Hi, I suppose you are talking about protonated Histidine, since that’s what is in the picture as far as I can tell. However, your coordinates are at most a fragment of HIP. My 3D vision isn’t good enough to see structure from coordinates, and I don’t know all of OpenBabel’s formats well enough to tell which one you have. So, I therefor can’t really tell what your coordinates are showing and hence I cannot say if the SMILE is a good representation or not. But I can say that it is a difficult problem to assign proper bondorders to molecules when only coordinates are given, especially with missing charges and even more so if we are talking about fragments. Further, I don’t really understand the part where you state that the coordinates back-converted are different. Since SMILES don’t carry any information about coordinates, it will obviously be lost in the conversion.
If you provide your input file and the commands you use for the conversion, I could try to look at it again. Kind regards, Fredrik 14 maj 2014 kl. 20:00 skrev Jiaguo <comingn...@hotmail.com>: > <http://forums.openbabel.org/file/n4657433/GV_hip.png> > > The SMILES given by Open Babel for the Hip (protonated Histine), coordinates > shown below, is "CCC1=CNCN1". > >> From the coordinates, it should be easily seen that Hip (protonated Histine) > is +1 charge. However, from the SMILES, this information (and the > coordination pattern) is lost. In fact, the coordinates back-converted from > SMILES is quite different. > > I would think this is wrong, but I wonder whether this is be design ? > > 16 > Hip (protonated Histine) > C -5.83770117 -1.72505544 0.00000000 > H -6.46253417 -1.64825244 -0.88982300 > C -6.72432417 -1.57893344 1.23214100 > H -7.46855917 -2.37525544 1.24137300 > H -6.11155117 -1.64458144 2.13119600 > C -7.48375317 -0.27683644 1.32108500 > N -8.33394317 0.00896456 2.38296700 > C -7.52063117 0.80076756 0.49245500 > H -8.52477017 -0.59484244 3.16979800 > C -8.84813417 1.20805556 2.18249600 > N -8.37444817 1.69329156 1.06166200 > H -7.03093917 1.04067456 -0.45133900 > H -9.54804417 1.62859556 2.90455700 > H -8.60883517 2.59721956 0.67685400 > H -5.14137252 -0.91263534 0.00000000 > H -5.33042678 -2.66716620 0.00000000 > > > > -- > View this message in context: > http://forums.openbabel.org/The-SMILES-of-Hip-protonated-Histine-is-wrong-tp4657433.html > Sent from the General discussion mailing list archive at Nabble.com. > > ------------------------------------------------------------------------------ > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE > Instantly run your Selenium tests across 300+ browser/OS combos. > Get unparalleled scalability from the best Selenium testing platform available > Simple to use. Nothing to install. Get started now for free." > http://p.sf.net/sfu/SauceLabs > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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