[Chimera-users] changing HIS to HIP

Elaine Meng meng at cgl.ucsf.edu
Thu Dec 16 09:46:27 PST 2010

Hi Francesco,
Your procedure is unnecessary.   Here are two much easier approaches:

Just use a text-editor to edit the PDB file and change the names of those residues to HIP, then open in Chimera and use AddH with default settings (histidine protonation "Residue-name-based")

- OR -

If it is OK if the residues are still named HIS, but you want certain ones protonated like HIP (positively charged sidechain, hydrogens on both nitrogens) you can avoid the text-editing part.  Just open the PDB file and use AddH with the histidine protonation option "Specified individually..." and then simply indicate with checkboxes all the histidine sidechain nitrogens you want protonated.

I recommend getting version 1.5 of Chimera if you are using something older.

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 Dec 15, 2010, at 10:45 PM, Francesco Pietra wrote:

> Hello:
> I need to change several histidine residues (both HIS and HIE,
> although both called HIS) to HIP. I tried manually. In case of
> monoprotonation at NE2:
> modify structure
> element N
> bonds 3
> geom trigonal
> connect to preex atoms
> color by element
> change modified residue's name to HIP
> set atom names to ND1
> or
> retain current atom names
> In both cases the proton attached to ND1 takes the name "H1" instead
> of the expected HD1.
> Is that error in the above procedure or chimera bug? (chimera alpha
> version 1.5 (build 30702) on GNU/LINUX 32bit)
> Addendum: is there any other method of accomplishing the task with
> chimera? It is rather troublesome to go through all monoprotonated
> histidines of this large homomer (in different chains HIS of the same
> number have been differently protonated by reduce). A problem with
> reduce (if not my misuse of reduce) is that all histidines become
> monoprotonated, while the experimental pH is such that all should be
> diprotonated. I must add that I  am bound to reduce because the
> program that I use subsequently goes through reduce.
> thanks for help
> francesco pietra

More information about the Chimera-users mailing list