[phenixbb] phenix.refine command line

Simon Kolstoe s.kolstoe at ucl.ac.uk
Wed Jan 30 03:35:59 PST 2013

Thanks for the help. I tried also pointing the .bash_profile and .bash_login to the .bashrc and now get the following.

[~]bash -x
+ export 'PS1=[\w]'
+ PS1='[\w]'
+ alias 'll=ls -lrt'
+ alias setphenix=/Applications/PHENIX-1.8.1-1168/Contents/phenix-1.8.1-1168/phenix_env.sh
+ alias 'setccp4=source /Applications/ccp4-6.3.0/bin/ccp4.setup-sh'
+ /Applications/PHENIX-1.8.1-1168/Contents/phenix-1.8.1-1168/phenix_env.sh
+ phenix.refine
bash: phenix.refine: command not found


I am wondering if something in the phenix_env.sh is wrong? I found phenix.refine in the directory and sure enough it works if run here: 




On 30 Jan 2013, at 01:08, Ben Eisenbraun wrote:

> On Tue, Jan 29, 2013 at 10:54 AM, Kip Guja <kip at pharm.stonybrook.edu> wrote:
>> You need to use .profile not .bashrc on a Mac
> Actually that's not true.
> In the case of bash, a login shell will read /etc/profile,
> ~/.bash_profile, ~/.bash_login, and ~/.profile in that order. A
> subshell, i.e. an interactive shell that is not a login shell, will
> read ~/.bashrc.
> In the traditional UNIX windowing environment of X11, the X11 session
> will invoke a login shell, reading one or all of the various profile
> files, and all subsequent shells started via terminal emulators and
> the like will usually be subshells, which will read your ~/.bashrc.
> If you look at /Applications/Utilities/XQuartz.app/Contents/MacOS/X11,
> you'll see that the Xorg ported to OS X does exactly this. A snippet:
> case $(basename "${SHELL}") in
>    bash)          exec -l "${SHELL}" --login -c 'exec "${@}"' - "${@}" ;;
> Where users get tripped up on OS X is that many of them will use
> Terminal.app as their terminal emulator, and since it's not an X11
> application, it uses a login shell as the default shell in its
> interface.
> The solution is to just follow the Bash FAQ suggestion to have your
> ~/.bash_profile contain:
> test -f ~/.bashrc && . ~/.bashrc
> Which will ensure you always pick up your base shell environment
> regardless of how the shell is started.
> Hopefully some of that explanation helps you, Simon, but if you're
> still stuck, you can run 'bash -x' to put the shell into debug mode as
> it interprets your shell start up files. It should give you some clues
> as to what's going wrong. Annoyingly that option is not documented in
> the manpage on this machine. Here is some additional explanation:
> http://wiki.bash-hackers.org/scripting/debuggingtips#use_shell_debug_output
> -ben
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