Hi Thomas,
thank you very much for the answer, I'm beginning to understand the
actual problem now.
dss state=1
helps, but it changes the problem: I would like to see the secondary
structure that corresponds to the single snapshot. When I use dss
state=1, I just see the secondary structure of the first snapshot in all
snapshots.
Is there a way to calculate the secondary structure for each individual
snapshot stored in this single .pdb file?
Cheers,
Alexander
Am Mittwoch, den 26.10.2011, 12:18 +0200 schrieb Thomas Holder:
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
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