Hi Richard, There is no direct way to prevent the minimize command from attempting to add hydrogens. I will be opening a ticket in our Trac bug database to get this remedied. So for right now your only recourse is to modify Chimera's Python code. Luckily the change is pretty simple. Lines 86-87 of <your Chimera installation>/share/MMMD/ MMTKinter.py should currently look like this: if nogui or chimera.nogui: DockPrep.prep(mols, nogui=nogui, **kw) change that to: if nogui or chimera.nogui: kw["addHFunc"] = None DockPrep.prep(mols, nogui=nogui, **kw) This change will prevent hydrogens from being added in nogui mode. One caveat is that if Chimera believes that hydrogens should be added then it's possible it will estimate the charge wrong for those ligands. So: 1) You should use the release candidate since that has the most accurate atom-type assessment. 2) If Add Charge fails because of wrong charge estimation, you may have to either run the failures through "by hand" or enforce correct atoms types with the "setattr" command (and the "idatmType" attribute, see http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html) I would be interested in knowing about ligands where Chimera fails to correctly type the atoms. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 19, 2009, at 8:35 AM, richardbonnet wrote:

Dear users

Would you give me the best way to minimize the hydrogens in ligands with chimera used without GUI and without addh?

I use : chimera --nogui --nostatus ligand_1.mol2 ./script.py

here is script.py : from chimera import runCommand runCommand("select @H=") runCommand("minimize freeze unselected nsteps 1000") runCommand("write format mol2 0 out.mol2")

However, chimera add wrong hydrogen because of the load of addh with minimize. I have a lot of ligands to process and I can not use GUI.

thank you much for your help,

Richard Bonnet Universite Auvergne