or directory

[chengde@1393-Mao01 ~]$ e2version.py
EMAN 2.11 (CVS 2015/06/05 19:02:06)
Your EMAN2 is running on:  Linux-2.6.32-504.8.1.el6.x86_64-x86_64-with-redhat-6.6-Santiago 2.6.32-504.8.1.el6.x86_64 x86_64
Your Python version is:  2.7.3

[chengde@1393-Mao01 ~]$ e2projectmanager.py
Traceback (most recent call last):
  File "/home/chengde/EMAN2/bin/e2projectmanager.py", line 33, in <module>
    from EMAN2 import *
  File "/home/chengde/EMAN2/lib/EMAN2.py", line 44, in <module>
    from EMAN2_cppwrap import *
  File "/home/chengde/EMAN2/lib/EMAN2_cppwrap.py", line 33, in <module>
    from libpyAligner2 import *
ImportError: /home/chengde/EMAN2/lib/libpyAligner2.so: undefined symbol: _ZN4EMAN8EMAN2Ctf20compute_1d_fromimageEifPNS_6EMDataE

The result for "echo $LD_LIBRARY_PATH" is:
/usr/local/bin/EMAN/lib:/usr/local/bin/eman2/EMAN2/lib:/usr/local/bin/ccp4-6.2.0/lib:/home/chengde/EMAN2-2.07/EMAN2/lib:/home/chengde/EMAN2/lib:/usr/local/bin/EMAN/lib:/usr/local/bin/eman2/EMAN2/lib:/usr/local/bin/ccp4-6.2.0/lib

And for "echo $PYTHONPATH" is:
/home/chengde/EMAN2/lib:/home/chengde/EMAN2/bin:/home/chengde/EMAN2/lib:/home/chengde/EMAN2/bin:/home/chengde/EMAN2/lib:/home/chengde/EMAN2/bin:/usr/local/bin/EMAN/lib:/usr/local/bin/eman2/EMAN2/lib:/usr/local/bin/eman2/EMAN2/bin:/usr/local/bin/ccp4-6.2.0/share/python:/home/chengde/EMAN2-2.07/EMAN2/lib:/home/chengde/EMAN2-2.07/EMAN2/bin:/home/chengde/EMAN2/lib:/home/chengde/EMAN2/bin:/usr/local/bin/EMAN/lib:/usr/local/bin/eman2/EMAN2/lib:/usr/local/bin/eman2/EMAN2/bin:/usr/local/bin/ccp4-6.2.0/share/python:

That EMAN2-2.07 was the folder for the older version. I renamed that folder before installation. The new path is just /home/chengde/EMAN2

The notice after installation was:
Please add the following line to the end of your /home/chengde/.bashrc :
source /home/chengde/EMAN2/eman2.bashrc

I've tried "echo source /home/chengde/EMAN2/eman2.bashrc >>.bashrc".
What exactly should I do for the situation?

[Steven Ludtke]

Presumably your installation is set up in 

/home/chengde/EMAN2

If so, then you need to edit the file called ".bashrc" in your home directory, and add

"source $HOME/EMAN2/.bashrc" to the end of the file

Finally, make sure that there are no other references in this file to previous installations of EMAN2. If you previously had a standard EMAN2 installation, there should have been a similar line in your .bashrc file already. If you did something nonstandard, then you may have 'export' or 'set' commands in this file which reference your old installation and will need to be removed. Ideally, find someone there who knows a bit of Linux to help you out. Otherwise, you could post the contents of your current .bashrc file and we can advise how to change it.

----------------------------------------------------------------------------

Steven Ludtke, Ph.D.

Professor, Dept of Biochemistry and Mol. Biol.         (www.bcm.edu/biochem)

Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu)

Co-Director CIBR Center                          (www.bcm.edu/research/cibr)

Baylor College of Medicine                             

slu...@bcm.edu

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[吴思彧]

Hi. I found someone help me changed the .bashrc file in home directory. We deleted the line with EMAN2-2.07 and added the new line: source /home/chengde/EMAN2/eman2.bashrc

The content of the .bashrc file now shows the following:

# .bashrc

# User specific aliases and functions
PATH=$PATH:/usr/local/bin
export PATH
alias rm='rm -i'
alias cp='cp -i'
alias mv='mv -i'

# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

. /usr/local/bin/setup-scripts/sh/ccp4.setup
#. /usr/local/bin/setup-scripts/sh/ccp4-others.setupsource
. /usr/local/bin/eman2/EMAN2/eman2.bashrc
. /usr/local/bin/EMAN/eman.bashrc source
. /usr/local/phenix-1.7.2-869/phenix_env.sh
source /home/chengde/EMAN2/eman2.bashrc

~                                                                              
~                                                                              
".bashrc" 21L, 489C                                           21,0-1        All



However the problem is not fixed.

[chengde@1393-Mao01 ~]$ e2projectmanager.py
Traceback (most recent call last):
  File "/home/chengde/EMAN2/bin/e2projectmanager.py", line 33, in <module>
    from EMAN2 import *
  File "/home/chengde/EMAN2/lib/EMAN2.py", line 44, in <module>
    from EMAN2_cppwrap import *
  File "/home/chengde/EMAN2/lib/EMAN2_cppwrap.py", line 33, in <module>
    from libpyAligner2 import *
ImportError: /home/chengde/EMAN2/lib/libpyAligner2.so: undefined symbol: _ZN4EMAN8EMAN2Ctf20compute_1d_fromimageEifPNS_6EMDataE

Is there anything else we should change in that file?

[Steven Ludtke]

Hi, 

you still have another EMAN2  being sourced, and you have a bunch of strange things with 'source' at the end of lines. 

The last few lines of your file should really look like this:

source /usr/local/bin/setup-scripts/sh/ccp4.setup
source /usr/local/bin/EMAN/eman.bashrc source
source /usr/local/phenix-1.7.2-869/phenix_env.sh
source /home/chengde/EMAN2/eman2.bashrc

Technically, you can replace 'source ' with '. ', but most people find that more obscure...

If you still have issues after doing this (and opening a new window), try putting the EMAN2 line before the other 3 lines rather than after.

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[吴思彧]

I've made the change. Now it shows this:

[chengde@1393-Mao01 ~]$ e2projectmanager.py
Traceback (most recent call last):

  File "/home/chengde/EMAN2/bin/e2projectmanager.py", line 34, in <module>
    from PyQt4 import QtCore, QtGui
ImportError: /home/chengde/EMAN2/extlib/lib/python2.7/site-packages/PyQt4/QtCore.so: undefined symbol: _ZN7QLocale14scriptToStringENS_6ScriptE

Is it a python problem?

[Steven Ludtke]

Hi. I think this issue is addressed on the installation page?

Sent from my iPhone