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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Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
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