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

Marek Maly marek.maly at ujep.cz
Tue Jun 18 09:47:32 PDT 2013

Dear Elaine,

thanks for the explanation.

Now I verified that if the input file is in MOL2 and I use all atom  
Chimera is able to show correct structure although if I try to use the  
original PDB
input file, Chimera still fails to show the right structure perhaps  
because of
the "bond"/connectivity complexity of this structure.

   Best wishes,


Dne Tue, 18 Jun 2013 18:49:39 +0200 Elaine Meng <meng at cgl.ucsf.edu>  

> Hi Marek,
> Just to add to Rebecca's answer, the problem is only that Chimera tries  
> to show the structure as ribbons.  You can simply show all atoms, as  
> Rebecca mentioned (for example: Presets… Interactive 2 (all atoms)), or  
> change the preferences to show all atoms when you open a structure  
> (Favorites… Preferences, category: New Molecules, set "smart initial  
> display" to "false", Save if you want it to apply to later uses of  
> Chimera).   The smart initial display wasn't smart about this graphene  
> fragment, probably because the carbons are named CA, like amino acid  
> alpha-carbons.
> However, without smart initial display you will just get (initially) all  
> atoms without any color-coding, so you might prefer to leave it on,  
> especially if you often view macromolecules.
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Jun 18, 2013, at 9:23 AM, "R.J. Swett" <rswett at chem.wayne.edu> wrote:
>> 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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