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

Eric Pettersen pett at cgl.ucsf.edu
Tue Jun 18 10:58:05 PDT 2013

Hi Marek,
	The reason the PDB doesn't work right is because you are using ATOM records and are also putting each carbon in a separate residue.  ATOM records are for standard polymeric residues and therefore Chimera tries to form a "chain", as much as it can, between adjacent "residues".  If you change the PDB file to all be one residue, Chimera handles it fine.  I've attached such a PDB file.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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On Jun 18, 2013, at 9:47 AM, "Marek Maly" <marek.maly at ujep.cz> wrote:

> Dear Elaine,
> thanks for the explanation.
> Now I verified that if the input file is in MOL2 and I use all atom representation
> 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,
>      Marek
> Dne Tue, 18 Jun 2013 18:49:39 +0200 Elaine Meng <meng at cgl.ucsf.edu> napsal/-a:
>> 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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