DSSP not work on MACOS

[Former user]

Hi, I have an issue calling the dssp function. I have dssp installed and can be called in R using system("/Users/zs/work/software/bin/dssp") with the following output: mkdssp 2.2.1 options: -h [ --help ] Display help message -i [ --input ] arg Input file -o [ --output ] arg Output file, use 'stdout' to output to screen -v [ --verbose ] Verbose output --2.2.1 Print 2.2.1 -d [ --debug ] arg Debug level (for even more verbose output) However, when i call the dssp function : dssp(pdb,exefile="/Users/zs/work/software/bin/dssp"), it give an error: Error in dssp.pdb(pdb, exefile = "/Users/sheng/work/software/bin/dssp") : Launching external program 'dssp' (or 'mkdssp') failed make sure '/Users/sheng/work/software/bin/dssp' is in your search path

Can anyone help with this?

Thanks

[Xinqiu Yao]

Have you checked the path? It is confusing that the command you tested uses the path "/Users/zs/work/software/bin/dssp" but the error message displays a different path "/Users/sheng/work/software/bin/dssp"...

[shengzz]

Sorry the directory is a typo mistake. It is '/Users/zs/work/software/bin/dssp' for all output.

[Xinqiu Yao]

Not sure what's going on here. I've tested on my Linux box and it works fine. What version of bio3d are you using?

[shengzz]

I am curious too since every places are set correctly. It sounds like dssp function refuses to check the path by saying 'not found '. Is there a way i can check the code of dssp function?

[Xinqiu Yao]

The source code should be fine, if you are using the latest version (2.3-1). Old versions may have the problem.

There are a couple ways to solve the problem:

• Check your bio3d version with sessionInfo(). If it is lower than 2.3-1, update the package with install.packages('bio3d').

• Add '/Users/zs/work/software/bin/dssp' to the search path of shell. For linux, it is usually stored in the '~/.bashrc' file. For MacOS, it could be '~/.profile' (Not sure because I'm not familiar with mac). Write down 'export PATH=$PATH:/Users/zs/work/software/bin/dssp' at the end of the file and save it. In shell, type source ~/.profile. Then, restart R and try it again.

Btw, you can check the source code of the function by either edit(dssp.pdb) or simply typing dssp.pdb and return.

[shengzz]

I fixed the problem. I used dssp v2.2.1, which doesn't have the '--version' option. So i just switched the version detection off in dssp.pdb.