Re: [PyMOL] Drawing chain to visualize backbone

[Sampson, J. <Jar...@ny...>]

Hi Simon - 

I don't think you need to do any deleting of atoms at all--there are a few settings that will be helpful here.  Here's how I would do what I think you're asking for:

# load and set basic representation
load structure.pdb
as cartoon

# create the smooth version
create smooth, structure
cartoon tube, smooth
set cartoon_tube_radius, 1.5
set cartoon_smooth_loops, on, smooth
set cartoon_transparency, 0.5, smooth

# give everything a "loop" secondary structure for the smooth version
alter smooth, ss="L"
rebuild

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/






On Nov 14, 2013, at 8:41 AM, Simon Schweizer <sch...@tu...> wrote:

> Dear all,
> 
> I have a complex protein (with a knot in the polypeptide chain)
> and want to show the rough course of the chain, so everyone can
> easily see that there is a knot inside.
> 
> I don't know how to draw such a complex 3D object in a drawing
> program, so I want to do that in PyMol (or another similar program).
> 
> What I did is copying a part of the protein sequence and transformed
> it in a new object. I want to superimpose the new object drawed
> in ribbons with the whole protein in cartoon representation. I made
> the ribbons big. How can I make it transparent, too, by the way?
> 
> For showing the rough course of the polypeptide chain, the ribbon
> should not follow every alpha-helix, loops and so on. What I want to
> do is like box filtering the chain.
> I tried to delete atoms, but then the ribbon is broken. How can
> I connect these atoms, must the c-alpha carbons be connected
> by peptide bonds so the ribbon is drawed? But I want to delete
> atoms, so the connections between the remaining atoms that
> form the ribbon will have larger distances than normal bonds.
> Is that possible to do that at all in PyMol?
> 
> Another option would be: taking some c-alpha carbons that
> show the rough course of the chain, and building a povray
> file that draws it like a ribbon or flexible tube, and input that
> povray code into the povray-file of the rendered protein.
> 
> Any help is greatly apprechiated!
> Thanks!
> Simon
> 
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