[Chimera-users] adding hydrogens

Eric Pettersen pett at cgl.ucsf.edu
Wed Jan 6 17:26:59 PST 2010

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 at hd1,dd1,td1 #handle deuterium/tritium as well
setattr r type HIP :HID at 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 Pettersen
                         UCSF Computer Graphics Lab

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