Question regarding Bash program

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# 8  
Old 10-06-2013
I mean actual file. Not the code that you are trying to use to generate it. Can you manually prepare one log.pml file that contains all the data for a single directory, that when run with "/usr/bin/pymol log.pml" will produce exepcted output for that directory? Test it by running "/usr/bin/pymol log.pml" and see if it is really working for that single directory.
# 9  
Old 10-06-2013
Hello bartus11,

Thanks for your reply. I am attaching a zip files containing the folders and respective bash script and a dummy Pymol log file.

Thanks once again for the help Smilie
# 10  
Old 10-06-2013
Try this:
for dir in Frog-mol-ryan_*; do
  if [ -d "${dir}" ]; then
    echo Loading structures in Pymol: $dir
    cat /dev/null > log.pml
    for file in $dir/*.pdbqt; do
      echo "load /server/John/Docking-Studies/Insilico-mod-FC996/docking-FC996-analog/MR1004/test/$file" >> log.pml
    cat <<EOF>>log.pml
load /server/John/Docking-Studies/Insilico-mod-FC996/docking-FC996-analog/PDBs/Holo-with-Bpore.pdb
cmd.hide("everything","holo-with-Bpore")"cartoon"   ,"holo-with-Bpore")
    for file in $dir/*.pdbqt; do
      echo "\"sticks\", \"`basename $file`\")" >> log.pml
    /usr/bin/pymol log.pml

# 11  
Old 10-06-2013
Hello bartus11,
Thank you so much for the help. The script is working like charm. With so little knowledge about the scripting I would have never figured that out.
I am trying to learn some scripting so that I could use if for my small analysis work, mostly copying, transferring and sorting type works. I have a linux machine at my lab with bash shell.
Could you suggest me some good reference to learn bash scripting (books or online) will be greatly appreciated Smilie

Thanks once again for the help Smilie
# 12  
Old 10-06-2013
This site is quite comprehensive guide to BASH (with many examples too): Advanced Bash-Scripting Guide
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