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
> <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
>> <mailto: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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your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
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