[phenixbb] help with pdbtools -- file name

[Pavel Afonine]

Type

  phenix.pdbtools

then spend a few moments looking at all available parameters..

Then you will see that to specify an output file name you need

output.file_name=some_name

Hope this works. Let me know otherwise.

Of course doing this in the GUI should be waaay obvious -;)

Pavel


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 = 
> 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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