Hi Jared,
yes your method works as you described, it does NOT follow every turn.
I'm sorry, I was mistaken.
Your method is very good, however I wanted do simplify it even more,
and showing a very rough course of the protein.
I ended up with a pdb file consisting of only 27 amino acid residues
(wh
Hi Simon -
Glad you figured out a method that worked for you.
However, I'm wondering why you ended up with "un-smoothed" helices using the
`cartoon_smooth_loops` method. Are you sure you typed the last two commands in
my example correctly (`alter` and `rebuild`)? I'm getting a single, relati
Hi Carlos and Jared,
thanks for your answers!
Jared, your method is quick to do, but the ribbon follows every
turn of a helix, which I wanted do avoid.
Carlos, your method did what I wanted. I commented
out amino acids which c-alphas I did not want to be included,
and ran the script zero_residues.
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, structu
ecule. (Or else I didn't understand what you want to
do). There is also a command > set ribbon_transparency that might do what you
want, but I never used it myself. Carlos From: Simon Schweizer
(schwei...@tum.de) Sent: Thursday, November 14, 2013 02:41 PM To:
pymol-users@lists.sourceforge.ne
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 simil
