[phenixbb] help with pdbtools

[Edward A. Berry]

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.
Ed


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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