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This can be done in a few lines of script in any structural biology 
package that provides a Python (or other) shell. Here's how I'd do it in 
ChimeraX, for example:

Assuming your model is the only one loaded and atom names are all 
standard:

m = session.models.list()[0]
histidines = m.residues.filter(m.residues.names == 'HIS')
for his in histidines:
     names = his.atoms.names
     he2 = 'HE2' in names
     hd1 = 'HD1' in names
     if hd1 and not he2:
         his.name = 'HID'
     elif he2 and not hd1:
         his.name = 'HIE'
     elif hd1 and he2:
         his.name = 'HIP'
     else:
         raise RuntimeError('HIS {}:{} is missing both 
hydrogens!'.format(
             h.chain_id, h.number))

Cheers,

Tristan

On 2017-06-29 07:09, Briggs, David C wrote:
> I believe the ProPka or Pdb2pqr webservers can do this.
> 
>  ProPka.org
> 
>  http:// [1]nbcr [1]-222.ucsd.edu/pdb2pqr_2.0.0/ [1]
> 
>  HTH,
> 
>  Dave
> 
>  --
> 
>  Dr David C Briggs
> 
>  Hohenester Lab
> 
>  Department of Life Sciences
> 
>  Imperial College London
> 
>  UK
> 
>  http://about.me/david_briggs [2]
> 
> -------------------------
> 
> FROM: CCP4 bulletin board <[log in to unmask]> on behalf of
> Sampson, Jared <[log in to unmask]>
>  SENT: Wednesday, June 28, 2017 11:34:05 PM
>  TO: [log in to unmask]
>  SUBJECT: [ccp4bb] Correcting 3-letter codes based on protonation
> states in a PDB file
> 
> Dear all -
> 
>  I'm working with a PDB file with explicit hydrogens where many of the
> histidines are in protonated form due to crystallization at low pH.
> Unfortunately, although the additional protons are present in the
> model for the positively charged histidines, the residues in question
> are indicated in both the SEQRES and the ATOM records as 3-letter code
> `HIS` regardless of protonation state (i.e. instead of `HIP` for
> positively charged, and `HID` or `HIE` for the neutral tautomers).
> 
>  Are there existing tools available to determine the proper 3-letter
> residue code for titratable amino acid residues based on which
> hydrogens are present, and output a corrected PDB file?
> 
>  Thank you in advance for your suggestions.
> 
>  Cheers,
> 
>  Jared Sampson
>  Ph.D. Candidate
>  Columbia University
> 
> Links:
> ------
> [1] http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/
> [2] http://about.me/david_briggs