JME to JSMol (2d-->3D) fails to load the coordinate file

NIH CADD service https://cactus.nci.nih.gov/ went down. This functionality
should work when it returns.

On Fri, Oct 30, 2020 at 6:33 PM Eduard Bitto ebitto@users.sourceforge.net
wrote:

---

• [bugs:#617] https://sourceforge.net/p/jmol/bugs/617/ JME to JSMol
  (2d-->3D) fails to load the coordinate file*

Status: open
Group: v14
Created: Fri Oct 30, 2020 11:33 PM UTC by Eduard Bitto
Last Updated: Fri Oct 30, 2020 11:33 PM UTC
Owner: nobody
Attachments:

• Screen Shot 2020-10-30 at 19.31.26.png
  https://sourceforge.net/p/jmol/bugs/617/attachment/Screen%20Shot%202020-10-30%20at%2019.31.26.png
  (255.0 kB; image/png)

Hi,
As of Oct 30th 2020 I noticed that JME to JSMol communication fails. Quick
demonstration of the problem can be done using "
https://chemapps.stolaf.edu/jmol/jsmol/hackamol.htm" with cyclopentane.
Attempt to generate a 3D model leads to following error message:

script ERROR: unrecognized file format for filehttps://cactus.nci.nih.gov/chemical/structure/C1CCCCC1/file?format=sdf&get3d=true
NetworkError: Failed to execute 'send' on 'XMLHttpRequest': Failed to load 'https://cactus.nci.nih.gov/chemical/structure/C1CCCCC1/file?format=sdf&get3d=true'.

It seems NCI changed something on their end, as this type of action worked
fine until several days ago.

The link in the error message returns following file, so the NCI server is
fine.

C6H12APtclcactv10302016003D 0 0.00000 0.00000

18 18 0 0 0 0 0 0 0 0999 V2000
0.0335 -1.4421 0.2550 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2321 -0.7501 -0.2550 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2657 0.6920 0.2550 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0335 1.4421 -0.2550 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2321 0.7501 0.2550 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2657 -0.6920 -0.2550 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0335 -1.4421 1.3450 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0574 -2.4695 -0.1083 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.2321 -0.7501 -1.3450 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.1100 -1.2844 0.1083 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.1673 1.1851 -0.1083 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.2657 0.6920 1.3450 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0335 1.4421 -1.3450 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0574 2.4695 0.1083 H 0 0 0 0 0 0 0 0 0 0 0 0
2.1100 1.2844 -0.1083 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2321 0.7501 1.3450 H 0 0 0 0 0 0 0 0 0 0 0 0
2.1673 -1.1851 0.1083 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2657 -0.6920 -1.3450 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
1 6 1 0 0 0 0
1 7 1 0 0 0 0
1 8 1 0 0 0 0
2 9 1 0 0 0 0
2 10 1 0 0 0 0
3 11 1 0 0 0 0
3 12 1 0 0 0 0
4 13 1 0 0 0 0
4 14 1 0 0 0 0
5 15 1 0 0 0 0
5 16 1 0 0 0 0
6 17 1 0 0 0 0
6 18 1 0 0 0 0M END
$$$$

When this file is saved as *.mol and loaded locally to JSMol, structure
shows up fine, so the problem seems to be in the parsing during the
Jmol.show2d(jmol, true).
I hope this is enough information for initial diagnostics.

Thank you for all your work!

EB.

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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

We stand on the homelands of the Wahpekute Band of the Dakota Nation. We
honor with gratitude the people who have stewarded the land throughout the
generations and their ongoing contributions to this region. We acknowledge
the ongoing injustices that we have committed against the Dakota Nation,
and we wish to interrupt this legacy, beginning with acts of healing and
honest storytelling about this place.

Dr.Hanson, thanks for looking into this, I had students using these tools for an assignment and ended up having a mailbox filled with franctic e-mails just before the deadline hour! I managed to give them a quick workaround by using load :smiles:xxx via a command line in the meantime. EB.