Hello I have recently been encountering problems with MultiFit within Chimera on both Ubuntu and Windows 10 (trace from reply log below--I get the same error on both operating systems). Even fitting with datasets that was working earlier in the year (~August-September) is not working anymore. My guess is that some changes have happened on the server that hosts Multifit. Could someone please try and reproduce the bug and let me know how I should troubleshoot this? I am trying to fit a single protein structure to an EM map and as I said, this was working earlier this year. I also tried downloading IMP on my Windows machine and using MultiFit from in there. This was running into some separate issues which I will not go into here since they are not directly related to Chimera. Thanks and best Nimit Trace from reply log: Application stderr ----- Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/generate_assembly_input.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/create_all_surfaces.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/generate_assembly_anchor_graph.py", line 3, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/run_fitting_fft.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/generate_indexes_from_fitting_solutions.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/create_auto_proteomics_file.py", line 6, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/align_proteomics_em_atomic_plan.py", line 3, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/usr/local/opal-local/bin/multifitWS.py", line 438, in <module> main() File "/usr/local/opal-local/bin/multifitWS.py", line 46, in main VersionMap[cf["version"]](cf) File "/usr/local/opal-local/bin/multifitWS.py", line 98, in v1_run asymWriteSolution(cf) File "/usr/local/opal-local/bin/multifitWS.py", line 411, in asymWriteSolution raise RuntimeError("Unable to find file combinations.output") RuntimeError: Unable to find file combinations.output -----
Hi Nimit, This does not answer your specific question, but you might want to try using the “fitmap” command in Chimera (or ChimeraX). It has options for • global search with random initial placement • sequential fitting of multiple different structures • symmetric fitting of copies of the same structure See <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> …or in ChimeraX: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 16, 2019, at 12:57 PM, Nimit Jain <nimit@stanford.edu> wrote:
Hello
I have recently been encountering problems with MultiFit within Chimera on both Ubuntu and Windows 10 (trace from reply log below--I get the same error on both operating systems). Even fitting with datasets that was working earlier in the year (~August-September) is not working anymore. My guess is that some changes have happened on the server that hosts Multifit. Could someone please try and reproduce the bug and let me know how I should troubleshoot this? I am trying to fit a single protein structure to an EM map and as I said, this was working earlier this year.
I also tried downloading IMP on my Windows machine and using MultiFit from in there. This was running into some separate issues which I will not go into here since they are not directly related to Chimera.
Thanks and best Nimit
Trace from reply log:
Application stderr ----- Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/generate_assembly_input.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/create_all_surfaces.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/generate_assembly_anchor_graph.py", line 3, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/run_fitting_fft.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/generate_indexes_from_fitting_solutions.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/create_auto_proteomics_file.py", line 6, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/align_proteomics_em_atomic_plan.py", line 3, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/usr/local/opal-local/bin/multifitWS.py", line 438, in <module> main() File "/usr/local/opal-local/bin/multifitWS.py", line 46, in main VersionMap[cf["version"]](cf) File "/usr/local/opal-local/bin/multifitWS.py", line 98, in v1_run asymWriteSolution(cf) File "/usr/local/opal-local/bin/multifitWS.py", line 411, in asymWriteSolution raise RuntimeError("Unable to find file combinations.output") RuntimeError: Unable to find file combinations.output -----
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Hi Nimit, I tried just now running MultiFit with Chimera 1.14 using EMDB 1080 and PDB 1grl chain A and I get a different error from yours shown below. A little investigation showed that MultiFit is a 32-bit executable and we recently updated our server that runs all our web services and it only supports 64-bit executables. MultiFit is very old and we did not develop it, so you will need to use the version from the lab that developed it, ie get it through the IMP package. Sorry for the trouble, we will remove MultiFit from our next Chimera release. Tom Reply log output running multifit: Wrote /var/folders/xr/p3w335_s5_g397mx1j17qdc00000gn/T/tmpknfAYW/1grl.pdb Web Service: MultiFit is a Python wrapper that calls cn_MultiFit in IMP for protein structure fitting into cryoEM data with cyclic symmetry. Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/MultiFitWebService Opal job URL: http://webservices.rbvi.ucsf.edu/appMultiFitWebService1576534867767-37465711... Running MultiFit: 1grl to emd_1080.map failed; see Reply Log for more information Application stderr ----- sh: /home/socr/a/yz/local/imp-repository/modules/cn_multifit/bin/msdots: /lib/ld-linux.so.2: bad ELF interpreter: No such file or directory ----- Application stdout ----- now executing: /home/socr/a/yz/local/imp-repository/modules/cn_multifit/bin/msdots 1grl.pdb vdw.lib out 10.0 1.8
On Dec 16, 2019, at 12:57 PM, Nimit Jain <nimit@stanford.edu> wrote:
Hello
I have recently been encountering problems with MultiFit within Chimera on both Ubuntu and Windows 10 (trace from reply log below--I get the same error on both operating systems). Even fitting with datasets that was working earlier in the year (~August-September) is not working anymore. My guess is that some changes have happened on the server that hosts Multifit. Could someone please try and reproduce the bug and let me know how I should troubleshoot this? I am trying to fit a single protein structure to an EM map and as I said, this was working earlier this year.
I also tried downloading IMP on my Windows machine and using MultiFit from in there. This was running into some separate issues which I will not go into here since they are not directly related to Chimera.
Thanks and best Nimit
Trace from reply log:
Application stderr ----- Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/generate_assembly_input.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/create_all_surfaces.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/generate_assembly_anchor_graph.py", line 3, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/run_fitting_fft.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/generate_indexes_from_fitting_solutions.py", line 2, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/create_auto_proteomics_file.py", line 6, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/home/socr/a/yz/local/imp-repository/modules/multifit2/bin/align_proteomics_em_atomic_plan.py", line 3, in <module> import IMP.multifit File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 25, in <module> _IMP_multifit = swig_import_helper() File "/home/socr/a/yz/local/imp-debug/build/lib/IMP/multifit/__init__.py", line 17, in swig_import_helper import _IMP_multifit ImportError: libfftw3.so.3: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/usr/local/opal-local/bin/multifitWS.py", line 438, in <module> main() File "/usr/local/opal-local/bin/multifitWS.py", line 46, in main VersionMap[cf["version"]](cf) File "/usr/local/opal-local/bin/multifitWS.py", line 98, in v1_run asymWriteSolution(cf) File "/usr/local/opal-local/bin/multifitWS.py", line 411, in asymWriteSolution raise RuntimeError("Unable to find file combinations.output") RuntimeError: Unable to find file combinations.output -----
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participants (3)
-
Elaine Meng -
Nimit Jain -
Tom Goddard