Bugs item #3448379, was opened at 2011-12-02 07:37 Message generated for change (Tracker Item Submitted) made by kevinrue You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3448379&group_id=40728
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. 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 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3448379&group_id=40728 ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel