Miguel wrote:
Jan wrote:
The RasMol script command to create bonds is called bond.
bond <source> <dest> +
unbond <source> <dest>
...
bond because it is the RasMol script command
Since RasMol uses the command 'bond' then I would feel some obligation to
use the same syntax & semantics.
As I said, I do not like using atom numbers to specify bonds.
Q: Thoughts?
why not
bond <src atom selection> <dest atom selection> [+-]
e.g.
bond ([CYS]1.CA) ([ARG]2.CA)
bond (carbon) (hydrogen and within(1.5, carbon))
The evaluation engine generally assumes that there is a 'current' set in
the accumulator.
make the first selection the current
I don't see the problem to split
bond (src select) (dest select) +
using
s/bond (\d+|\(.+\)) (\d+|\(.+\)) \+/select $1; link $2/i
to
select (src select); link (dest select)
In addition, there are no script commands that take more than one atom
expression set as an argument.
why not (copied from above):
>> The 'link' command should use atom sets to specify the atoms.
>>
> as the monitor command :-)
Agreed.
Therefore, it would be difficult to make it work in this manner.
since atom selection in bond is new, I don't would be too sad if the
link command would extend the RasMol bond command, but it would be
better to overload the bond command.
yes, distance is important and an iterating distance command would be
superior over the within command.
let distant evaluate <source> and <dest>
bond distant(1.5, (carbon) (hydrogen))
I do not see this as an improvement over:
select carbon; link hydrogen and within(1.5, carbon);
a linear alignment H C1 C2 would link H with both carbons
an iterating "within" should only link the H-C1 and not H-C2 as with the
current within()
I would say, the command without distance is useless, distance need not
to be optional.
I am now thinking that the distance is not necessary. Everything can be
done using the existing atom expression operators.
I agree employing operators for this would be the best solution, but an
extension of the within operator would be nice.
Using select, in various cases I have wished to have an iterating "within"
select hydrogen and within(1.5, carbon within(1.5, hydrogen))
Ops! is this the solution in any of the cases, I had problems with? I doubt.
#select carbon within(1.5, hydrogen); link hydrogen within(1.5, carbon);
No! H1 C1 C2 H2
would connect all H with all C
an iterating "within" would be nice
wireframe single | double | triple | aromatic | hydrogen | <diameter>
With RasMol script, I use the bond command before the wireframe command,
if I want to draw a ligand with correct bond order.
I do not like the RasMol script implementation of
bond <atom-number-1> <atom-number-2> +
where it increases the bond order if the bond already existed.
But, that is at least 90% of the use I take of the bond command,
generating the (missing) double bonds of a ligand for detailed display.
Regards, Jan
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