On Fri, Mar 24, 2017 at 11:17 PM, Edward A. Berry <BerryE@upstate.edu> wrote:

1. I'm trying to use pdbtools and I don't quite get the syntax.
How can I specify the output file name on the command line?
these don't work:
phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 output file_name = shake1.pdb
phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 file_name = shake1.pdb
phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 --output file_name = shake1.pdb
phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 --file_name = shake1.pdb
phenix.pdbtools --output file_name = shake1.pdb 2chr_refine_001.pdb sites.shake=0.5
phenix.pdbtools output.file_name = shake1.pdb 2chr_refine_001.pdb sites.shake=0.5

2. for the "shake" operation, is there a random seed so that it comes out differently each time?
(If I do this five times with different output file names, will they all be the different?)
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