Re: [PyMOL] Pymol visualization problem

[Martin H. <ma...@bl...>]

Hi Abida
Is it possible that you have multiple states in your PDB file? Try 
clicking the ">" arrow in the bottom right corner of PyMOL and see if 
you can display the other protein. If so, you probably need to delete 
the "MODEL" and "END" from your PDB file. Then all should appear at once.

Martin





On 08.01.13 06:12, Abida Siddiqa wrote:
> Hello,
>
> I have docked one protein named 'L1'( 450 amino acid)  with another protein
> named 'E2'(68 amino acid, Chain A) and used  pymol-v1.3r1-edu-Win32.msi to visualize
> the complex. my system is  windows 7 , 64 bit. The problem is, i am unable
> to see the sequence of 'E2' protein and so as its structure. In order to
> confirm, if it is docking problem or visualization problem, i have used
>   swiss pdb viewer. it has shown me sequence and structure of both proteins. i
> wonder why can not i see it in pymol.
> secondly, i docked L1 and E2 ( this time used chain A and B of it), and
> visualized the complex in pymol. i was only able to see L1, and chain A of
> E2 (both chain A and B are alike).  Then in order to see if it is docking
> error or visualization error, i rendered the complex in swiss pdb viwer and
>   saw the L1 and E2 (both chain A and B).
> Thirdly, i changed the docking software and generated a complex using
> another software, this time i still was unable to visualize complete complex
> in pymol.
> Any help will be much appreciated.
> Kind regards
> Abida
>
>
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