SourceForge.net wrote:
Bugs item #981799, was opened at 2004-06-29 03:42Altering the drawing, e.g. inserting a bond in the drawing where the experiment has placed two atoms which are known as bound too far away.
Message generated for change (Comment added) made by migueljmol
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Category: Scripting Group: None Status: Open Resolution: None Priority: 5 Submitted By: JR (interessent) Assigned to: Miguel (michaelthoward) Summary: bond selection
Initial Comment: it would be very helpful, if Jmol would accept something like
bond [T]1:D.O4 [T]1:D.C5M +
too, in addition to
bond 259 261 +
(which itself is not implemented yet:-)
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Comment By: Miguel (migueljmol)
Date: 2004-12-13 12:28
Message:
Logged In: YES user_id=1050060
Several things.
1. Allowing sets in addition to atom numbers would be very
difficult, given the current interpreter infrastructure. The
statements which take expressions as arguments are
well-defined. Having a statement which sometimes takes an
expression and sometimes takes other things is currently not
possible.
2. I do not understand the RasMol 2.7 doc for 'bond <number>
<number> +'
Q: What possible motivation could there have been for
requiring the '+' ?
Nice drawing of double bonds without the need to alter the PDB file (CONECT records)
In conjunction with rotate bond � you may want to add a 'bond' between two sub units and than rotate them around this 'bond' (which will alter the structure).
Q: Shouldn't the third parameter to 'bond' be a bond order?if
bond 1 2 +
and
bond 1 2 2
would result in the same graph, starting from a single bond between atom 1 and 2.
3. I will not implement 'rotate around a bond'
not now :-) Regards, Jan
Miguel
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