Local calculation of residue depth in python and MacOS >10.15.x
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8 months ago
Albert • 0

Hi,

I'm trying to integrate a residue depth calculation in my python script pipeline using MacOS Big Sur. Biopython's Bio.PDB.ResidueDepth module uses MGLtool's MSMS, which is a 32 bit app and thus I get the hateful "Bad CPU type in executable" error when trying to execute it separately.

"RuntimeError: Failed to generate surface file using command:
msms -probe_radius 1.5 -if"

pops if called from biopython using the Bio.PDB.ResidueDepth test code.

I've been using the Depth web application, which is not handy for script integration. I've tried the local installation, but the CMake install fails with:

clang: error: unsupported option '-fopenmp'

And none of this (or any other in stackoverflow) worked, even not adding the -Xpreprocessor flag before the -fopenmp one in depth_source/bin/makefile, which gives the error:

clang: error: linker command failed with exit code 1 (use -v to see invocation)

Any workarounds to solve any of these issues? Of course I'd prefer using biopython not being forced to switch OS, although being able to call Depth locally would also do.

python protein structure • 332 views
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I tend to remember that the default clang on Mac does not support openmp. I think you have to install an openmp-ready clang version, such as from here: https://cran.r-project.org/bin/macosx/tools/

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32-bit programs simply can't run on big sur. Apple dropped support for those starting with catalina. You will have to use a virtual environment (with an older macOS)/ Parallels.

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Sure this would fix the issue, it's just so annoying to be forced to change OS for such an issue. I was wondering whether somebody found a way around this, like an alternative python package for residue depth calculations for instance.

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