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August 23, 2019

Lookup Molecule Problems (Ongoing)... Log Out | Topics | Search
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Soren Eustis
Unregistered guest
Posted on Wednesday, March 16, 2016 - 10:19 pm:   

The lookup molecules feature was a fantastic addition to WebMO. However, some time after it was introduced, a WebMO or Java update broke it.

For some time now, we have been getting the "Error: could not resolve molecular structure" message with any input we have tried (see attachments).

I believe this was once thought to be an issue on the NIH(?) server. Is there a problem with the database or is this a known WebMO issue?

v. 16.0e

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JR Schmidt
Moderator
Username: Schmidt

Post Number: 496
Registered: 11-2006
Posted on Wednesday, March 16, 2016 - 10:24 pm:   

Odd. Seems to be working fine everywhere I test, including the Working Demo. Maybe try the demo and see if it works for you.

Are your running up-to-date WebMO 16?
Soren Eustis
Unregistered guest
Posted on Saturday, March 19, 2016 - 2:56 pm:   

JR,

It does work for me there. It seems that this problem is something site specific, as everyone using our WebMO (v 16.0.005e, btw) sees this error. My recollection is that it failed shortly after it was introduced here. I noticed when I went to your demo site, it did work, but it had me accept a security warning (Java) that I do not remember seeing. Is it possible that some sort of campus site restriction is preventing the external query here at Bowdoin?

This feature was like a dream come true for teaching. The students find a significant hurdle to finding and uploading the structures they want to play around with. The error for them is just kind of deflating, and they turn back to their twitter feed, etc.

Authorization screen just seen for demo server lookup.  This might be simply because it is a new host, but I do not recall seeing this particular warning for our server.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 497
Registered: 11-2006
Posted on Saturday, March 19, 2016 - 2:58 pm:   

Soren,

Two comments:
1) Are you running your WebMO installation of SSL/HTTPS?
2) If so, upgrade to the newest version of WebMO 16.1. There were issues related to the NIH lookup when running over HTTPS, related to changes at NIH. These are fixed in 16.1.
Soren Eustis
Unregistered guest
Posted on Saturday, March 19, 2016 - 2:58 pm:   

JR: As a related issue, I would find it super helpful if the minor releases were documented on WebMO.net. I know it would cut down on a lot of questions as well.

My $0.02.
Soren Eustis
Unregistered guest
Posted on Saturday, March 19, 2016 - 3:00 pm:   

Yes! That is it! We run everything with as many 'S' features as possible. I will forward this info to our HPC Director. Thanks!
John Keller
Unregistered guest
Posted on Wednesday, July 06, 2016 - 9:39 pm:   

Don't want to pay $$$ to upgrade to v 16 just to fix this problem?
Use a text editor to change "http" to "https" in line 53 of build_molecule.html of WEbMO v 15.
Anonymous
 
Posted on Tuesday, August 21, 2018 - 1:55 pm:   

Lookup Molecule by name is not working on the demo site, or our webmo 17. Can the lookup website(s) be tested independently from webmo?
JR Schmidt
Moderator
Username: Schmidt

Post Number: 618
Registered: 11-2006
Posted on Tuesday, August 21, 2018 - 1:58 pm:   

The NIH Cactus Resolver changed their server configuration. I have a workaround, but it will take a bit of time to deploy.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 619
Registered: 11-2006
Posted on Tuesday, August 21, 2018 - 2:17 pm:   

OK, this is resolved in 18.1.002, available for download.
Anonymous
 
Posted on Tuesday, August 21, 2018 - 2:33 pm:   

For those of us still back in in the stoneage (v. 17), can you reveal the file to be edited in the workaround?
JR Schmidt
Moderator
Username: Schmidt

Post Number: 620
Registered: 11-2006
Posted on Tuesday, August 21, 2018 - 2:54 pm:   

Unfortunately the changes requires a new version of the compiled editor, which is not human readable / editable; it is not a simple change to HTML or human readable javascript.

FYI the issue has to do with changes to NIH's API for molecule lookup. They replaced an API call with a newer version. While the older version remains it place, it now (appears) to return the molecule in a random/unpredictable file format!
Anonymous
 
Posted on Sunday, September 16, 2018 - 2:09 pm:   

Hooray! Lookup by Name is now functioning correctly with the default settings of WebMO v. 17.0.012e. No changes have been made at our end, so something must have happened at the NIH site.
Anonymous
 
Posted on Sunday, September 16, 2018 - 6:19 pm:   

Yes, It works! Thank you NIH (and WebMO)!

Here's "aspirin":

aspirin

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