If I type phenix.pdbtools | grep seed I get random_seed = None which tells me random seeds sets each time you run the command. If you want to fix it so that you get a reproducible result each time you the tool just set it to some number random_seed=2217384 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]