[Chimera-users] Chimeras limited capability to visualize correctly molecular structure

R.J. Swett rswett at chem.wayne.edu
Tue Jun 18 09:23:10 PDT 2013

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 at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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