1. Fall 2015 Course
  2. Discussion

Discussion

Sunghwan Kim | Thu, 11/05/2015 - 10:25
Just in case some people are not familiar with comparing a long list of compounds with another, I've uploaded a file named "Similarity Search Comparison.pdf" that illustrates how this task can be done using "search histories". Like many other databases, PubChem automatically stores your search results as a "history". By using these histories (in conjunction with operators such as AND, OR, NOT), you can combine results from different searches. The file is available at the bottom of this page (<a href="http://olcc.ccce.divched.org/2015OLCCModule6TLO2">http://olcc.ccce.divched.org/2015OLCCModule6TLO2</a>)

Sunghwan Kim | Thu, 11/05/2015 - 09:16
Please compare 3-D similarity search results with each of the 2-D similarity search results at different thresholds.

Judat Yazigi (not verified) | Thu, 11/05/2015 - 08:51
For question 4, when we're comparing the 3-D and 2-D similarity, do we compare all the different threshold (95%,90%,85%,80%) to the 3-D similarity or do we just pick one and compare???

Sunghwan Kim | Thu, 11/05/2015 - 08:35
I've fixed the link. Thank you for notifying us of the error.

John Turner (not verified) | Thu, 11/05/2015 - 08:17
For the second question the link is incomplete. The text suggest its attempting to go to <a href="https://pubchem.ncbi.nlm.nih.gov/search/search.cgi">https://pubchem.ncbi.nlm.nih.gov/search/search.cgi</a> however the search/search.cgi is not included so the link instead goes to <a href="https://pubchem.ncbi.nlm.nih.gov">https://pubchem.ncbi.nlm.nih.gov</a>

Robert Belford's picture
Robert Belford | Wed, 11/04/2015 - 16:23
All, In response to this comment David Sharpe of RSC has added a bit to this module on ChemSpider Spectra searches that I think everyone should look at, play around with, and comment on. Although it is embedded into this page, you have to click on the link 7.2.1:ChemSpider Spectra Search to see the full post, and comment directly on it. Here is the direct link, <a href="http://olcc.ccce.divched.org/2015FallOLCCM7P1TLO5">http://olcc.ccce.divched.org/2015FallOLCCM7P1TLO5</a> Cheers, Bob

OLCC s12's picture
OLCC s12 | Tue, 11/03/2015 - 23:02
I went to the ChemSpider Spectral page that was listed in this section to access all of the spectral data and it did not work after entering my token. Im interested in seeing how the response code looks in the API service. Would this be something that may need to be approved by the site administrators to use? Seems like it may use a lot of server resources in calling this API.

Robert Lancashire | Tue, 11/03/2015 - 18:17

Sarah,
If you are seeing the file data on screen are you able to then do a file save through Safari?
When I go to ChemSpider and click on a spectrum logo I get the option to display as the JSpecView Java application or the option above that which is for the JavaScript version which should run OK on the MAC.
The file should look something like...
##TITLE= a description
##JCAMP-DX= 5.0

...

##END=

Sarah House (not verified) | Tue, 11/03/2015 - 17:32
Hello, I am using a mac with safari as a browser. Every time I attempt to save the spectra data for one of the xylene isomers on chemspider it does not send it to my downloads or my documents, it just spits out a new web tab with a list of data. I don't know how to get it to actually save the spectra data in its original format to my computer.

Alex Williams (not verified) | Tue, 11/03/2015 - 12:38
Although it does cost, I believe MNova to be the best NMR software that is out there. It is really well produced, and its comparison tool will allow you to compare a predicted molecule to an experimental spectrum and tell you if there are any mismatched peaks. It even has a built in solvent database so it wont integrate peaks of said solvents!