mic3
May 2nd, 2016, 08:14 PM
I use Ubuntu and already have Pymol 1.7.x installed, but I get errors when I try to use the APBS plugin. I read online that installing the latest version of Pymol from source solves this error
I followed this link to try to compile the latest version of Pymol from source http://tubiana.me/how-to-install-and-compile-pymol-windows-linux-mac/
However, I only see a Pymol shell script created, not an executable. When I then try to run "./pymol" or "./pymol.sh", I get the error
File "/home/Softwares/Pymol/modules/pymol/__init__.py", line 72, in <module>
import pymol
File "/home/Softwares/Pymol/modules/pymol/__init__.py", line 536, in <module>
import pymol._cmd
ImportError: /home/Softwares/Pymol/modules/pymol/_cmd.so: undefined symbol: png_check_sig
Here are the contents of the newly created pymol script
#!/bin/bash
export PYMOL_PATH="/home/Softwares/Pymol/modules/pymol/pymol_path"
"/home/username/anaconda2/bin/python" "/home/Softwares/Pymol/modules/pymol/__init__.py" "$@"
And here are the contents of the previous pymol script that worked for Python 1.7.x
#!/bin/sh
# debian wrapper script for pymol
test -r ${HOME}/.pymol && . ${HOME}/.pymol
PYMOL_PATH=${PYMOL_PATH:=`/usr/bin/python2.7 -c "from imp import find_module; print find_module('pymol')[1]"`}
PYMOL_DATA=${PYMOL_DATA:=/usr/share/pymol/data}
PYMOL_SCRIPTS=${PYMOL_SCRIPTS:=/usr/share/pymol/scripts}
CHEMPY_DATA=${CHEMPY_DATA:=/usr/share/pymol/data/chempy}
export PYMOL_PATH
export PYMOL_DATA
export PYMOL_SCRIPTS
export CHEMPY_DATA
/usr/bin/python2.7 -m pymol.__init__ ${1+"$@"}
I followed this link to try to compile the latest version of Pymol from source http://tubiana.me/how-to-install-and-compile-pymol-windows-linux-mac/
However, I only see a Pymol shell script created, not an executable. When I then try to run "./pymol" or "./pymol.sh", I get the error
File "/home/Softwares/Pymol/modules/pymol/__init__.py", line 72, in <module>
import pymol
File "/home/Softwares/Pymol/modules/pymol/__init__.py", line 536, in <module>
import pymol._cmd
ImportError: /home/Softwares/Pymol/modules/pymol/_cmd.so: undefined symbol: png_check_sig
Here are the contents of the newly created pymol script
#!/bin/bash
export PYMOL_PATH="/home/Softwares/Pymol/modules/pymol/pymol_path"
"/home/username/anaconda2/bin/python" "/home/Softwares/Pymol/modules/pymol/__init__.py" "$@"
And here are the contents of the previous pymol script that worked for Python 1.7.x
#!/bin/sh
# debian wrapper script for pymol
test -r ${HOME}/.pymol && . ${HOME}/.pymol
PYMOL_PATH=${PYMOL_PATH:=`/usr/bin/python2.7 -c "from imp import find_module; print find_module('pymol')[1]"`}
PYMOL_DATA=${PYMOL_DATA:=/usr/share/pymol/data}
PYMOL_SCRIPTS=${PYMOL_SCRIPTS:=/usr/share/pymol/scripts}
CHEMPY_DATA=${CHEMPY_DATA:=/usr/share/pymol/data/chempy}
export PYMOL_PATH
export PYMOL_DATA
export PYMOL_SCRIPTS
export CHEMPY_DATA
/usr/bin/python2.7 -m pymol.__init__ ${1+"$@"}