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	<title>Comments on: NMRShiftDB On and Off Again</title>
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		<title>By: Markus Sitzmann</title>
		<link>http://www.chemspider.com/blog/nmrshiftdb-on-and-off-again.html/comment-page-1#comment-195161</link>
		<dc:creator>Markus Sitzmann</dc:creator>
		<pubDate>Wed, 12 May 2010 21:41:34 +0000</pubDate>
		<guid isPermaLink="false">http://www.chemspider.com/blog/?p=1711#comment-195161</guid>
		<description><![CDATA[Egon,

Maybe this helps for the &quot;SMILES bond order problem&quot; at least temporarily (setting the usearo flag to false is important):

http://cactus.nci.nih.gov/chemical/structure/c1cccc2c1c(c(\C=C)n2)CCN/smiles?usearo=false
NCCC1=C([NH]C2=CC=CC=C12)C=C

http://cactus.nci.nih.gov/chemical/structure/c1ccccc1/smiles?usearo=false
C1=CC=CC=C1]]></description>
		<content:encoded><![CDATA[<p>Egon,</p>
<p>Maybe this helps for the &#8220;SMILES bond order problem&#8221; at least temporarily (setting the usearo flag to false is important):</p>
<p><a href="http://cactus.nci.nih.gov/chemical/structure/c1cccc2c1c(c(" rel="nofollow">http://cactus.nci.nih.gov/chemical/structure/c1cccc2c1c(c(</a>\C=C)n2)CCN/smiles?usearo=false<br />
NCCC1=C([NH]C2=CC=CC=C12)C=C</p>
<p><a href="http://cactus.nci.nih.gov/chemical/structure/c1ccccc1/smiles?usearo=false" rel="nofollow">http://cactus.nci.nih.gov/chemical/structure/c1ccccc1/smiles?usearo=false</a><br />
C1=CC=CC=C1</p>
]]></content:encoded>
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	<item>
		<title>By: Wolfgang Robien</title>
		<link>http://www.chemspider.com/blog/nmrshiftdb-on-and-off-again.html/comment-page-1#comment-195153</link>
		<dc:creator>Wolfgang Robien</dc:creator>
		<pubDate>Mon, 03 May 2010 05:56:51 +0000</pubDate>
		<guid isPermaLink="false">http://www.chemspider.com/blog/?p=1711#comment-195153</guid>
		<description><![CDATA[Dear Stefan;

benzene (Compound #236) gives now 1.45 ppm for 1H and 27.1ppm for C13 (Mon, May 3rd 2010m 7:26am MET; screendump available on request), obviously again lost double bonds.

1) Please keep in mind that &#039;Chemspider&#039; and Tony Williams have established a lot of reputation within the scientific community - this is the best way to destroy it !
2) Open Software and Open Data doesnt mean that every program is untested 
3) I have detected this error a long time ago and have written a private email to Tony, because I think this topic is not suitable for my webpage located on http://nmrpredict.orc.univie.ac.at/chemspider_nmrshiftdb.html; on this webpage only problems showing that NMRSHIFTDB is state-of-the-art of ca. 1980 are summarized.
4) When you know that the problem is connected to some parser-error dealing with double bonds then YOUR RESPONSIBILITY IS TO TEST THAT BEFORE (!!!!!!!) you make it available to the community. I think it is NOT an obscene desire, that a program author of a prediction program has tested his/her program with benzene. Maybe a second test with a heterocycle like imidazole can be expected by the community - maybe only when your &#039;Open Time&#039; allows that ! 

Recommendation for Chemspider users: Do a prediction on Chemspider, then take a textbook and apply the &#039;old&#039; increment rules, if you are still unsure apply another prediction program like ACD, KnowItAll, NMRPredict, SPECINFO ........ be careful, those programs produce reliable values, but they are not free-of-charge ! Hopefully, you understand now, why those programs are NOT FREE-OF-CHARGE ! They are tested und the underlying data are curated !

Have a nice day ! Wolfgang Robien]]></description>
		<content:encoded><![CDATA[<p>Dear Stefan;</p>
<p>benzene (Compound #236) gives now 1.45 ppm for 1H and 27.1ppm for C13 (Mon, May 3rd 2010m 7:26am MET; screendump available on request), obviously again lost double bonds.</p>
<p>1) Please keep in mind that &#8216;Chemspider&#8217; and Tony Williams have established a lot of reputation within the scientific community &#8211; this is the best way to destroy it !<br />
2) Open Software and Open Data doesnt mean that every program is untested<br />
3) I have detected this error a long time ago and have written a private email to Tony, because I think this topic is not suitable for my webpage located on <a href="http://nmrpredict.orc.univie.ac.at/chemspider_nmrshiftdb.html" rel="nofollow">http://nmrpredict.orc.univie.ac.at/chemspider_nmrshiftdb.html</a>; on this webpage only problems showing that NMRSHIFTDB is state-of-the-art of ca. 1980 are summarized.<br />
4) When you know that the problem is connected to some parser-error dealing with double bonds then YOUR RESPONSIBILITY IS TO TEST THAT BEFORE (!!!!!!!) you make it available to the community. I think it is NOT an obscene desire, that a program author of a prediction program has tested his/her program with benzene. Maybe a second test with a heterocycle like imidazole can be expected by the community &#8211; maybe only when your &#8216;Open Time&#8217; allows that ! </p>
<p>Recommendation for Chemspider users: Do a prediction on Chemspider, then take a textbook and apply the &#8216;old&#8217; increment rules, if you are still unsure apply another prediction program like ACD, KnowItAll, NMRPredict, SPECINFO &#8230;&#8230;.. be careful, those programs produce reliable values, but they are not free-of-charge ! Hopefully, you understand now, why those programs are NOT FREE-OF-CHARGE ! They are tested und the underlying data are curated !</p>
<p>Have a nice day ! Wolfgang Robien</p>
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		<title>By: Egon Willighagen</title>
		<link>http://www.chemspider.com/blog/nmrshiftdb-on-and-off-again.html/comment-page-1#comment-195152</link>
		<dc:creator>Egon Willighagen</dc:creator>
		<pubDate>Mon, 03 May 2010 05:26:13 +0000</pubDate>
		<guid isPermaLink="false">http://www.chemspider.com/blog/?p=1711#comment-195152</guid>
		<description><![CDATA[Antony, I looked at the CSID 553949 (thanx to hko for posting CSIDs!); it looks to me like a problem with the NMRShiftDB incorrectly accounting for the missing information in the SMILES (&quot;c1cccc2c1c(c(\C=C)n2)CCN&quot;): the latter does not define all bond orders; moreover, the CDK currently does not have a SINGLE_OR_DOUBLE bond order to match the SMILES for that compound (and, no, not all bonds between to &#039;c&#039; atoms in SMILES are really aromatic; if it only was that easy).

The NMRShiftDB is then left to guess where the double bonds are, which is tricky, and the CDK does not have a universal solution. I do not know what solution the NMRShiftDB is using, but please do consider having ChemSpider send SMILES *with* explicit bond orders.

Say what you want; say what you mean. Semantic chemistry starts with being explicit with your data, and not with wrapping in CML or RDF :)]]></description>
		<content:encoded><![CDATA[<p>Antony, I looked at the CSID 553949 (thanx to hko for posting CSIDs!); it looks to me like a problem with the NMRShiftDB incorrectly accounting for the missing information in the SMILES (&#8220;c1cccc2c1c(c(\C=C)n2)CCN&#8221;): the latter does not define all bond orders; moreover, the CDK currently does not have a SINGLE_OR_DOUBLE bond order to match the SMILES for that compound (and, no, not all bonds between to &#8216;c&#8217; atoms in SMILES are really aromatic; if it only was that easy).</p>
<p>The NMRShiftDB is then left to guess where the double bonds are, which is tricky, and the CDK does not have a universal solution. I do not know what solution the NMRShiftDB is using, but please do consider having ChemSpider send SMILES *with* explicit bond orders.</p>
<p>Say what you want; say what you mean. Semantic chemistry starts with being explicit with your data, and not with wrapping in CML or RDF <img src='http://www.chemspider.com/blog/wp-includes/images/smilies/icon_smile.gif' alt=':)' class='wp-smiley' /> </p>
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	</item>
	<item>
		<title>By: hko</title>
		<link>http://www.chemspider.com/blog/nmrshiftdb-on-and-off-again.html/comment-page-1#comment-195151</link>
		<dc:creator>hko</dc:creator>
		<pubDate>Sun, 02 May 2010 10:20:00 +0000</pubDate>
		<guid isPermaLink="false">http://www.chemspider.com/blog/?p=1711#comment-195151</guid>
		<description><![CDATA[Further bug predicting cnmr spectra using NMRShiftDB in ChemSpider.
CSID 776, 773, 1118, 83867, 553949. Lost double bond.]]></description>
		<content:encoded><![CDATA[<p>Further bug predicting cnmr spectra using NMRShiftDB in ChemSpider.<br />
CSID 776, 773, 1118, 83867, 553949. Lost double bond.</p>
]]></content:encoded>
	</item>
	<item>
		<title>By: Antony Williams</title>
		<link>http://www.chemspider.com/blog/nmrshiftdb-on-and-off-again.html/comment-page-1#comment-195150</link>
		<dc:creator>Antony Williams</dc:creator>
		<pubDate>Thu, 29 Apr 2010 11:34:12 +0000</pubDate>
		<guid isPermaLink="false">http://www.chemspider.com/blog/?p=1711#comment-195150</guid>
		<description><![CDATA[It was on the NMRSHiftDB side with one of the intermediate parsers. It has been fixed and we are now looking for further feedback as people use the system.]]></description>
		<content:encoded><![CDATA[<p>It was on the NMRSHiftDB side with one of the intermediate parsers. It has been fixed and we are now looking for further feedback as people use the system.</p>
]]></content:encoded>
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		<title>By: Chris Singleton</title>
		<link>http://www.chemspider.com/blog/nmrshiftdb-on-and-off-again.html/comment-page-1#comment-195149</link>
		<dc:creator>Chris Singleton</dc:creator>
		<pubDate>Thu, 29 Apr 2010 02:33:13 +0000</pubDate>
		<guid isPermaLink="false">http://www.chemspider.com/blog/?p=1711#comment-195149</guid>
		<description><![CDATA[Is this issue strictly with structures translating and being drawn correctly, or with the algorithms in NMRShift DB?]]></description>
		<content:encoded><![CDATA[<p>Is this issue strictly with structures translating and being drawn correctly, or with the algorithms in NMRShift DB?</p>
]]></content:encoded>
	</item>
	<item>
		<title>By: melle B.fouzia</title>
		<link>http://www.chemspider.com/blog/nmrshiftdb-on-and-off-again.html/comment-page-1#comment-195147</link>
		<dc:creator>melle B.fouzia</dc:creator>
		<pubDate>Wed, 28 Apr 2010 10:53:21 +0000</pubDate>
		<guid isPermaLink="false">http://www.chemspider.com/blog/?p=1711#comment-195147</guid>
		<description><![CDATA[Bonjour,
 je suis doctorante en sciences agronomiques, une partie de mon travail concerne l&#039;identification chimique de deux extraits polyphenolique et huile essentielle d&#039;une plante médicinale (Thymus vulgaris L.) j&#039;ai trois spectre pour chaque extrait (IR, RMN, CG-MS) mais je n&#039;arrive pas a interpréter ces spectres.
Pour cela je cherche l&#039;aide afin d&#039;identifier la composition chimique des extraits.
Dans l&#039;attente de votre réponse, veuillez agréer mes respectueuses salutations]]></description>
		<content:encoded><![CDATA[<p>Bonjour,<br />
 je suis doctorante en sciences agronomiques, une partie de mon travail concerne l&#8217;identification chimique de deux extraits polyphenolique et huile essentielle d&#8217;une plante médicinale (Thymus vulgaris L.) j&#8217;ai trois spectre pour chaque extrait (IR, RMN, CG-MS) mais je n&#8217;arrive pas a interpréter ces spectres.<br />
Pour cela je cherche l&#8217;aide afin d&#8217;identifier la composition chimique des extraits.<br />
Dans l&#8217;attente de votre réponse, veuillez agréer mes respectueuses salutations</p>
]]></content:encoded>
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		<title>By: Antony Williams</title>
		<link>http://www.chemspider.com/blog/nmrshiftdb-on-and-off-again.html/comment-page-1#comment-195146</link>
		<dc:creator>Antony Williams</dc:creator>
		<pubDate>Tue, 27 Apr 2010 13:54:17 +0000</pubDate>
		<guid isPermaLink="false">http://www.chemspider.com/blog/?p=1711#comment-195146</guid>
		<description><![CDATA[Based on my exchanges with Stefan Kuhn the issue was in the CDK. Stefan can probably give you details but I would expect it to be the SMILES parser.]]></description>
		<content:encoded><![CDATA[<p>Based on my exchanges with Stefan Kuhn the issue was in the CDK. Stefan can probably give you details but I would expect it to be the SMILES parser.</p>
]]></content:encoded>
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	<item>
		<title>By: Egon Willighagen</title>
		<link>http://www.chemspider.com/blog/nmrshiftdb-on-and-off-again.html/comment-page-1#comment-195145</link>
		<dc:creator>Egon Willighagen</dc:creator>
		<pubDate>Tue, 27 Apr 2010 13:50:39 +0000</pubDate>
		<guid isPermaLink="false">http://www.chemspider.com/blog/?p=1711#comment-195145</guid>
		<description><![CDATA[Can you elaborate on the double bond problem? Where was the double bond information lost? Or was it just the not taking into account cis/trans?]]></description>
		<content:encoded><![CDATA[<p>Can you elaborate on the double bond problem? Where was the double bond information lost? Or was it just the not taking into account cis/trans?</p>
]]></content:encoded>
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