Re: [PyMOL] Pymol: Cartoon representation for .pdb file with multible entries

[Thomas H. <sp...@us...>]

Hi Alexander,

by default PyMOL recognized secondary structure as the minimum consensus 
over all states. So if a residue is not recognized as helix or sheet in 
_all_ states, it will be assigned as loop. You might be happy with this:

# type after loading the file
dss state=1

For detailed explanation what values are valid for the "state" argument 
see the PyMOLWiki page:
http://pymolwiki.org/index.php/Dss

Cheers,
   Thomas

On 10/26/2011 11:04 AM, Alexander Schulz wrote:
> Hi everyone,
>
> I'm quite new to Pymol and I hope that I don't ask something that has
> been answered several times before, but I didn't find anything about
> this topic that could solve my problem.
>
> I've prepared a .pdb file containing one protein at different times in
> the simulation. I'd like to prepare a video from this file, which is why
> I'd like to keep everything in one .pdb file.
>
> When I select "cartoon" as a representation, the backbone is visualized
> as a tibe (as always), but no secondary strucutres are recognized. When
> I copy one of the snaphots out of the .pdb and open in seperately, the
> secondary structure is shown correctly.
>
> How can I make Pymol show the structure of the multible states in one
> file correctly?
>
> Thanks in advance for answers!
>
> Cheers,
> Alexander

-- 
Thomas Holder
MPI for Developmental Biology