On Dec 29, 2009, at 1:01 PM, Ravinder Abrol wrote:

We have Chimera installed and I hadn't thought of using it to add hydrogens. I just tried it and it worked. We have many pdbs that we need to run this on, so I found a --nogui mode in chimera. I tried using this to load a pdb and added hydrogens to waters using: addh hbond true spec :hoh but this command adds hydrogens to many of my Histidines also, which I don't want. Seems like spec option is not working? Do you know a way around this?

Hi Ravi, The "spec" argument to addh only specifies models. addh will always add hydrogens to the entire model(s) specified. To protonate water and yet preserve current histidine protonation you will have to get tricky. Namely, change the name of delta-protonated histidines to HID, epsilon-protonated to HIE, and doubly-protonated to HIP, then use "useHisName true" in the addh command. You can script this as: setattr r type HID :HIS@hd1,dd1,td1 #handle deuterium/tritium as well setattr r type HIP :HID@he2,de2,te2 setattr r type HIE :HIS addh useHisName true [+ any other args you want] setattr r type HIS :HIE:HIP:HID # set residue name back to HIS write [your args] --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu