It seems to work with SDF but not CML.Peter wrote: > Thanks. We have been analysing our MOPAC calculations and displaying the > results in Jmol. [snip] > ***What we would like to do is use a set of given bonds rather than have > Jmol calculate its own.***
Jmol will always use the bond information if it is provided.
I am using CML -
I am not familiar with MOPAC and do not understand which file format you are using to load the molecular models into Jmol.
CML
> This is demonstrated in: > http://wwmm.ch.cam.ac.uk/download/mopac/nci_proteus/nsc5220_view.html > where the input molecule is truly horrible and MOPAC rescues it.
I am not in a position to view these URLs at this time.
> The input > bonds are given and we would like to show them, not the join-the-dots > result. If Jmol does this, what is the switch, else can it be easily > fixed?
Here is the input... <molecule title="NSC5220"> <identifier version="0.932Beta" tautomeric="0"> <basic>C6H12BNO3,1H2-4H2-9-7-10-5H2-2H2-8(1)3H2-6H2-11-7</basic> <charge/> </identifier> <atomArray> <atom id="a1" elementType="O" x3="-0.0171" y3="1.4108" z3="0.0098"/> <atom id="a2" elementType="N" x3="-0.0222" y3="1.7161" z3="-1.9637"/> <atom id="a3" elementType="O" x3="1.63" y3="3.2905" z3="-0.2646"/> <atom id="a4" elementType="B" x3="0.9913" y3="2.075" z3="0.0037"/> <atom id="a5" elementType="O" x3="0.335" y3="3.1003" z3="-0.0574"/> <atom id="a6" elementType="C" x3="0.0021" y3="-0.0041" z3="0.0020"/> <atom id="a7" elementType="C" x3="0.542" y3="0.6806" z3="-1.1756"/> <atom id="a8" elementType="C" x3="0.8581" y3="3.781" z3="-1.3987"/> <atom id="a9" elementType="C" x3="1.2148" y3="2.5355" z3="-2.1473"/> <atom id="a10" elementType="C" x3="-1.1201" y3="2.7587" z3="-0.1377"/> <atom id="a11" elementType="C" x3="-0.8637" y3="2.7957" z3="-1.6707"/> <atom id="a12" elementType="H" x3="0.7156" y3="-0.5025" z3="0.66"/> <atom id="a13" elementType="H" x3="-0.9526" y3="-0.5197" z3="-0.1157"/> <atom id="a14" elementType="H" x3="0.4816" y3="-0.1666" z3="-1.9272"/> <atom id="a15" elementType="H" x3="1.61" y3="0.7157" z3="-1.1191"/> <atom id="a16" elementType="H" x3="0.0138" y3="4.367" z3="-1.2206"/> <atom id="a17" elementType="H" x3="1.5225" y3="4.615" z3="-1.8615"/> <atom id="a18" elementType="H" x3="2.1239" y3="2.0644" z3="-1.7862"/> <atom id="a19" elementType="H" x3="1.3497" y3="2.7495" z3="-3.2262"/> <atom id="a20" elementType="H" x3="-1.6094" y3="1.9163" z3="0.2644"/> <atom id="a21" elementType="H" x3="-1.7271" y3="3.6581" z3="0.1561"/> <atom id="a22" elementType="H" x3="-0.8459" y3="3.6623" z3="-2.228"/> <atom id="a23" elementType="H" x3="-1.8558" y3="2.376" z3="-2.0757"/> </atomArray> <bondArray> <bond atomRefs2="a1 a6" id="b1" order="1"/> <bond atomRefs2="a1 a4" id="b2" order="1"/> <bond atomRefs2="a2 a7" id="b3" order="1"/> <bond atomRefs2="a2 a11" id="b4" order="1"/> <bond atomRefs2="a2 a9" id="b5" order="1"/> <bond atomRefs2="a3 a8" id="b6" order="1"/> <bond atomRefs2="a3 a4" id="b7" order="1"/> <bond atomRefs2="a4 a5" id="b8" order="1"/> <bond atomRefs2="a5 a10" id="b9" order="1"/> <bond atomRefs2="a6 a7" id="b10" order="1"/> <bond atomRefs2="a6 a12" id="b11" order="1"/> <bond atomRefs2="a6 a13" id="b12" order="1"/> <bond atomRefs2="a7 a14" id="b13" order="1"/> <bond atomRefs2="a7 a15" id="b14" order="1"/> <bond atomRefs2="a8 a9" id="b15" order="1"/> <bond atomRefs2="a8 a16" id="b16" order="1"/> <bond atomRefs2="a8 a17" id="b17" order="1"/> <bond atomRefs2="a9 a18" id="b18" order="1"/> <bond atomRefs2="a9 a19" id="b19" order="1"/> <bond atomRefs2="a10 a11" id="b20" order="1"/> <bond atomRefs2="a10 a20" id="b21" order="1"/> <bond atomRefs2="a10 a21" id="b22" order="1"/> <bond atomRefs2="a11 a22" id="b23" order="1"/> <bond atomRefs2="a11 a23" id="b24" order="1"/> </bondArray> </molecule>
Jmol only calculates bond information if no bonds are given (However, .pdb files have some special rules).
Tell me which file format you are using.
Work with me on this and we will get it fixed.
Thanks - I think I mentioned this some time ago and it seems to be specific to CML.
P.
Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069
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