[phenixbb] help with pdbtools
Edward A. Berry
BerryE at upstate.edu
Sat Mar 25 11:38:02 PDT 2017
Thanks Pavel, Oleg, that works now.
I want the results to be different each time, so I guess I don't need to do anything about the seed.
I should have guessed about the spaces- I had no spaces in sites=0.5 and that part worked.
Oleg Sobolev wrote:
> Hi Edward,
> phenix.pdbtools output.file_name=shake1.pdb 2chr_refine_001.pdb sites.shake=0.5
> should work to specify file name. Note that I removed spaces around =.
> As Pavel pointed out, results will be different.
> Best regards,
> Oleg Sobolev.
> On Fri, Mar 24, 2017 at 11:17 PM, Edward A. Berry <BerryE at upstate.edu <mailto:BerryE at 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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