Newman projections in Marvin Sketch

Hi...

I have some questions

I've seen that it's
possible to draw newman projections in Marvin JS (It even seems that
there is a library template for that and buttons !)

I've tried to
import those projections in Marvin sketch (desktop version for Mac, last
version) but either the circle of the Newman proj disapears, or it
masks all the lateral bonds(as if it was in front of the molecule and
not between the two alligned carbons.

I need to draw newman projs and to copy them to illustrate my chemistry lessons...

Is it possible to get a Template library of Newman projections for Marvin Sketch?

Thanks for your help..

Pierre

Hi Pierre,

Sorry for the late reply. Could you send me a picture please what kind of Newman projection would you like to see, in which way?

Best regards,

Efi

Hi Efi

Thanks for your answer.

what I found to work is the Marvin JS at the web adress:

http://epoch.uky.edu/ace/public/rotateDihedral.jsp?prefersJava=false

Here you find those buttons and those 4  Newman proj (newman staggered 1 and 2 and eclipsed 1 and 2) would be of great use for me...  (by the way, the perspective staggered and eclipsed as well as the left and right chairs would be great too!! :-)

When I chose for example Newman staggered, I get this (which would be perfect!):

I export that (copying the source from the page into my Marvin sketch (downloaded the 15.3.16 version by the way...) and I get this:

 The disk seems to be in front of all the C-CH bonds!!)

I've tried the code below( found in one of your forums by... you (:-)  Posted: Wed Feb 22, 2012 11:21 pm (topic:atoms and graphical lines):

<?xml version="1.0"?>
<cml version="ChemAxon file format v5.9.0, generated by v5.9.0">
<MDocument>
  <MEllipse id="o1">
    <MPoint x="0.3876398474121192" y="0.3632200762939526"/>
    <MPoint x="1.2401404053115943" y="0.3632200762939526"/>
    <MPoint x="1.2401404053115943" y="-0.5167797997283863"/>
    <MPoint x="0.3876398474121192" y="-0.5167797997283863"/>
  </MEllipse>
  <MChemicalStruct>
    <molecule molID="m1">
     
<atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8" elementType="C C H H H H
H H" mrvValence="- 4 - - - - - -" mrvAlias="0 \u0020 0 0 0 0 0 0"
x3="0.8087771078644337 0.778953468886725 2.2327964279558
0.19126315920984283 -0.05881400725725234 -0.7000659902198645
1.341467350121369 1.5915444311062468" y3="-0.08431630646459229
-0.06754638265561996 -0.23561637913931413 1.2295029385099274
-1.2706340509846932 0.16625363410813046 -1.2988657160216701
1.2012712562660433" z3="0.9438075191826176 -0.6727702328477688
-1.2519898769599767 -1.3433562129609582 -1.2455952855297023
1.5230271450547614 1.6143934609408603 1.5166324700082723"/>
      <bondArray>
        <bond atomRefs2="a1 a2" order="1"/>
        <bond atomRefs2="a2 a3" order="1"/>
        <bond atomRefs2="a2 a4" order="1"/>
        <bond atomRefs2="a2 a5" order="1"/>
        <bond atomRefs2="a1 a6" order="1"/>
        <bond atomRefs2="a1 a7" order="1"/>
        <bond atomRefs2="a1 a8" order="1"/>
      </bondArray>
    </molecule>
  </MChemicalStruct>
</MDocument>
</cml>

and I get this in marvin sketch:

(the upper model was rotated in order to see that the disc is located on the C-C bond... but as you see this time we see all the CH bonds... even those behind the disk...

Can you help me?

Thanks forward for your answer:-)

Pierre

Hi Pierre,

There is a bug in MarvinSketch, that is why we display the graphical object on the top always.

On the page which you refers, there is a button under the editor "Switch to Java Applet", pressing this a MSketch applet opens, and you can reach the same template in MSketch compatible format. I think this is the best how you can have it in MSketch currently. I hope it helps, please let me know.

Thanks,

Efi

Hi, I can explain this. MarvinJS and MarvinSketch are not exactly equivalent. In particular, MarvinJS behaves differently with respect to objects on the z-axis than does MarvinSketch. In MarvinSketch, the circular graphical object either obscures all of the atoms with which it overlaps along the z axis, or it obscures none of them. In MarvinJS, the circular graphical object obscures only those atoms that have a z coordinate less than the circle. The latter behavior is obviously better.

If you switch to the MarvinSketch Java applet on the indicated page, you will see that it also shows some Newman projections. Here, I was able to obscure the C atom in the back of the Newman projection by giving it an alias of a space character. Unfortunately, a fairly recent bug in MarvinSketch means that the bonds around the space character are no longer being obscured properly; instead, "bloody stumps" appear where the bonds should be obscured.

I'm attaching the files that contain the templates for MarvinJS (3DTemplatesMJS.mrv) and for MarvinSketch (ACENewmanProjs.mrv). To invoke the templates for MarvinSketch on a Web page, use:

msketch_param('ttmpls0', '*Generic*chemaxon/marvin/templates/ACENewmanProjs.mrv');

where ACENewmanProjs.mrv is located in marvin/chemaxon/marvin/templates/. To invoke the templates for MarvinJS, include the following in the <iframe> invocation:

data-templateurl="templates/3DTemplatesMJS.mrv"

 where 3DTemplatesMJS.mrv is located in marvinJS/templates/.

In the latest version of MarvinSketch, 15.3.23.0, the bloody stumps have shrunk to the point of being negligible.

Hi Bob,

I have also checked the files, the problem with the version for MarvinSketch is that there are atom set ids in the mrv for the "hidden" atoms, and that is why the bonds connecting to those atoms gets partly red, since they get colored with the color for the atom set, and because the MDocument tag does not define the color for the atomset MarvinSketch use the default red color (for the 1st atom set it is red, and the file defines the atom to be in the 1st atom set).

So if you change the mrv and delete all atom set information, the red parts of the bonds in the background will be colored black also.

Regards,
Istvan 

Yes, that solved the problem! The Newman projections are still not perfect, because the back bonds that should be obscured by the circle are still a little bit visible, but it's definitely better than it was.

The optimal solution would be for the circle to be able to obscure atoms and bonds behind it and to reveal atom and bonds in front of it, just like happens in MarvinJS.

Hey...

interested in your discussion...

I opened the mrv in smultron...

My question: how do you "delete all atom set in the MRV" please?

deleting which information in the line:

<MDocument atomSetRGB="0:D,1:D" atomSetFont="1:SansSerif-PLAIN-16" bondSetRGB="0:N">

??

Thanks for your explanation

Pierre.

In the file ACENewmanProjs.mrv, delete the lines beginning with mrvSetSeq. 

By the way...

when I copy my projection with substituents changed from H to diverse atoms in pages for mac,(pages 9 version 4.3)

I get the projection but not the atom symbols at the end of the bonds... is that also a usual problem?

(what I need actually is to create Newman projections to copy them in documents (exams and exercices to give to my students...)

someone can help?

Thanks anyway :-)

Pierre

Same problem with copying into MS Word. Appears to be a bug. Workaround: take a screen shot of your MarvinSketch drawing, then paste the image into your document. Drawback of workaround: doesn't allow you to paste the structure back into MarvinSketch to edit it.

The problem also exists with the java applet ...

hope that it will be solved (with the " bloody stumps problem") in a future release of Msketch?

Thanks  for your help and rapid answers :-)

Pierre

Indeed it seems to be a bug in the copied data on Mac, we will check this soon, and we will try to fix it fast.

Thank you for  reporting it, we are quite in the middle of heavy code changes, inside the painting algorithms, to make it extendable with new features we would like to implement in the near future, and these kind of regressions unfortunatelly occur with the new tools and techniques we are starting to use. This one we did not noticed yet, so I have added a ticket into our issue tracker about it, and we will notify you in this topic if it has been fixed.

Bob, thank you for the workaround suggestion!

Regards,
Istvan 

Will wait patiently for the next releases... thanks bob for the "workaround" they will help until then :-)

Istvan, what is priceless is not getting a "flawless" software when you guys are trying to make it better, but knowing  that you  are working hard to get it better and better, trying to listen to users in the process...

Thanks for your work

Pierre

Hello,

I am happy to inform you that the pdf copy with label issue is fixed and will be released in version 15.4.27

Best regards,

Efi

Confirmed that the fix is in version 15.4.27, and it now works properly.