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 <CCP4BB@JISCMAIL.AC.UK> on behalf of
Sampson, Jared <jms2...@cumc.columbia.edu>
SENT: Wednesday, June 28, 2017 11:34:05 PM
TO: CCP4BB@JISCMAIL.AC.UK
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
