Bugs item #3448379, was opened at 2011-12-02 07:37
Message generated for change (Tracker Item Submitted) made by kevinrue
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Category: Stereochemistry
Group: 2.3.x
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Kévin RUE-ALBRECHT (kevinrue)
Assigned to: Nobody/Anonymous (nobody)
Summary: SERINE residue incorrectly converted when last residue
Initial Comment:
Considering a peptide sequences, the SERINE residue is recognized and converted
correctly (from Smiles string to any 3D structure) at any position EXCEPT the
last one.
In other words. when its smiles string sequence is N[C@@]([H])(CO)C=O or
N[C@@]([H])(CO)C(=O) , you will notice that one of the carboxylate's oxygens is
missing, which corresponds to a SERINE residue bound to another residue by its
carboxylate carbon.
On the contrary, when the SERINE is the Cterminal residue of the peptide; i.e.
its Smiles string is ...N[C@@]([H])(CO)C(=O)O , then OpenBabel will not
recongnize the SERINE residue and write it in the PDB file as an unknown
residue ("UNK"), and its atoms will be considered as "HETATM", which prevents
them from being typed (alpha carbon: CA, etc...). Which gives the following for
the SERINE residue.
HETATM 60 N UNK A 9 4.954 -4.052 8.717 1.00 0.00 N
HETATM 61 C UNK A 9 4.694 -4.357 10.134 1.00 0.00 C
HETATM 62 C UNK A 9 3.665 -3.415 10.762 1.00 0.00 C
HETATM 63 O UNK A 9 4.268 -2.161 11.068 1.00 0.00 O
HETATM 64 C UNK A 9 4.178 -5.783 10.233 1.00 0.00 C
HETATM 65 O UNK A 9 3.663 -6.429 9.325 1.00 0.00 O
HETATM 66 O UNK A 9 4.330 -6.325 11.454 1.00 0.00 O
IMPORTANT:
The error is specific to the SERINE residue. Any other residue is correctly
recognized at any position in the peptide.
I enclosed files which provide a full example:
"0019_QGNVTSIHS_orig.smi" is a file containing a correct smiles string (the
last SERINE has a complete carboxlate function)
"0019_QGNVTSIHS_orig.pdb" is the file produced by openBabel from the conversion
of the previous one using the options: "-d" and "--gen3d"
look at the SERINE at the end of the peptide, you will see the above lines.
"0019_QGNVTSIHS.smi" is a file where I manually tweaked the Smiles string,
taking off one of the oxygens of the carboxylate group of the last SERINE. This
is NOT the correct Smiles string. An incomplete carboxylate function is
biologically incoherent.
"0019_QGNVTSIHS.pdb" is the file produced by OpenBabel from the conversion of
the previous one, using the same options as above. Now it works... but the
peptide will look - and be - incorrect in any visualization tool, because of
the missing oxygen of the carboxylate function.
I do need to get a new release, where this bug is fixed, as soon as possible
to go on with my PhD project. I have a script looking for the alpha carbon of
the different residues, and as long as this bug is not fixed (which should be
really fast as soon as someone will get to consider it), I can't go on with my
project.
Thank you for all the work you put in this nice piece of software, otherwise
perfect to me!
All the best
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