<div dir="ltr">But I forgot to mention that <tt><span>phenix.composite_omit_map is not in the list...<br></span></tt></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Apr 21, 2014 at 1:05 PM, Chen Zhao <span dir="ltr"><<a href="mailto:c.zhao@yale.edu" target="_blank">c.zhao@yale.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Thank you Tom,<br><br>I understand what "command not found" mean, but I already sourced "phenix_env" in my bashrc. "phenix.list" works, also I have already run "phenix.autosol", "phenix.autobuild", "phenix.refine" without any problems.<br>
<br></div><div>Thank you so much again!<br><br></div><div>Sincerely,<br>Chen<br></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Apr 21, 2014 at 1:01 PM, Terwilliger, Thomas C <span dir="ltr"><<a href="mailto:terwilliger@lanl.gov" target="_blank">terwilliger@lanl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Hi Chen,
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<div>"command not found" usually means the shell cannot find a particular command. �It often can be fixed by sourcing the right setup commands.�</div>
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<div>If you type:</div>
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<div>��phenix.list</div>
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<div>does it also say "command not found"? �If so, you just need to source the phenix version you want. �When you install it phenix lists where this directory is...If you are on a mac you will say something like this:</div>
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<div>��source�/Applications/PHENIX-1.8.3-1479/Contents/phenix-1.8.3-1479/phenix_env</div>
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<div>and you can put that in your .cshrc file too (if you are using csh).</div>
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<div>Let me know if that doesn't do it!</div><div>
<div>All the best,</div>
<div>Tom T</div>
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<div>On Apr 21, 2014, at 10:53 AM, Chen Zhao wrote:</div>
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<div>Dear all,<br>
<br>
Hello! I am now running into a simple technical problem but I just cannot figure it out. I am trying to create a composite omit map by phenix, but when I typed in the command<tt><span> phenix.composite_omit_map XXX.eff</span></tt> based on
the instructions on <a href="http://www.phenix-online.org/version_docs/dev-1579/composite_omit_map.htm" target="_blank">
http://www.phenix-online.org/version_docs/dev-1579/composite_omit_map.htm</a>, I got the error message "command not found". Could anybody help me out?<br>
<br>
Thank you so much in advance!<br>
<br>
</div>
Sincerely,<br>
Chen<br>
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