Hi Guys, I am trying to use ChimeraX with Modeller to fill in a few small gaps in my PDB file. However, when I run modeller from ChimeraX I get the following error: dyld[77819]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python Referenced from: <498CB722-A7BC-378D-A38D-3A690F9D635B> /Library/modeller-10.6/bin/mod10.6_mac10v4 Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file) Exception in thread Thread-10 (threaded_run): Traceback (most recent call last): File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/modeller/common.py", line 708, in threaded_run _ = subprocess.run(cmd, capture_output=True, text=True, check=True, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py", line 571, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/Library/modeller-10.6/bin/mod10.6_mac10v4', '/var/folders/wn/dw9ws1756cjfsv3p6m3lphmc0000gn/T/tmpj5w_luqj/ModellerModelling.py']' died with <Signals.SIGABRT: 6>. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038, in _bootstrap_inner self.run() File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975, in run self._target(*self._args, **self._kwargs) File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/modeller/common.py", line 720, in threaded_run raise UserError("Modeller execution failed; output and errors in log") chimerax.core.errors.UserError: Modeller execution failed; output and errors in log It seems that the python2.7 is the issue, but I’m not sure which file to edit to point it to a new version (I’m on python 3.12). I’ve also tried this with ChimeraX 1.9 and 1.8 with the same error. Can you point me in the right direction? Thanks! Matt Goff
Hi Matt, This seems to be a problem with your Modeller installation. I guess I would recommend going to https://salilab.org/modeller/10.6/release.html#osx and following step 4 to uninstall any old versions you might have and then re-install the current version. If installed properly, the “modeller executable” would be the full path to python3 (if you used the Homebrew install that would be /opt/homebrew/bin/python3l otherwise probably /usr/bin/python3). If you still then get this problem (or a related problem), I would use ChimeraX’s Help→Report a Bug menu item to file a bug report. That will provide us with more information about your system. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Dec 9, 2024, at 3:45 PM, Matt Goff via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Guys, I am trying to use ChimeraX with Modeller to fill in a few small gaps in my PDB file. However, when I run modeller from ChimeraX I get the following error:
dyld[77819]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python Referenced from: <498CB722-A7BC-378D-A38D-3A690F9D635B> /Library/modeller-10.6/bin/mod10.6_mac10v4 Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
Exception in thread Thread-10 (threaded_run): Traceback (most recent call last): File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/modeller/common.py", line 708, in threaded_run _ = subprocess.run(cmd, capture_output=True, text=True, check=True, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py", line 571, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/Library/modeller-10.6/bin/mod10.6_mac10v4', '/var/folders/wn/dw9ws1756cjfsv3p6m3lphmc0000gn/T/tmpj5w_luqj/ModellerModelling.py']' died with <Signals.SIGABRT: 6>.
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038, in _bootstrap_inner self.run() File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975, in run self._target(*self._args, **self._kwargs) File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/modeller/common.py", line 720, in threaded_run raise UserError("Modeller execution failed; output and errors in log") chimerax.core.errors.UserError: Modeller execution failed; output and errors in log
It seems that the python2.7 is the issue, but I’m not sure which file to edit to point it to a new version (I’m on python 3.12). I’ve also tried this with ChimeraX 1.9 and 1.8 with the same error. Can you point me in the right direction? Thanks! Matt Goff _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
It looks to me like you're trying to run the Modeller binary /Library/modeller-10.6/bin/mod10.6_mac10v4 directly. As you've seen, that doesn't work, as it's not meant to be run directly (if you wanted to run that, use the mod10.6 script, which amongst other things sets the search path correctly so that Python 2 can be found). As Eric says, the best way to use Modeller with ChimeraX is to use the full path to your Python 3 install instead. (This looks like you installed Modeller using the standalone package, which is designed to work with Apple's Python 3, which is /usr/bin/python3.) Ben On 12/9/24 4:54 PM, Eric Pettersen via ChimeraX-users wrote:
Hi Matt, This seems to be a problem with your Modeller installation. I guess I would recommend going to https://salilab.org/modeller/10.6/ release.html#osx <https://salilab.org/modeller/10.6/ release.html#osx> and following step 4 to uninstall any old versions you might have and then re-install the current version. If installed properly, the “modeller executable” would be the full path to python3 (if you used the Homebrew install that would be /opt/homebrew/bin/ python3l otherwise probably /usr/bin/python3). If you still then get this problem (or a related problem), I would use ChimeraX’s Help→Report a Bug menu item to file a bug report. That will provide us with more information about your system.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Dec 9, 2024, at 3:45 PM, Matt Goff via ChimeraX-users <chimerax- users@cgl.ucsf.edu> wrote:
Hi Guys, I am trying to use ChimeraX with Modeller to fill in a few small gaps in my PDB file. However, when I run modeller from ChimeraX I get the following error: dyld[77819]: Library not loaded: /System/Library/Frameworks/ Python.framework/Versions/2.7/Python Referenced from: <498CB722-A7BC-378D-A38D-3A690F9D635B> /Library/ modeller-10.6/bin/mod10.6_mac10v4 Reason: tried: '/System/Library/Frameworks/Python.framework/ Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/ Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/ Python' (no such file), '/System/Library/Frameworks/Python.framework/ Versions/2.7/Python' (no such file, not in dyld cache), '/Library/ Frameworks/Python.framework/Versions/2.7/Python' (no such file)
Exception in thread Thread-10 (threaded_run): Traceback (most recent call last): File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/ Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ modeller/common.py", line 708, in threaded_run _ = subprocess.run(cmd, capture_output=True, text=True, check=True, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/ Python.framework/Versions/3.11/lib/python3.11/subprocess.py", line 571, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/Library/modeller-10.6/bin/ mod10.6_mac10v4', '/var/folders/wn/dw9ws1756cjfsv3p6m3lphmc0000gn/T/ tmpj5w_luqj/ModellerModelling.py']' died with <Signals.SIGABRT: 6>.
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/ Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038, in _bootstrap_inner self.run() File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/ Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975, in run self._target(*self._args, **self._kwargs) File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/ Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ modeller/common.py", line 720, in threaded_run raise UserError("Modeller execution failed; output and errors in log") chimerax.core.errors.UserError: Modeller execution failed; output and errors in log It seems that the python2.7 is the issue, but I’m not sure which file to edit to point it to a new version (I’m on python 3.12). I’ve also tried this with ChimeraX 1.9 and 1.8 with the same error. Can you point me in the right direction? Thanks! Matt Goff _______________________________________________ ChimeraX-users mailing list --chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email tochimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax- users@cgl.ucsf.edu/ <https://mail.cgl.ucsf.edu/mailman/archives/list/ chimerax-users@cgl.ucsf.edu/>
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
-- ben@salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle
participants (3)
-
Ben Webb -
Eric Pettersen -
Matt Goff