Hi Simon, Maybe this will help. First create a molecule containing only the
Calphas: > create calphamol, whatever_your_pdb_name and n. ca then you can
delete your original pdb and continue: > set ribbon_trace_atoms, 1 > show
ribbon You are breaking your chain because of the amino acid numbering (Pymol
won't make a bond between residues 13 and 15). You'll have to renumber the
residues (either by text editing or with Pymol itself, the procedure is in the
wiki). The distance between the Calphas doesn't matter, as far as they belong
to the same chain and molecule. (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
([email protected]) Sent: Thursday, November 14, 2013 02:41 PM To:
[email protected] Subject: [PyMOL] Drawing chain to visualize
backbone 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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