Re: [PyMOL] Bash scripting and pymol

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 <jms...@gm...>:
> 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 <jms...@gm...>:
>> 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 <jwi...@gm...>:
>>> 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 <jwi...@gm...> 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 <jms...@gm...> 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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