[Chimera-users] problems with multifit in chimera

[Tom Goddard]

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/appMultiFitWebService1576534867767-374657110
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 at 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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