I just made a simple VBA-based workbook that downloads the images for a list of compounds. Please take a look whether this fits your needs: https://drive.google.com/file/d/0B5ln9gFZnHD4a080a0JqX19aRkk/viewBy default, it downloads the png files to the same folder where the workbook is.Hope it helps,Jordi
I think this is another interesting example. I think it is worth compiling all kinds of non-sense cases that we find in PubChem (or via PubChem) during this course, giving explanations that make sense out of them, and sharing with the chemical education community. It would be a very interesting work.
By the way, I am not going to tell you my answer for a while so that other people can enjoy this quiz, too.
The limit of WEBSERVICE/IMPORTDATA calls can be overcome by using some programming.
It is not super-easy but I have an example in Google Sheets here: https://docs.google.com/spreadsheets/d/1KUV3kbNWZ-ED57-E-J-J1MMOim1ljmz_MyaFuae6QUg/copy
Best,
Jordi
This question arised some days in a different TLO and I made a work-around in VBA for Excel. You may want to check it here: https://drive.google.com/file/d/0B5ln9gFZnHD4a0RtWWJCdWpKclE/viewBest,Jordi
`In the problem where we remove a hydrogen from the carboxylic acid and add it to the amine end of an amino acid to form a zwitterion, we can easily do this with the bond table, but the XYZ coordinates are off. Is there a way we can "see" where the coordinate of an atom are, and then adjust them?
I see we can "right click" and see the axis, but could we right click on an atom, and see its coordinates? It seems like that might be an option in "set picking"/"pick atom", but they do not seem to be active
Also, is the "optimize structure" option disabled?
Cheers,
Bob
This is just a follow-up on my previous JSME note. This is a test page that puts a smiles query string ( | delimited ) quickly into JSME depict. Not the # must be URL encoded in the string to %23. This capability is now part of the JSME installation.
By the way, this test page generates a bunch of default structures if you do not include a query string. Feel free to play:
http://chemagic.org/molecules/JSMEdepict.htm?smis=CCCC|C/C=C\C|C%23C|C1=CC=CC(O)=C1
Otis
JSME is also a thought here. JSME allows the pasting of a SMILES into the interface to produce a structure in the editor.
On a broader note, both JMSE and Jmol are cheminformatics powerhouses. Put them together into a single browser app, and you have a real power tool. Writing such a power tool for a specific course spreadsheet would make an excellent project.
Also note that Jmol can compare 2 SMILES from different sources and determing match/no-match.
Otis
Students -- now that you are getting acquainted with how to get chemical information, I have a question for discussion:
What is the pKa of aniline?
Provide us your source as a link. Tell us how that number makes chemical sense.
:)
Alternatively you can store the SDF in a column.
I tried this and it works fine and then copy and paste into Jmol or into the JSmol console...
I had the same problem recently. Our stockroom manager gave me an Excel sheet with all of our chemicals listed. I needed a set of unknowns and also was interested in proofing the list for spelling. I found the best way was to move that to a Google Sheet and use a links such as =IMAGE("https://cactus.nci.nih.gov/chemical/structure/" & substitute(A2," ","%20") & "/image") -- which I learned how to do here, by the way! That worked great. There were about 950 structures. They did finally come in, but it was not fast. Fortunately, I wasn't in a hurry, either. Didn't seem to be an issue with a limit of 50 for whatever reason. Maybe because different times I would open it I would get more. Or perhaps the 50-hit limit is not strictly enforced. Just now I opened it up, structures are flooding in, and way more than 50 structures are present. What I see is a series of calls that look like this:
https://docs.google.com/a/stolaf.edu/spreadsheets/d/1Czpe-yyZla0t1wxDvrTiXEmz5bg-5MgxG6bCovQ/externaldata/fetchData
so perhaps it is a limit of 50 for each of those. Don't know....