Hi,
You need
for i in ${pdb_array[@]}
do
...
done
Cheers,
Tsjerk
On Apr 27, 2016 4:44 PM, "James Starlight" <jmsstarli...@gmail.com> wrote:
> so As I tried to do it but it was not worked :-O)
>
> #pdbs list
> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
> #where to save
> pdb_array_store=$template/pymol/
>
>
> # A simple FETCHER: download pdbs to the folder and pre-process them!
> #mkdir ${pdb_array_store}
> for i in `cat ${pdb_array}` ; do wget
> http://www.rcsb.org/pdb/files/${i}.pdb ${pdb_array_store}/${i}.pdb ;
> done
>
> result
> cat: 1UBI: No such file or directory
>
> 2016-04-27 12:29 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> > Please give me an example of the list of 3 pdbs instead of just cat $1 :)
> > as well as proper syntax of how to save each pdb after fetching in
> > pymol using same command line
> > Forgot to mention important points:
> > 1) that list should be physically in my script like in python
> > 2) I use pymol because I will need to process each of the pdb- e,g to
> > remove from them ligands or water etc
> >
> > Thanks!
> >
> > 2016-04-27 12:18 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> >> Please give me an example of the list of 3 pdbs instead of cat $1 as
> >> well as how to save syntax of how to save each pdb
> >>
> >>
> >> Thanks!
> >>
> >> J
> >>
> >> 2016-04-27 12:09 GMT+02:00 Jordan Willis <jwillis0...@gmail.com>:
> >>> If you really want to use pymol, this works
> >>>
> >>> #!/bin/bash
> >>> #myscript.bash
> >>> for i in `cat $1` ; do pymol -d "fetch $i" -c ; done
> >>>
> >>>
> >>> Then on the command line
> >>>>chmod +x myscript.bash; ./myscript.bash mylist.txt
> >>>
> >>>
> >>> On Apr 27, 2016, at 2:55 AM, Jordan Willis <jwillis0...@gmail.com>
> wrote:
> >>>
> >>> Must you use pymol?
> >>>
> >>>
> >>> Try directly from the PDB
> >>>
> >>> #!/bin/bash
> >>> #myscript.bash
> >>>
> >>> for i in `cat $1` ; do wget http://www.rcsb.org/pdb/files/${i}.pdb ;
> done
> >>>
> >>>
> >>>
> >>>
> >>> Then on the command line
> >>>>chmod +x myscript.bash; ./myscript.bash mylist.txt
> >>>
> >>>
> >>> J
> >>>
> >>> On Apr 27, 2016, at 2:41 AM, James Starlight <jmsstarli...@gmail.com>
> wrote:
> >>>
> >>> Dear Pymol users!
> >>>
> >>> I need to add a few strings to my simple bash script which will creat
> >>> a list of pdb files and than will call pymol without GUI from the
> >>> terminal to fetch all the pdbs and save it to the desired location.
> >>> For one pdb it should be smth like
> >>>
> >>> pdbs="1f88"
> >>>
> >>> pymol -c -q -d "fetch ${pdbs}; save $template/pymol/*.pdb " >
> >>> ${tmp}/pymol_${pdbs}.log
> >>>
> >>> will be thankful for the correction of this string as well as example
> >>> how it can be adapted for a list of pdbs in bash.
> >>>
> >>> Thanks!
> >>>
> >>> J
> >>>
> >>>
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