>>>like in RasMol, if I said: >>> set picking distance >>>Atom #1: [ARG]97:E.NH2 (1062) >>>Atom #2: [ARG]173:E.NH2 (1722) >>>Distance [ARG]97:E.NH2 - [ARG]173:E.NH2 = 19.211 >> >>Are you saying that you get all this text sent to you as a single >> string? >> > yes, in RasMol
But does it happen in Chime?
Chime is similar but not identical:
First click messages back Atom #1: HOH46.O (598)
Second clidk messages back Atom #2: Distance -: 9.021
Chime's #2 report is inferior to RasMol's because it omits the atom ID and hence you can't be sure you hit the intended atom.
[snip]
Parsing this information out of strings is ridiculous.
(I may change my mind later ... but that is how I feel today :-(
Well, I agree -- except that it provides a totally general communication channel for getting all sorts of information, everything from the entire header of the PDB file (can be several 100 Kbytes) to the list of residues currently selected to the number of models present, to the current orientation of the molecule, to whether or not the latest select command selected zero or more atoms.
The code to interpret these strings (if needed) is up to the user. This avoids needing a specific mechanism to report each of over 100 kinds of information within the applet, perhaps reducing bloating.
[snip]
Does a script stop execution when you say 'set picking distance'?
No. That just changes the response to the next mouse click (the picking mode). Normally, one is not clicking the mouse while a script is running. Whether or not one can do that may depend on the platform (macs differ from Windows in the ability to pause script execution with the mouse).
>>When you are selecting multiple items doesn't the same mouse gesture >> generally 'toggle' the selection? >> >> > That is good in deed, my I cite the already discussed Java guidelines: > http://java.sun.com/products/jlf/ed2/book/HIG.Behavior.html#35603 > Follow the general JFC-provided rules for selection in selectable lists > > and tables: > 1. A click on an object deselects any existing selection and selects the > object. > 2. A Shift-click on an object extends the selection from the most > recently selected object to the current object. > > this means in context of biopolymere, follow the chain. > > 3. A Control-click on an object toggles its selection without affecting > the selection of any other objects. This operation can result in > disjoint selections.
Correct.
>>In response to 'show selected atoms', does MessageCallBack send the >> string exactly as RasMol would send it? What happens with the newline >> characters? >> >> > no, > show selected group > lists all the groups that have atoms selected and how many atoms e.g > (2/17) if only two atoms of the group are currently selected > one group per line > show selected atom > lists one atom per line
Do I understand correctly that you want to try to extract all of this information out of a string?
Yes, it is extraordinarly useful!
Protein Explorer relies very heavily on this kind of communication, including this specific instance. In some cases, a single "operation" consists of a series of scripts, parsing messages between each script to dynamically construct the next script.
I am not against a different/better mechanism in Jmol. However, for backwards compatibility, we need all the modes and reports that Chime now sends via messageCallback and pickCallback.
[snip]
At this point I am not going to implement anything beyond what Chime does.
OK with me!
-Eric Martz
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