<div dir="ltr">Hi Edward,<div><br></div><div><span style="font-size:12.8px">phenix.pdbtools output.file_name=shake1.pdb 2chr_refine_001.pdb sites.shake=0.5</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">should work to specify file name. Note that I removed spaces around =.</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">As Pavel pointed out, results will be different.</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Best regards,</span></div><div><span style="font-size:12.8px">Oleg Sobolev.<br></span><div><br></div><div><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Mar 24, 2017 at 11:17 PM, Edward A. Berry <span dir="ltr"><<a href="mailto:BerryE@upstate.edu" target="_blank">BerryE@upstate.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">1. I'm trying to use pdbtools and I don't quite get the syntax.<br>
How can I specify the output file name on the command line?<br>
these don't work:<br>
phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 output file_name = shake1.pdb<br>
phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 file_name = shake1.pdb<br>
phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 --output file_name = shake1.pdb<br>
phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 --file_name = shake1.pdb<br>
phenix.pdbtools --output file_name = shake1.pdb 2chr_refine_001.pdb sites.shake=0.5<br>
phenix.pdbtools output.file_name = shake1.pdb 2chr_refine_001.pdb sites.shake=0.5<br>
<br>
2. for the "shake" operation, is there a random seed so that it comes out differently each time?<br>
(If I do this five times with different output file names, will they all be the different?)<br>
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