Marek,
I had no problem opening the mol2 file, and displaying the atoms. I simply hid the ribbon structure,
displayed the atoms, and saved an image. There are some excellent tutorials on the chimera
website on visualization of structures which I'm sure will help you in the future. Chimera makes
more guesses on initial display than VMD or VegaZZ, and for protein structures this is very convenient.
I have attached an image generated with Chimera which you will see is nearly identical to yours.

R.J. Swett
Wayne State University
357 Chemistry
Detroit, MI 48201

Lab Phone 313-577-0552
Cell Phone 906-235-0768

On 6/18/2013 9:55 AM, Marek Maly wrote:

Hello all,

recently was sent to the Amber mailing list question about
how to proceed here with simulation of the piece of graphene.

I was just curious about the molecular structure so I tried
to visualize attached PDB file in Chimera which was not able to
show correct structure so I visualized it using VMD and also Vega ZZ
in both cases without any problem. Then I used Vega ZZ to create MOL2
file and tried again to use Chimera for visualizing graphene saved now
in MOL2 format but again without success.

So maybe there is still some space for improvement of Chimera visualizing
capability. Especially in case of MOL2 format I was surprised that Chimera
is not able to show correct molecular structure as in this case all the information
(including bonds/connectivity info) is included in the input file.

All files are attached.
(my version of Chimera is: candidate version 1.8 (build 38694))

Best wishes,

Marek
_______________________________________________
Chimera-users mailing list
Chimera-users@cgl.ucsf.edu
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users