MarvinSketch 5.3.x freezes while drawing 1-EF arrow

User 62a37f4796

24-08-2010 20:11:02

I don't really want to pour oil on the fire, but there's another serious error in the implementation of the new electron-flow arrow code.

I know the chemistry isn't correct in the following example, but bear with me.

In 5.2.4 I can draw a 1-electron flow arrow from F to Na (see the attached image).

When I try to do the same in 5.3.4 (or .5 or .6 or .7), the whole applet freezes up. In "phase 1" the image shows the arrow and destination. If you switch to a different window (like this browser to post a message), then back, it goes to "phase 2" where the arrow has magically disappeared. (see the second set of attached images).

None of the buttons on the applet itself will respond. Only the red X at upper right works, and prompts me if I want to save the structure before exiting.

Since the whole file/directory structure changed from 5.2.4 to 5.3.x I can't really readily revert to 5.2.4. Additionally, any files received in 5.3.x format are not interpretable by 5.2.4.

Does anyone have a suggestion how to get out from between this rock and a hard place?

Thanks,

Michiel

This happens on a local installation of MarvinSketch (XP SP3) as well as on our servers. It has been observed in IE8.06 and FF3.6 on Win boxes, and in FF3.6 and Safari4.x on OS/X. By my reckoning this is either an applet issue or a Java issue. Since 5.2.4 works under the same Java environment (1.6.0_21-b07 on my local machine) I figure it's not Java.

ChemAxon 990acf0dec

24-08-2010 21:13:28

Hi Michiel,

Thanks for the bug report. We will fix this together with the other electron-flow arrow issues soon.

Best regards,

Akos

ChemAxon 990acf0dec

26-08-2010 13:56:16

Hi Michiel,

We tried to reproduce the freeze of the applet (both with embedded and detached examples) on our site, but we cannot reproduce the freezing of the applet after switching between windows. Could you please tell us more details?

Could you also try this example:

https://www.chemaxon.com/devel/marvin/examples/applets/view/transfering.html

Double-click on any of the structure to open it in a detached MSketch, delete the structure from it, and draw your example there. Can you reproduce the freeze with it? We could not...

Best regards,

Akos

User 62a37f4796

26-08-2010 15:53:57

akospapp wrote:

Hi Michiel,

We tried to reproduce the freeze of the applet (both with embedded and detached examples) on our site, but we cannot reproduce the freezing of the applet after switching between windows. Could you please tell us more details?

Could you also try this example:

https://www.chemaxon.com/devel/marvin/examples/applets/view/transfering.html

Double-click on any of the structure to open it in a detached MSketch, delete the structure from it, and draw your example there. Can you reproduce the freeze with it? We could not...

Best regards,

Akos

The arrow doesn't seem to freeze there, but I do get a stack trace error when I try to save it ...

When I pulled the About it said 5.3.7beta1, which is not any one of the versions I checked.

The freezing actually occurs without any need to switch windows. If you try to "move" an electon from a F atom to a Na atom, it will stop dead in its tracks right there with the destination circle still visible.

Let me refine that: if you only have an Na and an F atom on the canvas it works just fine.

If you add 1 radical to Na and 3 lone pairs + 1 radical to F, it triggers the freeze. ... some incompatibility between a 1 electron problem and a 1 electron-flow arrow?

I did note that you have autocalc lone pairs on on your website, whereas we always have it switched off. Possibly another difference to investigate.

After you switch windows back and forth, the arrow has disappeared but the frozen state stays. I've let it run as long as 30 min, and it doesn't come back, so it doesn't look like a Java load issue.

Does that give you any pointers?

Michiel

User 62a37f4796

26-08-2010 17:03:20

I can't seem to post more than 3 images at a time.