can not run JChem base Installation on linux web server

I have installed JChem on a linux web server.

but the command line tools are not running eg:  jcman. This is the case for both a local development server where I can confirm the gui tools are working and also on a web vserver were I have no access to gui tools:
root@v14908:~/ChemAxon/JChem/bin# jcman -h
-bash: jcman: command not found.

Please advise my next step, Many thanks, Bernard.

here is the listing of the bin directory:

root@v14908:~/ChemAxon/JChem/bin# ls -lF
total 236
-rwxr-xr-x 1 root root 3977 Jun 12 10:03 bm*
-rwxr-xr-x 1 root root 3974 Jun 12 10:03 compr*
-rwxr-xr-x 1 root root 3974 Jun 12 10:03 config*
-rwxr-xr-x 1 root root 3978 Jun 12 10:03 count*
-rwxr-xr-x 1 root root 4090 Jun 12 10:03 creact*
-rwxr-xr-x 1 root root 3977 Jun 12 10:03 crview*
-rwxr-xr-x 1 root root 3973 Jun 12 10:03 cxcalc*
-rwxr-xr-x 1 root root 3970 Jun 12 10:03 cxtrain*
-rwxr-xr-x 1 root root 3978 Jun 12 10:03 enumerate*
-rwxr-xr-x 1 root root 3969 Jun 12 10:03 evaluate*
-rwxr-xr-x 1 root root 3986 Jun 12 10:03 exampleCount*
-rwxr-xr-x 1 root root 3977 Jun 12 10:03 fragment*
-rwxr-xr-x 1 root root 3985 Jun 12 10:03 fragstat*
-rwxr-xr-x 1 root root 3978 Jun 12 10:03 generatemd*
-rwxr-xr-x 1 root root 3973 Jun 12 10:03 generfp*
-rwxr-xr-x 1 root root 3980 Jun 12 10:03 hitstatistics*
-rwxr-xr-x 1 root root 3980 Jun 12 10:03 jarp*
-rw-r--r-- 1 root root   75 Jun 21 10:15 java.ini
-rwxr-xr-x 1 root root 4038 Jun 12 10:03 jcman*
-rwxr-xr-x 1 root root 3967 Jun 12 10:03 jcsearch*
-rwxr-xr-x 1 root root 3967 Jun 12 10:03 jcunique*
-rwxr-xr-x 1 root root 3977 Jun 12 10:03 jklustor*
-rwxr-xr-x 1 root root 4069 Jun 12 10:03 libmcs*
-rwxr-xr-x 1 root root 4063 Jun 12 10:03 license*
-rwxr-xr-x 1 root root 3991 Jun 12 10:03 markushview*
-rwxr-xr-x 1 root root 3970 Jun 12 10:03 mcs*
-rwxr-xr-x 1 root root 4100 Jun 12 10:03 metabolize*
-rwxr-xr-x 1 root root 3975 Jun 12 10:03 molconvert*
-rwxr-xr-x 1 root root 4013 Jun 12 10:03 moledit*
-rwxr-xr-x 1 root root 3990 Jun 12 10:03 molfragment*
-rwxr-xr-x 1 root root 3968 Jun 12 10:03 msketch*
-rwxr-xr-x 1 root root 3978 Jun 12 10:03 mspace*
-rwxr-xr-x 1 root root 3966 Jun 12 10:03 mview*
-rwxr-xr-x 1 root root 3983 Jun 12 10:03 nneib*
drwxr-xr-x 2 root root 4096 Jun 21 10:15 np/
-rwxr-xr-x 1 root root 3983 Jun 12 10:03 optimizemetrics*
-rwxr-xr-x 1 root root 3976 Jun 12 10:03 pmapper*
-rwxr-xr-x 1 root root 4144 Jun 12 10:03 react*
-rwxr-xr-x 1 root root 4013 Jun 12 10:03 redit*
-rwxr-xr-x 1 root root 3970 Jun 12 10:03 rgdecomp*
-rwxr-xr-x 1 root root 3986 Jun 12 10:03 rmap*
-rwxr-xr-x 1 root root 3985 Jun 12 10:03 rtest*
-rwxr-xr-x 1 root root 4030 Jun 12 10:03 scedit*
-rwxr-xr-x 1 root root 3975 Jun 12 10:03 screen3d*
-rwxr-xr-x 1 root root 3985 Jun 12 10:03 screeningoptimizer*
-rwxr-xr-x 1 root root 3975 Jun 12 10:03 screenmd*
-rwxr-xr-x 1 root root  626 Jun 12 10:03 setup*
-rwxr-xr-x 1 root root 4105 Jun 12 10:03 standardize*
-rwxr-xr-x 1 root root 4022 Jun 12 10:03 standedit*
-rwxr-xr-x 1 root root 4098 Jun 12 10:03 structurechecker*
-rwxr-xr-x 1 root root 3970 Jun 12 10:03 toxic*
-rwxr-xr-x 1 root root 4003 Jun 12 10:03 toxicView*
-rwxr-xr-x 1 root root 3989 Jun 12 10:03 toxiccalc*
-rwxr-xr-x 1 root root 3990 Jun 12 10:03 toxicophore*
-rwxr-xr-x 1 root root 3971 Jun 12 10:03 ward*

Hello Bernard,

Is . added to your path? Could you try it by executing

./jcman -h

?

Regards,

Tamas

Hi Tamas

OK, this works with the "." 

....and I think I understand more...

When I cd into the ...\bin\ directory I need to add the "."

I now need to find the place where I set this ...\bin\ directory into PATH environment variable. Is this correct?

Thanks!

Bernard

Hi,

You can add the "." to the path, so you can access every file in your current directory without the ./  prefix.

Or you can add ~/ChemAxon/JChem/bin to your path to access all commands from that directory even when your current directory is different.

You can add that to your path by the export command:

export PATH=$PATH:<added path>

You can also add this line to your .bash_profile file in your home directory to automatically use the new path after login.

Regards,

Tamas