Xscore Installation Issue using Bash

Question

[Neuls]

Dear all,

I am trying to install xscore v1.3 (Xscore Manual). They provide instructions to set up some environmental variables in the .cshrc file under C-shell.

setenv XTOOL_HOME   the_installation_directory_of_X-Score
setenv XTOOL_PARAMETER  $XTOOL_HOME/parameter
setenv XTOOL_BIN  $XTOOL_HOME/bin
set path = ($path  $XTOOL_BIN)

If you are using other types of shell, please add the equivalent contents to your configuration file.

Since I am using Bash, I tried modifying .profile file with equivalent commands as they recommend:

# set PATH so it includes user's private bin directories
XTOOL_HOME=/home/marta/Peptide/oficial-MC/sf/xscore_v1.3
XTOOL_PARAMETER=$XTOOL_HOME/parameter
XTOOL_BIN=$XTOOL_HOME/bin

PATH="$HOME/bin:$HOME/.local/bin:$PATH:$HOME/Programs/VMD/:$PATH:$XTOOL_HOME:$PATH:$XTOOL_PARAMETER:$PATH:$XTOOL_BIN"

However, I get the following error when i run the program:

marta@dagon:~$ xscore -fixpdb HER21.pdb try.pdb

X-Score starts to run ... Wed Sep 26 09:26:29 2018

Warning: XSCORE_PARAMETER is not set ... use default setting

Error: cannot open the file ../parameter/RESIDUE_DEF_XTOOL Please make sure it exists.

The folder exist as the file does but the program seems to be unable to locate them. I wonder if there is something wrong in the environment variables' settings.

Any help would be appreciated!

[Benn]

What are the rwx permissions of the ../parameter/RESIDUE_DEF_XTOOL file?

[Neuls]

They are : -rw-r--r-- 1 marta marta 38801 mag 25 2016 RESIDUE_DEF_XTOOL. Is it a permission problem?

[Benn]

Try to put the x everywhere with chmod

[Neuls]

It is not working, same error as before

[Benn]

Okay, sorry then it's not a permission problem.

Answer 1

[John Marshall]

Warning: XSCORE_PARAMETER is not set ... use default setting

That's because that variable is indeed not set in the environment.

The shell equivalent of C-shell's setenv is export, so you need

export XTOOL_PARAMETER=$XTOOL_HOME/parameter
# etc