I need to do an animation about bacteriorhodopsin, and I need to have the 3D
model of the bacteria; before starting do try to build it myself (taking lot of
time), has somebody the POV file or similar (for example mdl file for Moray) to
give me, or knows where I can find it?

Thank you

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> I need to do an animation about bacteriorhodopsin, and I need to have the 3D
> model of the bacteria; before starting do try to build it myself (taking lot of
> time), has somebody the POV file or similar (for example mdl file for Moray) to
> give me, or knows where I can find it?
>
> Thank you
>
>

If you have a file containing the location of the various atoms forming 
the molecule, you can easily create a blob object representing it. You 
can also place spheres to represent those atoms.
Using both aproach, you can color code the various atoms or specific 
parts of the model.



Alain

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On 24-9-2010 17:21, Giuela wrote:
> I need to do an animation about bacteriorhodopsin, and I need to have the 3D
> model of the bacteria; before starting do try to build it myself (taking lot of
> time), has somebody the POV file or similar (for example mdl file for Moray) to
> give me, or knows where I can find it?
>
> Thank you

You can find the structure e.g. on
http://www.pdbj.org/emnavi/emnavi_detail.php?id=pdb-1brd
i.e. the position of all atoms (except hydrogen, you are supposed to 
figure those out yourself).
Use blobs or ball and stick models to create the protein.

It is a bit of work, but rather straightforward. You can e.g. paste the 
relevant portion in a spreadsheet, reorganize it so it only include the 
data you need and add pov-sdl in the columns where required. Export it 
as a textfile and you have a basic include file. Perhaps you need to 
write some macros also to make life easy.

Unless someone wrote a pdb to pov convertor or something similar... 
There may be something usefull in 
http://www.povray.org/resources/links/3D_Programs/Chemical_Molecular_Modelling_Programs/

For the cell you need other references. but blobs may again be suited to 
get a basic shape.

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"Giuela" <mgi### [at] selex-sicom> wrote:
> I need to do an animation about bacteriorhodopsin, and I need to have the 3D
> model of the bacteria; before starting do try to build it myself (taking lot of
> time), has somebody the POV file or similar (for example mdl file for Moray) to
> give me, or knows where I can find it?
>
> Thank you

You can look for the model as andrel suggested and then you might use
biodesigner:
http://www.pirx.com/biodesigner/index.shtml
which can output a pov-ray scene file which you then can adapt to your needs.

Cheers,

Simone

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Giuela saw fit to write:

> I need to do an animation about bacteriorhodopsin, and I need to have the
> 3D model of the bacteria; before starting do try to build it myself
> (taking lot of time), has somebody the POV file or similar (for example
> mdl file for Moray) to give me, or knows where I can find it?

Do you mean a model of the bacteriorhodopsin (the protein) or a model of the 
bacterium (the organism)? If it's the former, as others have interpreted, my 
advice is to use VMD (<http://www.ks.uiuc.edu/Research/vmd/>), which as a 
visualization program that can export to POV-Ray. It can also load 
structures from the PDB directly, just write "1brd" in the file load dialog, 
and it gets fetched from the net.

-- 
light_source{9+9*x,1}camera{orthographic look_at(1-y)/4angle 30location
9/4-z*4}light_source{-9*z,1}union{box{.9-z.1+x clipped_by{plane{2+y-4*x
0}}}box{z-y-.1.1+z}box{-.1.1+x}box{.1z-.1}pigment{rgb<.8.2,1>}}//Jellby

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"Giuela" <mgi### [at] selex-sicom> wrote:
> I need to do an animation about bacteriorhodopsin, and I need to have the 3D
> model of the bacteria; before starting do try to build it myself (taking lot of
> time), has somebody the POV file or similar (for example mdl file for Moray) to
> give me, or knows where I can find it?
>
> Thank you


You may want to try the program Mol2mol to convert chemical pdb coordinate files
to POVray format.
The program creates povray input files and you can modify them as you want.
http://www.gunda.hu/mol2mol

You can find several bacteriorhodopsin files from here:
http://www.rcsb.org./pdb/search/advSearch.do

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andrel <byt### [at] gmailcom> wrote:
> On 24-9-2010 17:21, Giuela wrote:
> > I need to do an animation about bacteriorhodopsin, and I need to have the 3D
> > model of the bacteria; before starting do try to build it myself (taking lot of
> > time), has somebody the POV file or similar (for example mdl file for Moray) to
> > give me, or knows where I can find it?
> >
> > Thank you
>
> You can find the structure e.g. on
> http://www.pdbj.org/emnavi/emnavi_detail.php?id=pdb-1brd
> i.e. the position of all atoms (except hydrogen, you are supposed to
> figure those out yourself).
> Use blobs or ball and stick models to create the protein.
>
> It is a bit of work, but rather straightforward. You can e.g. paste the
> relevant portion in a spreadsheet, reorganize it so it only include the
> data you need and add pov-sdl in the columns where required. Export it
> as a textfile and you have a basic include file. Perhaps you need to
> write some macros also to make life easy.
>
> Unless someone wrote a pdb to pov convertor or something similar...
> There may be something usefull in
>
http://www.povray.org/resources/links/3D_Programs/Chemical_Molecular_Modelling_Programs/
>
> For the cell you need other references. but blobs may again be suited to
> get a basic shape.


Thank you Andrel for your suggestions.
I found the Pov Ray file of the bacteria at the address
http://www.rcsb.org/pdb/explore/jmol.do?structureId=1BRD&opt=3
Here it's possible to wiev in different ways and to save the image in different
formats, also in .pov.

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