1

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.

6

To set an environment variable, you must both assign a value to a shell variable and export it. This can be done in one go with

export variable=value

or in two steps with

variable=value
export variable

In your case:

XTOOL_HOME=/home/marta/Peptide/oficial-MC/sf/xscore_v1.3
XTOOL_PARAMETER="$XTOOL_HOME/parameter"
XTOOL_BIN="$XTOOL_HOME/bin"

export XTOOL_HOME XTOOL_PARAMETER XTOOL_BIN

PATH="$PATH:$XTOOL_BIN"

Note the setting of PATH. Your code needlessly includes the old value of PATH four times. The above replicates the suggested csh code.

Also, the error message mentions XSCORE_PARAMETER but I'm unsure what this is. It's either something set by your program based on one or several of the environment variables above (automatically), or something that you are supposed to manually set to something that is not mentioned in the manual.

According to comments, this may in fact be a typo in the manual, and the various XTOOL variables should in fact be prefixed with the string XSCORE rather than XTOOL.

  • Thank your for your reply. Unfortunatelly, I still get the same error following your advice. I rigorously followed the instructions given in the program manual page (hyper link on the post) so that is why I think there was a problem when i was trying to set up this variables on bash. – Neuls Sep 26 '18 at 9:23
  • @Neuls Just in case there's a typo in the manual, try export XSCORE_PARAMETER="$XTOOL_PARAMETER" and see what happens... It could be that all the XTOOL variables should actually be XSCORE variables (or both). – Kusalananda Sep 26 '18 at 9:25
  • Dear Kusa.. YES IT WAS A TYPO IN THE MANUAL >_< – Neuls Sep 26 '18 at 9:31

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.