[Chimera-users] Question: Dock Prep

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 14 09:49:20 PST 2016

Dear Aaran,
If you just want to convert the format (not do all the other Dock Prep stuff), you can use the “open” command to open the PDB file and the “write” command to save it as a Mol2 file.  There are also commands to add hydrogens (addh) and charges (addcharge), but not for every part of Dock Prep.  Once you have tried the commands and figured out how to use them, then you would probably want to put them into a Python script that will loop through a lot of files, see:


See also the command manual pages for the options:


However, if you only wanted to convert formats, it might be more efficient to use something else like Babel instead of Chimera.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 11, 2016, at 6:32 AM, wang_q at tib.cas.cn wrote:
> Dear Colleagues,
>         I am a beginner in docking(using DOCK 6.7). I learned from DOCK6 tutorial that I could use UCSF chimera to prepare my inputs file for DOCK6 and I prepared the inputs mol2 format file ( converting from PDB to mol2) successfully indeed. And now I have a question, is there a way that I can use in commend line to convert PDB to mol2 format file in chimera, because I want to use this format conversion function in server. I would be very grateful if someone could help me solve the puzzle.
> Thanks very much!
> Aaran

More information about the Chimera-users mailing list