C60 modeling

[baizq]

Hi，

Here is a question about the C₆₀ modeling: In VNL, how to align the centers of two opposite hexagons of a C₆₀ fullerene molecule along the z axis of cartesian coordinates?

Thanks in advance!
baizq

[Anders Blom]

1. Select all 6 atoms in the first hexagon. Click the "Centroid" tool to insert an atom in the middle of the hexagon.
2. Do the same thing for the second hexagon.
3. Select all atoms, then click the Move tool. Click the two newly inserted atoms (make them red) and then enter 0,0,1 for the vector between them in the Move tool widget.
4. Close the Move tool and delete the extra atoms.

[baizq]

Hi Anders,

Thanks a lot.

I have followed the first two steps. But I cannot select the inserted atoms on my machine. This is actually an old problem with choosing an atom by clicking it: it always deviate from the target one to another which I don't want to choose... This may be a machine-specific problem... Any idea how to solve it?

By the way, could you please kindly lend me a hand to align the molecule? I have attached the model processed after the first two steps(you can find two opposite hexagons with additional atoms in their center.). Thank you very much.

baizq

[Anders Blom]

Aligned! (I mean, attached! )

The issue about selection has been solved, it was a bug somewhere in an older version (12.2 I think). It should be fixed in 12.8. If I recall correctly, the bug only appears for click-selection, so you can perhaps work around it by using rectangle-drag-selection.

[baizq]

Hi Anders

There it is! Thank you very much for your kind help! 

Yeah, I am always using drag-selection... But under the Move tool widget, it seems that the rectangular-drag selection doesn't work...

baizq

[Anders Blom]

But you are seeing the click-select issue in 12.8? That's very odd, because I know precisely what triggered it and we fixed it, it was a rounding error.

[baizq]

Yes, I am currently using atk ver.12.8.0, but the clicking problem seems still there... 

[Anders Blom]

Can you make sure you are not actually using Builder in the preview 13.8? We just realized that indeed the fix has been unfixed in 13.8 (but we have time to fix that, fortunately), but it really should be fixed in 12.8.2 at least (can't speak 100% for 12.8.0 although the fix was made well ahead of release, so it should be fixed there too).

[baizq]

Hi Anders,

I've made a double-check and I am pretty sure that I am using 12.8.0 when I meet the problem. 

Actually the problem is only within the linux version. Earlier windows version (even as early as 11.2 or so) doesn't have such a problem.

baizq

[Anders Blom]

Apart from the odd fact that I really think this should be fixed, it is expected that the problem is new to 11.8. Also, it seems to be dependent on the driver; it appeared on my machine (under Windows) after updating the video driver once, so perhaps the first thing to check is that you have the latest video driver (although in my case the newer driver had the problem and the older not).

I will see if we can make some test that you can run which can tell us more about why the problem can appear on your system.

[baizq]

Hi Anders,

Yeah, this may be a machine-specific problem. I will try to upgrade the driver and see whether the problem is still there or not.

Thanks！
baizq