electron-flow arrows, minor bug

If I have an atom that is at the front or end of an electron-flow arrow, and I draw another bond to that atom, the electron-flow arrow disappears. It should not.





Also, could you make the dashed line that shows an incipient bond resulting from an electron-flow arrow in gray instead of black? It is not conventional to show a dashed line; we need to show it for unambiguity's sake, but it should not be very prominent.

Quote:

f I have an atom that is at the front or end of an electron-flow arrow, and I draw another bond to that atom, the electron-flow arrow disappears. It should not.

Can you explain it more deeply? I do not understand which atom disappears? A snapshot would be very useful to understand the problem.

Quote:

Also, could you make the dashed line that shows an incipient bond resulting from an electron-flow arrow in gray instead of black? It is not conventional to show a dashed line; we need to show it for unambiguity's sake, but it should not be very prominent.

We will consider your request about gray incipient bonds.

Hm, can't seem to reproduce it now. I'll get back to you if it pops up again.

OK, here's an example. Start with this file:

Code:

<?xml version="1.0" ?> <MDocument>   <MEFlow arcAngle="171.0" headSkip="0.15" headLength="0.5" headWidth="0.4"           tailSkip="0.25">     <MAtomSetPoint atomRefs="m1.a7" />     <MAtomSetPoint atomRefs="m1.a7 m1.a8" />   </MEFlow>   <MChemicalStruct>     <molecule molID="m1">       <atomArray           atomID="a1 a2 a3 a4 a5 a6 a7 a8"           elementType="C C C C O C O H"           formalCharge="0 0 0 0 0 0 0 1"           x2="-11.42533556266691 -11.42533556266691 -10.091666221618652 -8.757996880570394 -10.091666221618652 -8.757996880570394 -8.757996880570394 -6.416666507720947"           y2="7.536683829749714 5.996649948631633 5.226633008072593 5.996649948631633 8.306700770308755 7.536683829749714 9.076683829749715 7.758333206176758"           />       <bondArray>         <bond atomRefs2="a5 a1" order="1" />         <bond atomRefs2="a5 a6" order="1" />         <bond atomRefs2="a1 a2" order="1" />         <bond atomRefs2="a2 a3" order="1" />         <bond atomRefs2="a3 a4" order="1" />         <bond atomRefs2="a4 a6" order="1" />         <bond atomRefs2="a6 a7" order="1" />       </bondArray>     </molecule>   </MChemicalStruct> </MDocument>

Now press the Cl button, click and hold on H⁺, and drag to change it to HCl. I get this:

Code:

<?xml version="1.0" ?> <MDocument>   <MChemicalStruct>     <molecule molID="m1">       <atomArray           atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9"           elementType="C C C C O C O H Cl"           formalCharge="0 0 0 0 0 0 0 1 0"           x2="-11.42533556266691 -11.42533556266691 -10.091666221618652 -8.757996880570394 -10.091666221618652 -8.757996880570394 -8.757996880570394 -6.416666507720947 -6.416666507720947"           y2="7.536683829749714 5.996649948631633 5.226633008072593 5.996649948631633 8.306700770308755 7.536683829749714 9.076683829749715 7.758333206176758 6.218333206176758"           />       <bondArray>         <bond atomRefs2="a5 a1" order="1" />         <bond atomRefs2="a5 a6" order="1" />         <bond atomRefs2="a1 a2" order="1" />         <bond atomRefs2="a2 a3" order="1" />         <bond atomRefs2="a3 a4" order="1" />         <bond atomRefs2="a4 a6" order="1" />         <bond atomRefs2="a6 a7" order="1" />         <bond atomRefs2="a8 a9" order="1" />       </bondArray>     </molecule>   </MChemicalStruct> </MDocument>

The electron-flow arrow has disappeared.





Oddly enough, if I copy the figure and paste it into a new window, then the electron-flow arrow DOESN'T disappear. ???!

Thanks for the bug report. We will fix it.

This bug is fixed.

Tamas wrote:

This bug is fixed.

Is the fix contained in JChem 3.1.7?

Next (major) Marvin / JChem release will include it.

bobgr wrote:

Also, could you make the dashed line that shows an incipient bond resulting from an electron-flow arrow in gray instead of black? It is not conventional to show a dashed line; we need to show it for unambiguity's sake, but it should not be very prominent.

I would like to modify this request. I would like the incipient bond to be invisible, *except* during mouseover over the electron-flow arrow, while drawing the electron-flow arrow, and during mouseover over the atom-atom axis; in these cases the incipient bond can be thin and gray or green or blue, maybe dashed (just so it doesn't look like an ordinary bond). This way, the picture is more consistent with the convention, in which the incipient bond is not drawn, but it is easy for the user to check that the electron-flow arrow is indeed pointing to the right place.

I have posted your request to Peti.