Dear Engin,

Thank you so much for your reply! Yes, this is the problem because I am using phenix-1.8.4-1496. I will download the newest version!

Best,

Chen

On Mon, Apr 21, 2014 at 1:10 PM, Engin Özkan <eozkan@uchicago.edu> wrote:

Dear Chen,

What version of Phenix are you using? phenix.composite_omit_map was recently added (post 1.8.4 release). Are you using a recent nightly (presumably dev-1579 as you suggest or even newer, like the release candidate for 1.9)?

Engin

On 4/21/14, 12:05 PM, Chen Zhao 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!

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

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Assistant Professor
Dept of Biochemistry and Molecular Biology
University of Chicago

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