[Chimera-users] problems with multifit in chimera

[Elaine Meng]

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 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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