> Hi,
>
> I am writing a program as part of a masters course at Imperial college
> London. The program searches a set of given molecules and finds certain
> substructures that the molecules all have in common. I would like to
> display my results using the jmol applet. I would like to therefore be
> able to
> have jmol highlight just certain specified atoms within the molecule
> e.g. all O-H groups all C=0 groups. Can anyone give me some help with
> how to do this?
Using scripting commands one can hilite the selected atoms with a halo
load {some-molecule}; select {some-atoms}; set display selected
Alternatively, you could change the colors of the selected atoms
select {some-atoms}; color atoms orange
... or display a solvent-accessible-surface around the selected atoms ...
whatever.
select {some-atoms}; set solvent on; dots on
Now, the trick for you is going to be identifying the atoms that need to
be selected.
You will need to learn about how to use atom expressions. For details look
at the RasMol documentation:
http://www.openrasmol.org/doc/#chexprs
A simple way is to select by atom number. For file types other than .pdb,
atoms are ordered sequentially starting at 1
select atomno=1,atomno=5,atomno=6; set display selected
Alternatively, you could select specific groups by constructing atom
expressions in jmol. For example, the following *might* (or might not)
specifically select C=O:
select within(1.3, carbon) & within(1.3, oxygen)
Let us know if/when you have more questions.
Miguel
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