[phenixbb] Phenix composite omit map

Terwilliger, Thomas C terwilliger at lanl.gov
Mon Apr 21 10:12:59 PDT 2014

Hi Chen,
I think Engin's answer is the right one then!  Just download a more recent phenix and try that!
All the best,
Tom T

On Apr 21, 2014, at 11:11 AM, Chen Zhao wrote:

But I forgot to mention that phenix.composite_omit_map is not in the list...

On Mon, Apr 21, 2014 at 1:05 PM, Chen Zhao <c.zhao at yale.edu<mailto:c.zhao at yale.edu>> wrote:
Thank you Tom,

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.

Thank you so much again!


On Mon, Apr 21, 2014 at 1:01 PM, Terwilliger, Thomas C <terwilliger at lanl.gov<mailto:terwilliger at lanl.gov>> wrote:
Hi Chen,

"command not found" usually means the shell cannot find a particular command.  It often can be fixed by sourcing the right setup commands.

If you type:


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:

  source /Applications/PHENIX-1.8.3-1479/Contents/phenix-1.8.3-1479/phenix_env

and you can put that in your .cshrc file too (if you are using csh).

Let me know if that doesn't do it!
All the best,
Tom T

On Apr 21, 2014, at 10:53 AM, Chen Zhao wrote:

Dear all,

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 phenix.composite_omit_map XXX.eff based on the instructions on http://www.phenix-online.org/version_docs/dev-1579/composite_omit_map.htm, I got the error message "command not found". Could anybody help me out?

Thank you so much in advance!


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