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!

Sincerely,
Chen

On Mon, Apr 21, 2014 at 1:01 PM, Terwilliger, Thomas C <terwilliger@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:

��phenix.list

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!

Sincerely,
Chen