Joost, I was playing with your file. Check out:
http://www.stolaf.edu/people/hansonr/jmol/test/test_jmol.html
Here's the deal:
You are using TER to set off those rotomers. This won't work for two reasons.
First, Jmol is connecting all close atoms, so you are seeing lots of connected atoms. Not only that, though, there's a limit on number of bonds, and since you
are exceeding that in the basic model, you won't ever be able to see the bonds
the way you expect.
Second, Jmol can't read "TER" anything more than "termination"
My fiddling suggests that you need to reconsider how you create this file.
One problem is that the different "TER" block tyrosine residues are duplicates
of Tyr A 155. So it's not clear how you would remove that group and show the others. (In the animation above, I removed it manually.)
So I think it's up to you to create a model file with more standard format.
Bob Hanson
Joost Van Durme wrote:
Hello!
I'm investigating rotamer distributions of residues and I write a new PDB file including the found rotamers for one position. These are written at the end of the PDB file. The result is that multiple rotamers of one residue are displayed in the molecule.
Unfortunately, Jmol starts to make bonds between those rotamer atoms, and that's not really what I want. It gets pretty messy that way.
Is there a way to get this fixed? Or a workaround somewhere?
you can view the model here: http://iri-pc87.ulb.ac.be/sample/sample/test_jmol.html
and download the PDB file here: http://iri-pc87.ulb.ac.be/sample/sample/JOOST.PDB
For info, you see the rotamers of a Tyrosine. ;-)
Joost
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Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr
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