Re: [Jmol-users] Bond Selection

[Robert H. <ha...@st...>]

On Mon, Jun 21, 2010 at 4:46 PM, Otis Rothenberger <osr...@ch...>wrote:

> Bob,
>
> Three questions about bond selection:
>
> 1) It appears that in modelkitmode, bonds are identified by a zero based
> index. This index appears to be the only data going into the bond change
> script - e.g.:
>
> assign bond [{4}] "p"
>
> right, that [{n}] notation is very special.


> To affect the bond change, it seems that the relevant atom index numbers
> are required. Is this information picked up from the molfile connection
> table?
>
> Ah, that reminds me --- there is a bug in the SPT file. I have to get that
fixed!

2) Is the bond index simply the position of the bond in the connection
> table?
>
> yes, but the way it is supposed to work is that we rewrite the entire mol
file as part of the SPT state.



> 3) Cutting to the chase, is there any way that a hovered or clicked bond
> can feedback the indexes of the atoms connected by that bond? I think I
> asked you this question before. The answer was, if I recall, no.
>
> I'm pretty sure that as long as you have

set bondPicking true

bond picking, if not hovering, gives a callback report.




> I'm trying to grab the atom indexes because this would allow me to
> rotate connected branches, thus simulating conformational (dihedral
> angle) rotation. I do this now by a two click selection of the relevant
> atoms, but a single bond hover or click picking up these atoms indexes
> would be nice. The relevant bind script is
>
> bind 'ALT-WHEEL' 'select WITHIN(BRANCH,{atomIndex = rot1}, {atomIndex =
> rot2});rotateSelected {atomIndex = rot1} {atomIndex = rot2} @{_DELTAY*20};
>
> I'd like to fill the Jmol globals rot1 and rot2 with a bond hover or
> click. Technically, this should allow a simple mouse action to do a
> single bond rotation without a lot of pre rotation clicking.
>
> Otis
>
> --
> Otis Rothenberger
> chemagic.com
>
>
>
>
>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900