Command line interface help (3D screen)

I have installed the ChemAxon package, however I am not able to work out the command line interface. I have been trying to follow the manual I found online, but I think i am missing some basic user info. Could anyone help?

Hi, 

Unfortunately I didn't manage to reproduce the error that you sent us. So I will give you some clues on how to run the calculation:

screen3d g filename options

The letter g refers to the generation phase of the 3D virtual screening. This step pre-processes the molecules and prepares them for the actual screening. Your molecule file can be a file that we can import. You should either put the bin directory into the PATH or use absolute paths so that the screen3d command can reach the file.

You can use the 

screen3d -h

command to get full help for the command. 

Daniel

Hi Daniel,

 

I tried using the -h command but the only thing I seem to be getting is another error:

Michals-MacBook-Pro:~ mzzielinski$ cd /Applications/ChemAxon/JChem/bin

Michals-MacBook-Pro:bin mzzielinski$ screen3d -h

-bash: screen3d: command not found

Michals-MacBook-Pro:bin mzzielinski$ open screen3d -h

Unable to find header file matching screen3d

Michals-MacBook-Pro:bin mzzielinski$  

Hi, 

I think the path to screen3d in not in your PATH environmental variable. You should check it or re-run the JChem installer. The installer can put the bin directory in your PATH is this option is selected.

Daniel

Hi,

I'm not a Mac expert, but in Linux-style command-line environments usually the current directory (.) is not in the PATH either.

So once you are in the "bin" directory of JChem you should use a "./" prefix, and it should work, e.g:

./screen3d -h

Of course it's the most convenient if you add the "bin" directory of JChem to the PATH, then you can execute it from any other location as well (without the "./").

Best,

Szilard