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<div class="moz-cite-prefix">Marek,<br>
I had no problem opening the mol2 file, and displaying the atoms.
I simply hid the ribbon structure, <br>
displayed the atoms, and saved an image. There are some excellent
tutorials on the chimera<br>
website on visualization of structures which I'm sure will help
you in the future. Chimera makes <br>
more guesses on initial display than VMD or VegaZZ, and for
protein structures this is very convenient.<br>
I have attached an image generated with Chimera which you will
see is nearly identical to yours. <br>
<pre class="moz-signature" cols="72">R.J. Swett
Wayne State University
357 Chemistry
Detroit, MI 48201
Lab Phone 313-577-0552
Cell Phone 906-235-0768</pre>
On 6/18/2013 9:55 AM, Marek Maly wrote:<br>
</div>
<blockquote cite="mid:op.wyvnndlylc8gdf@pocitadlon.ujep.cz"
type="cite">Hello all,
<br>
<br>
recently was sent to the Amber mailing list question about
<br>
how to proceed here with simulation of the piece of graphene.
<br>
<br>
I was just curious about the molecular structure so I tried
<br>
to visualize attached PDB file in Chimera which was not able to
<br>
show correct structure so I visualized it using VMD and also Vega
ZZ
<br>
in both cases without any problem. Then I used Vega ZZ to create
MOL2
<br>
file and tried again to use Chimera for visualizing graphene saved
now
<br>
in MOL2 format but again without success.
<br>
<br>
So maybe there is still some space for improvement of Chimera
visualizing
<br>
capability. Especially in case of MOL2 format I was surprised that
Chimera
<br>
is not able to show correct molecular structure as in this case
all the information
<br>
(including bonds/connectivity info) is included in the input file.
<br>
<br>
All files are attached.
<br>
(my version of Chimera is: candidate version 1.8 (build 38694))
<br>
<br>
Best wishes,
<br>
<br>
Marek
<br>
<br>
<br>
<br>
<br>
<br>
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<br>
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</blockquote>
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