[phenixbb] help with pdbtools

Oleg Sobolev osobolev at lbl.gov
Sat Mar 25 00:11:21 PDT 2017


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>
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?)
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20170325/8f1f2cf7/attachment.htm>


More information about the phenixbb mailing list