molconvert command line help

Please excuse the simplicity of this question, but if i have a file named '1' saved in .sdf format and want to use a command line to output a file of the same molecule in 3D, what is the actual command line?

I have tried:

molconvert -3 -o test.mol 1.sdf

molconvert -3 -o 1.sdf test.mol

I can generate the correct type of file in the correct place, but they are blank. I assume this is because I am incorrectly trying to select the 1.sdf file for conversion to 3D.

Here is what I entered:

molconvert sdf -3 "1.sdf" -o 3D.sdf

Any hints on what I am doing wrong?

Thanks

Hi,

The expected format is to convert 1.sdf to 3d format in 3D.sdf:

molconvert -3 -o 3D.sdf sdf 1.sdf

or

molconvert -3 1.sdf -o 3D.sdf

or on linux:

molconvert -3 1.sdf >3D.sdf

You can get additional help and examples about molconvert here:

http://www.chemaxon.com/marvin/help/applications/molconvert.html

Best Regards,

Peter

Peter,

Thank you very much for the help. This worked well.

My next step is to make sure each molecule is 'cleaned' in 3D so that I have the lowest energy conformer.

Is there a simply command that will do this?

It looks like I should use S{fine} for this operation?

 

Thanks again for the help,

Graham

Graham,

Actually, the -3 option returns the lowest energy conformer according to the default 3D "cleaning" method. As you can read here

http://www.chemaxon.com/marvin/help/sci/cleanoptions.html#base.3d

the default cleaning option is "fast", but you can switch to "fine" using the S{fine} option.

Best regards,

Akos