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
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