Re: [PyMOL] Bash scripting and pymol

Yes thanks it works! Now assuming that I want to make alitle complicated script based on that template. Assuming that I have 3 pdbs used as references defined in variables ref1, ref2,ref3 now I need loop all of my pdbs from the array and superimpose each pdb from the array agains each of

Re: [PyMOL] Bash scripting and pymol

You need to add “,async=0” to your fetch calls. http://pymolwiki.org/index.php/Fetch > On Apr 28, 2016, at 4:51 AM, James Starlight wrote: > > Hi, > > My script is > > pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H") > pdb_array_store=$template/pymol > > > #

Re: [PyMOL] Bash scripting and pymol

Hi, My script is pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H") pdb_array_store=$template/pymol # A simple FETCHER via PYMOL: download pdbs to the folder and pre-process them! mkdir ${pdb_array_store} for i in ${pdb_array[@]}; do pdb_tit=$(basename "$i") pymol -d "fetch $i; save

Re: [PyMOL] Bash scripting and pymol

Hi, You need for i in ${pdb_array[@]} do ... done Cheers, Tsjerk On Apr 27, 2016 4:44 PM, "James Starlight" 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 >

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

Re: [PyMOL] Bash scripting and pymol

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

Re: [PyMOL] Bash scripting and pymol

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 wrote: > > Must you

Re: [PyMOL] Bash scripting and pymol

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