[phenixbb] help with pdbtools - ps
pafonine at lbl.gov
Sat Mar 25 00:08:49 PDT 2017
P.S.: Sounds like you are doing something that may benefit from a lower
level scripting - let me know and I might be able to help!
On 3/24/17 23:17, Edward A. Berry 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 =
> phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 file_name =
> 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 =
> phenix.pdbtools --output file_name = shake1.pdb 2chr_refine_001.pdb
> phenix.pdbtools output.file_name = shake1.pdb 2chr_refine_001.pdb
> 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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