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?) _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

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 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]