User 870ab5b546
25-08-2005 15:48:15
Please observe this behavior.
1. Go to http://epoch.chem.uky.edu/marvin.html. (It's Marvin 4.0 alpha4, but the same behavior happens with Marvin 3.5.5.)
2. Choose Insert -> Template -> Conformer
3. Choose the third or fourth structure and paste it.
4. Choose Edit -> Source, and select Format -> MDL Molfile. Note the 2D at the end of the first line. I assure you that the template file has a 3D there.
5. Choose File -> Import. Note how the structure shrinks!
6. Choose Edit -> Source again. Note the 3D now at the end of the line.
7. Now choose Edit -> Clean -> 3D.
8. Erase the structure.
9. Repeat 3-5. Note how this time the structure does NOT shrink.
10. Now choose Edit -> Clean -> 2D and repeat 3-5. Original behavior!
How do I get Marvin to initiate in the Clean -> 3D state, so structures don't shrink?
Interesting enough, if after step 3, I copy the structure, paste it into your Marvin 4.0 demo at http://www.chemaxon.com/demosite/marvin/index.html, and do steps 4-5, the structure grows instead of shrinking! Go figure.
1. Go to http://epoch.chem.uky.edu/marvin.html. (It's Marvin 4.0 alpha4, but the same behavior happens with Marvin 3.5.5.)
2. Choose Insert -> Template -> Conformer
3. Choose the third or fourth structure and paste it.
4. Choose Edit -> Source, and select Format -> MDL Molfile. Note the 2D at the end of the first line. I assure you that the template file has a 3D there.
5. Choose File -> Import. Note how the structure shrinks!
6. Choose Edit -> Source again. Note the 3D now at the end of the line.
7. Now choose Edit -> Clean -> 3D.
8. Erase the structure.
9. Repeat 3-5. Note how this time the structure does NOT shrink.
10. Now choose Edit -> Clean -> 2D and repeat 3-5. Original behavior!
How do I get Marvin to initiate in the Clean -> 3D state, so structures don't shrink?
Interesting enough, if after step 3, I copy the structure, paste it into your Marvin 4.0 demo at http://www.chemaxon.com/demosite/marvin/index.html, and do steps 4-5, the structure grows instead of shrinking! Go figure.