Have you sourced the setpaths.[c]sh file. Are you able to run any phenix
programs?
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov
On Tue, Nov 29, 2016 at 12:47 PM, NISHANT SINGH
Hi Everyone,
I am trying to run Phenix's rosetta refine. I seem to have downloaded and compiled the rosetta package fine, as I got the following statement after compiling was done:
scons: done building targets. but I am failing at running: rosetta.build_phenix_interface. It says that command not found. I am attaching my env page with this email.
bmbs-imac:rosetta_bin_mac_2016.32.58837_bundle Kumar$ env
ROSETTA3_DB=/Applications/rosetta_bin_mac_2016.32.58837_ bundle/PHENIX_ROSETTA_PATH//main/database
TERM_PROGRAM=Apple_Terminal
SHELL=/bin/bash
TERM=xterm-256color
TMPDIR=/var/folders/cb/5v492std3d31jr42j7h3jm9h0000gp/T/
Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd. KEC4L2Cjos/Render
TERM_PROGRAM_VERSION=387
OLDPWD=/Applications
TERM_SESSION_ID=A82EA51D-0920-4F3B-BE03-92AE0C40A44B
USER=Kumar
SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.tMihawGOC7/Listeners
__CF_USER_TEXT_ENCODING=0x1F6:0x0:0x0
ROSETTA_BIN=/Applications/rosetta_bin_mac_2016.32.58837_ bundle/PHENIX_ROSETTA_PATH//main/source/bin
PATH=/Library/Frameworks/Python.framework/Versions/3.5/ bin:/Library/Frameworks/Python.framework/Versions/3.5/ bin:/Users/Kumar/miniconda2/bin:/usr/local/bin:/usr/bin:/ bin:/usr/sbin:/sbin:/opt/X11/bin
PWD=/Applications/rosetta_bin_mac_2016.32.58837_bundle
LANG=en_US.UTF-8
XPC_FLAGS=0x0
XPC_SERVICE_NAME=0
SHLVL=1
HOME=/Users/Kumar
LOGNAME=Kumar
DISPLAY=/private/tmp/com.apple.launchd.BhETYwyInl/org.macosforge.xquartz:0
PHENIX_ROSETTA_PATH=/Applications/rosetta_bin_mac_ 2016.32.58837_bundle/PHENIX_ROSETTA_PATH/
_=/usr/bin/env
bmbs-imac:rosetta_bin_mac_2016.32.58837_bundle Kumar$ env
ROSETTA3_DB=/Applications/rosetta_bin_mac_2016.32.58837_ bundle/PHENIX_ROSETTA_PATH//main/database
TERM_PROGRAM=Apple_Terminal
SHELL=/bin/bash
TERM=xterm-256color
TMPDIR=/var/folders/cb/5v492std3d31jr42j7h3jm9h0000gp/T/
Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd. KEC4L2Cjos/Render
TERM_PROGRAM_VERSION=387
OLDPWD=/Applications
TERM_SESSION_ID=A82EA51D-0920-4F3B-BE03-92AE0C40A44B
USER=Kumar
SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.tMihawGOC7/Listeners
__CF_USER_TEXT_ENCODING=0x1F6:0x0:0x0
ROSETTA_BIN=/Applications/rosetta_bin_mac_2016.32.58837_ bundle/PHENIX_ROSETTA_PATH//main/source/bin
PATH=/Library/Frameworks/Python.framework/Versions/3.5/ bin:/Library/Frameworks/Python.framework/Versions/3.5/ bin:/Users/Kumar/miniconda2/bin:/usr/local/bin:/usr/bin:/ bin:/usr/sbin:/sbin:/opt/X11/bin
PWD=/Applications/rosetta_bin_mac_2016.32.58837_bundle
LANG=en_US.UTF-8
XPC_FLAGS=0x0
XPC_SERVICE_NAME=0
SHLVL=1
HOME=/Users/Kumar
LOGNAME=Kumar
DISPLAY=/private/tmp/com.apple.launchd.BhETYwyInl/org.macosforge.xquartz:0
PHENIX_ROSETTA_PATH=/Applications/rosetta_bin_mac_ 2016.32.58837_bundle/PHENIX_ROSETTA_PATH/
_=/usr/bin/env
bmbs-imac:rosetta_bin_mac_2016.32.58837_bundle Kumar$
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