pymol-users

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

[Alexander S. <sc...@dw...>]

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

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

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

[Alexander S. <sc...@dw...>]

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
> 

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

[Robert C. <rob...@qu...>]

Hi Alexander,

On Wed, 2011-10-26 12:53  EDT,  Alexander Schulz
<sc...@dw...> wrote:

> 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?

Yes, simply load the pdb file with the "discrete=1" flag:

load md_file.pdb, discrete=1
dss md_file

Setting the "discrete" flag causes PyMOL to store more information
(B-factors, secondary structure) with each atom of each state -- so it can
also be noticeably slower to load and uses more memory.

Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

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

[Alexander S. <sc...@dw...>]

Hi Robert,

this solves exactly my problem and gives me the pictures I wanted.

Thank you very much for the quick answer!

Cheers,
Alexander

Am Mittwoch, den 26.10.2011, 09:48 -0400 schrieb Robert Campbell:
> Hi Alexander,
> 
> On Wed, 2011-10-26 12:53  EDT,  Alexander Schulz
> <sc...@dw...> wrote:
> 
> > 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?
> 
> Yes, simply load the pdb file with the "discrete=1" flag:
> 
> load md_file.pdb, discrete=1
> dss md_file
> 
> Setting the "discrete" flag causes PyMOL to store more information
> (B-factors, secondary structure) with each atom of each state -- so it can
> also be noticeably slower to load and uses more memory.
> 
> Cheers,
> Rob
>