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I'm having trouble running 3DNA on my Mac. I followed the installation instructions exactly, and all the files are in the appropriate directory, but when I run the "find_pair" command, it doesn't work. Here's a log of my commands and the system's response:
Steve-Harveys-MacBook-Pro-2:bin steveharvey$ pwd
/Users/steveharvey/bin/x3dna-v2.3/bin
Steve-Harveys-MacBook-Pro-2:bin steveharvey$ ls
alc2img blocview ex_str frame_mol o1p_o2p rebuild stack2img x3dna_ensemble
analyze cehs fiber get_part pdb2img regular_dna std_base x3dna_setup
anyhelix comb_str find_pair mutate_bases r3d_atom rotate_mol step_hel x3dna_utils
Steve-Harveys-MacBook-Pro-2:bin steveharvey$ ./find_pair -h
Illegal instruction: 4
Steve-Harveys-MacBook-Pro-2:bin steveharvey$ find_pair -h
-bash: find_pair: command not found
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Hi Steve,
Thanks for posting the difficulty you experienced when trying to run 3DNA on Mac. A quick Google search with "Illegal instruction: 4 Mac" leads to the following link:
http://stackoverflow.com/questions/14268887/what-is-the-illegal-instruction-4-error-and-why-does-mmacosx-version-min-10
What version of Mac OS X are you using? Click the Apple icon on the upper-left corner, and then click "About This Mac" to get the info. As I am posting this message, my MacBook Air has "Version 10.11.6". Please post your info back.
The distributed version of 3DNA v2.3 for Mac was compiled with Mac OS 10.8 on SBGrid (https://sbgrid.org), which is more than 3 years old now. Since newer Mac OS X are free, so virtually all Mac users should be using newer versions than 10.8. I suspect yours may be older (10.6?). Certainly, you're the first one who's reported such an error message.
Alternatively, since 3DNA v2.3 is now distributed with source code, you could easily go to the src/ directory and type 'make'. Assuming you've the builder tools (Xcode/gcc) available on your Mac (which can compile the classic "Hello, World" C program), then everything should be alright. Have a try and let me know how it goes.
Xiang-Jun
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University