Viewing 3D molecules in 2D in MarvinView

When I load a 3D molecule into MarvinView, I have the following choices:





(1) Display in 3D, which allows the molecule to be rotated by the user.


(2) Display in 2D, which does not preserve the 3D perspective.





I want to be able to display the molecule as a projection onto the Z plane (3D perspective), but I don't want the user to be able to rotate the molecule. Any suggestions?

Dear Bob,


I do not understand exactly what your problem is with the displaying of 3D molecules.


Can you explain it in more details?

Consider this compound:

Code:

Marvin  03260508123D  18 18  0  0  0  0            999 V2000    -0.3721   -0.2451    1.4302 C   0  0  0  0  0  0  0  0  0  0  0  0     1.0632   -0.5292    0.9129 C   0  0  0  0  0  0  0  0  0  0  0  0     1.4188    0.3815   -0.2924 C   0  0  0  0  0  0  0  0  0  0  0  0     0.3721    0.2451   -1.4302 C   0  0  0  0  0  0  0  0  0  0  0  0    -1.0632    0.5292   -0.9129 C   0  0  0  0  0  0  0  0  0  0  0  0    -1.4188   -0.3815    0.2924 C   0  0  0  0  0  0  0  0  0  0  0  0    -0.6168   -0.9288    2.2462 H   0  0  0  0  0  0  0  0  0  0  0  0    -0.4137    0.7692    1.8380 H   0  0  0  0  0  0  0  0  0  0  0  0     1.7862   -0.3814    1.7183 H   0  0  0  0  0  0  0  0  0  0  0  0     1.1346   -1.5769    0.6060 H   0  0  0  0  0  0  0  0  0  0  0  0     2.4134    0.1315   -0.6684 H   0  0  0  0  0  0  0  0  0  0  0  0     1.4543    1.4229    0.0413 H   0  0  0  0  0  0  0  0  0  0  0  0     0.6168    0.9288   -2.2462 H   0  0  0  0  0  0  0  0  0  0  0  0     0.4137   -0.7692   -1.8380 H   0  0  0  0  0  0  0  0  0  0  0  0    -1.7862    0.3814   -1.7183 H   0  0  0  0  0  0  0  0  0  0  0  0    -1.1346    1.5769   -0.6060 H   0  0  0  0  0  0  0  0  0  0  0  0    -1.4543   -1.4229   -0.0413 H   0  0  0  0  0  0  0  0  0  0  0  0    -2.4134   -0.1315    0.6684 H   0  0  0  0  0  0  0  0  0  0  0  0   1  2  1  0  0  0  0   1  6  1  0  0  0  0   2  3  1  0  0  0  0   3  4  1  0  0  0  0   4  5  1  0  0  0  0   5  6  1  0  0  0  0   1  7  1  0  0  0  0   1  8  1  0  0  0  0   2  9  1  0  0  0  0   2 10  1  0  0  0  0   3 11  1  0  0  0  0   3 12  1  0  0  0  0   4 13  1  0  0  0  0   4 14  1  0  0  0  0   5 15  1  0  0  0  0   5 16  1  0  0  0  0   6 17  1  0  0  0  0   6 18  1  0  0  0  0 M  END

If I choose to display it in View 3D mode, I can rotate it around. If I choose to display it in View 2D mode, it looks like a flat structure -- a perfect hexagon with the H atoms sticking straight out. I want to display it like it looks in the 3D mode, but without the ability to rotate it. What I don't understand is why View 2D mode discards all the xy coordinate information when it displays the structure.





Another way of saying it: I want View 2D mode to look like the MarvinSketch view.

Hi Bob,


Tamas is off (it is holiday in Hungary today) so I am trying to help, but this is not clear for me either.

bobgr wrote:

If I choose to display it in View 3D mode, I can rotate it around. If I choose to display it in View 2D mode, it looks like a flat structure -- a perfect hexagon with the H atoms sticking straight out.

I attached the picture that I see without rotation.


I don't know what you mean by "2D mode", but if you set the navmode parameter to (for example) "zoom", then the structure will not rotate at mouse dragging.

bobgr wrote:

I want to display it like it looks in the 3D mode, but without the ability to rotate it. What I don't understand is why View 2D mode discards all the xy coordinate information when it displays the structure.

The structure is projected on the xy plane. (This projection is the most obvious.)

bobgr wrote:

Another way of saying it: I want View 2D mode to look like the MarvinSketch view.

I see the same view using both applications.

Ferenc wrote:

I don't know what you mean by "2D mode"

I mean, in MarvinSketch, choose View -> Open 2D Viewer. If you choose this option with the structure below, you will see a hexagon with C-H bonds sticking out. It won't look at all like a chair.

Ferenc wrote:

but if you set the navmode parameter to (for example) "zoom", then the structure will not rotate at mouse dragging.

Ah, that's helpful. It can't be set from the user interface, so I didn't know about it. You need one more value for navmode, though: off. But I guess we can use zoom or translate as a stopgap measure.





Happy holiday.

bobgr wrote:

It can't be set from the user interface, so I didn't know about it.

In the GUI of the present version, the same choices are available at the Move option of the pop-up menu.