As Miguel suggests and my demo shows, the thing you need to do is to separate the different models using
MODEL ENDMDL
as shown, for example, at
http://rcsb-deposit.rutgers.edu/adit/docs/pdb_atom_format.html
1 2 3 4 5 6 7 8 12345678901234567890123456789012345678901234567890123456789012345678901234567890 MODEL 1 ATOM 1 N ALA 1 11.104 6.134 -6.504 1.00 0.00 N ATOM 2 CA ALA 1 11.639 6.071 -5.147 1.00 0.00 C ... ... ATOM 293 1HG GLU 18 -14.861 -4.847 0.361 1.00 0.00 H ATOM 294 2HG GLU 18 -13.518 -3.769 0.084 1.00 0.00 H TER 295 GLU 18 ENDMDL
Of course the catch is that with this you need to duplicate ALL the entries. A nice benefit of this is that then you can run the animations and watch your rotomers interconvert.
With 80+ rotomers that's a BIG file. You might consider doing this in a way I've
done, where the single file is read in, then parsed, then reloaded as a set of models. The JavaScript sequence for this is really not that bad:
strModel="" Model=new Array()
function mycallback(app,msg){
var strMsg=msg+""
if(strMsg.length<1000)return
strModel=strMsg
Model=strModel.split("TER")
strModel=""
for(var i=1;i<=Model.length;i++){
strModel+="MODEL "+i+"\n"+Model[0]+Model[i]+"ENDMDL\n"
}
setTimeout("document.jmol.loadInline(strModel)",100)
}This is a bit crude, but I think it does the job. (It doesn't rip out the
Tyr A 155, though. If that's really what you need, that's a bit of a problem, I think.
One PARTIAL solution, actually a pretty nice one would be an option in Jmol such as
set interchainbonding ON/OFF
This would, I guess, have to be executed BEFORE a "load" command and would
direct the bond-generator to NOT connect atoms that are in separate TER sets.
What this would allow is for you to load your model with all those sets just the way you have them and then restrict them to separate rotomers by defining groups of atoms as, for example:
define mainchain 1-210 and not 155 define rotomer1 (mainchain or 1210) define rotomer2 (mainchain or 1211) define rotomer1 (mainchain or 1212) ... restrict rotomer1
except... How do you "unrestrict"? So that then later you can do:
restrict rotomer2
etc.
This will ONLY work if Miguel can allow for ignoring interchain bonding.
Bob
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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