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E/Z label bug
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Bob

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Link to postPosted: Mon Nov 23, 2009 5:57 pmPost subject: E/Z label bug Reply with quote

In the following structure, if the iPr group is contracted, Marvin 5.2.6 says that the double bond configuration is Z.  If the iPr group is expanded or ungrouped, it says that the double bond configuration is indeterminate.  It should give the same answer regardless of whether the group is expanded or contracted.  (In this case, indeterminate is a better answer.)

<?xml version="1.0" ?>
<cml>
<MDocument>
  <MChemicalStruct>
    <molecule molID="m1">
      <atomArray
          atomID="a1 a2 a3 a4 a5 a6 a7 a8"
          elementType="C C R C C C C H"
          sgroupRef="0 0 sg1 0 0 0 0 0"
          x2="-5.893644605745648 -4.353644605745648 -7.227323727573683 -6.29222593520353 -3.583644605745647 -3.9822259352035303 -2.043644605745648 -3.054269510378216"
          y2="-1.0398703531563447 -1.0398703531563447 -0.2698703531563442 0.4476554193288207 -2.3735494749843804 -3.861075247469546 -2.3735494749843804 0.0670046492278411"
          />
      <bondArray>
        <bond atomRefs2="a1 a2" order="2" />
        <bond atomRefs2="a1 a3" order="1">
          <bondStereo>W</bondStereo>
        </bond>
        <bond atomRefs2="a1 a4" order="1">
          <bondStereo>H</bondStereo>
        </bond>
        <bond atomRefs2="a2 a5" order="1">
          <bondStereo>W</bondStereo>
        </bond>
        <bond atomRefs2="a5 a6" order="1" />
        <bond atomRefs2="a5 a7" order="2" />
        <bond atomRefs2="a2 a8" order="1">
          <bondStereo>H</bondStereo>
        </bond>
      </bondArray>
      <molecule id="sg1" role="SuperatomSgroup" title="iPr" molID="m2">
        <atomArray
            atomID="a9 a10 a11"
            elementType="C C C"
            attachmentPoint="1 0 0"
            x2="-4.623343703044938 -5.957022824872972 -3.289664581216904"
            y2="-5.861316994712752 -5.091316994712753 -5.091316994712752"
            />
        <bondArray>
          <bond atomRefs2="a10 a9" order="1" />
          <bond atomRefs2="a9 a11" order="1" />
        </bondArray>
      </molecule>
    </molecule>
  </MChemicalStruct>
</MDocument>
</cml>
n style="font-family: Verdana, Arial, Helvetica, sans-serif;">
Akos
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Link to postPosted: Wed Nov 25, 2009 12:35 amPost subject: Reply with quote

Hi Bob,

I apologize for the late answer. There are two different problems:

1. AFAIK, wedge bond types are not taken into account in the determination of E-Z notaion. They are taken as single bonds, and only their position counts.

2. There is certainly an issue with SGroups, because until they are expanded, the indication of E or Z is wrong. We will investigate this problem and come back with more details soon.

Best regards,

Akos

Bob

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Link to postPosted: Wed Dec 02, 2009 10:57 pmPost subject: Reply with quote

Any chance you can give me an emergency build of Marvin with this shortcut groups bug fixed?  I have another exam in two weeks.

Akos
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Link to postPosted: Thu Dec 03, 2009 11:01 pmPost subject: Reply with quote

Hi Bob,

Hopefully we will release the 5.2.7 version sometimes next week.

Best regards,

Akos

Bob

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Link to postPosted: Fri Dec 04, 2009 4:47 pmPost subject: Reply with quote

Thanks, much appreciated.  Will the user-detachable sketcher window be reenabled in this version?  (See this discussion.)  

Volfi
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Link to postPosted: Mon Dec 07, 2009 5:33 pmPost subject: Reply with quote

Hi Bob,

Akos will return tomorrow.

But until know I let you know the info I have gathered.

We are focusing on the Marvin 5.3 release so it seems that the other problem will not be fixed neither in 5.2.7 nor in 5.3.

Sorry for the bad news.

Andras

Bob

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Link to postPosted: Tue Dec 22, 2009 3:07 pmPost subject: Reply with quote

My final exam has come and gone, so I no longer have quite the same sense of urgency.  My next exam is in February.  I hope you will have both the E/Z bug fixed and the user-controlled sketcher window restored by then?

Tamas
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Link to postPosted: Tue Dec 22, 2009 5:57 pmPost subject: Reply with quote

I hope we can do it. We will review task priorities after the releasing 5.3 so I can be more specific after it.

Hans-Ulrich

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Link to postPosted: Fri Dec 25, 2009 2:19 pmPost subject: Reply with quote

Hi, I have questions here. I have loaded the mrv-file given above in MarvinSketch, see attached image.

What is the meaning of this structure representation ? Does it show the upper double bond from the side ?

Regards, Hans-Ulrich




 Filename: EZ-Problem02.png    Filesize: 4.31 KB    Viewed: 10852 Time(s)
 Description:  EZ problem
EZ-Problem02.png


Last edited by Hans-Ulrich on Sun Dec 27, 2009 9:23 pm; edited 1 time in total
Bob

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Link to postPosted: Sat Dec 26, 2009 5:46 pmPost subject: Reply with quote

A student drew this structure in response to a question.  The problem was that Marvin told the student that the stereochemistry was Z, but when the shortcut groups were ungrouped by JChem, JChem interpreted it as indeterminate. Marvin should have told the student that the stereochemistry was indeterminate.  I don't think the wedge bonds are relevant to the bug.

Hans-Ulrich

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Link to postPosted: Sun Dec 27, 2009 9:22 pmPost subject: Reply with quote

Hi Bob,

yes, the wedge bonds are not relevant to the bug. It's a problem of the sgroups.

To show this I have produced the image below. It shows the bug once more on the left side for the sgroup iPr. Replacing this iPr by Cl gives the indeterminate icon (?). Moving the Cl-atom down produces the Z-configuration and now (Z) is correctly shown.

I have tested other sgroups. With Et sometimes it works correctly, sometimes not. With larger sgroups it gets worse. But it's difficult to reproduce the results.

Regards, Hans-Ulrich





 Filename: EZ-Problem03.png    Filesize: 17.85 KB    Viewed: 10853 Time(s)
 Description:  Sgroups EZ problem
EZ-Problem03.png
Bob

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Link to postPosted: Thu Dec 31, 2009 3:16 amPost subject: Reply with quote

Tamas wrote:

I hope we can do it. We will review task priorities after the releasing 5.3 so I can be more specific after it.

Can you tell me the following:

(1) When will the E/Z shortcut group bug be fixed?  If not in Marvin 5.3.0, then when?

(2) When will the user-detachable sketcher window be restored?

I'm sorry to keep bugging you about them, but these two requests are both very high priority for me, even if they are not so important for your other users.

Gabor
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Link to postPosted: Thu Dec 31, 2009 7:19 amPost subject: Reply with quote

Dear Bob, Dear Hans-Ulrich,

 

Tamas and Akos are on holiday. They will be back next week.

 

Regards,

Gabor

Tamas
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Link to postPosted: Mon Jan 04, 2010 3:41 pmPost subject: Reply with quote

Now, I can not answer for your questions.

Currently we are focusing on Marvin 5.3.0. It will be released in a couple of days. Immediatelly after the release, we hold an internal meeting about tasks priorities for 5.3.1 and about the milestones for 5.4. After this meeting, I can tell you how your tasks are scheduled.

Bob

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Link to postPosted: Sun Jan 24, 2010 1:46 amPost subject: Reply with quote

What is the status of the E/Z bug fix?  It's very important for it to be correct for students.

Akos
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Link to postPosted: Mon Jan 25, 2010 3:16 pmPost subject: Reply with quote

Hi Bob,

Sorry for the late answer; this bug will be fixed in 5.3.1.

Best regards,

Akos

Akos
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Link to postPosted: Thu Feb 25, 2010 3:11 pmPost subject: Reply with quote

Hi Bob,

I would like to inform you that we had to make an urgent patch release that was named 5.3.1, therefore the fix promised in this topic will be included only in the patch release coming at the end of March (probably named 5.3.2).

Best regards,

Akos

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