Question: Xscore Installation Issue using Bash
0
gravatar for Neuls
11 weeks ago by
Neuls0
Neuls0 wrote:

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!

ADD COMMENTlink modified 7 weeks ago by John Marshall1.4k • written 11 weeks ago by Neuls0

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

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by b.nota5.4k

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

ADD REPLYlink written 11 weeks ago by Neuls0

Try to put the x everywhere with chmod

ADD REPLYlink written 11 weeks ago by b.nota5.4k

It is not working, same error as before

ADD REPLYlink written 11 weeks ago by Neuls0

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

ADD REPLYlink written 11 weeks ago by b.nota5.4k
1
gravatar for John Marshall
7 weeks ago by
John Marshall1.4k
Glasgow, Scotland
John Marshall1.4k wrote:

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
ADD COMMENTlink written 7 weeks ago by John Marshall1.4k
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