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

Marek Maly marek.maly at ujep.cz
Tue Jun 18 10:10:37 PDT 2013


Thanks, I already confirmed this however as I already answered
to Elaine, the problem with PDB input file still persists, but
I do not see it as some critical err of course.

   Best,

      Marek


Dne Tue, 18 Jun 2013 18:23:10 +0200 R.J. Swett <rswett at chem.wayne.edu>  
napsal/-a:

> 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
>>
>>
>>
>>
>>
>>
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>
>
>
>
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