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 >> >> ------------------------------------------------------------------------------ >> 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 >> _______________________________________________ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> >> >> ------------------------------------------------------------------------------ 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 _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
