> RasMol commands return useful information e.g.
> select HIS
> returns something like 8 residues selected,
So, this information is displayed for the user to read, but the results
are never actually interpreted by any tools or external program ...
correct?
So the actual format of the output does not need to be RasMol/Chime
compatible ... correct?
> I think it is very useful if
> every command could return something like the command how it is
> interpreted, in this case HIS is interpreted as residue where the
> correct notation is [HIS] and useful result information.
> ('select [HIS]','8 residues selected')
Very good. I agree that if we are going to pass 'commands' back as user
information then they should be in valid syntax.
In fact, it will be easier for me to return a 'reformatted' version of the
command. The scripts get compiled/tokenized and it will be easier to
generate the command text from the tokenized format.
(It may also make it easier to build the script recorder in the future)
>>Is this just the count of selected atoms?
> it should be appropriate, if you make an atom selection it should
> return 60 atoms selected
OK
> if it is a chain selection should it report the number of chains
> selected or the number of residues?
Hmmm ... my initial reaction is that it will be more difficult to give
chain/residue information ... at least with the current implementation
of atom selections. We'll have to see.
Q: How would HOH molecules affect chain/residue counts?
> and if you need the information about residues you could use
> show selected residues
> ('show selected residues','[HIS]84:A/0 (8/11)\n[HIS]93:A/0 (14/14)')
> or should it report [HIS]93;A:A/0 (8/11)\n[HIS]93;B:A/0 (6/6)
> separately?
Is 'show selected residues' an existing RasMol/Chime command or a 'new'
command?
> but lets make it better than RasMol in reporting strings which could
> be used directly as selection expressions.
I agree 100%
> By the way, which is the syntax to address insertion codes (which
> RasMol lacks)?
When it comes to chemistry I am just a self-taught 'hacker' ... I don't
have any idea what an 'insertion code' is :-)
>>Is there any text or identifier that says it was a selection?
> I suggest use it as first value of the return array
So, your recommendation is that the value sent to the MessageCallBack be
an array rather than a single string?
That sounds OK to me but ...
What does Chime do?
Will it break existing scripts?
>>>- when an atom is clicked, its references are given
>>>
> but in correct notation, not in slang.
> and we should tolerate wildcards for
> insertion code (implementation and syntax)
> alternate location indicator
> model
> molecule (syntax)
You (the community) will have to give me input/direction on this because
it is not something I understand.
>>What do the atom 'references' look like?
>>
> complete like
> [Gly]1:E.CA;B/0(insertion=none,molecule=1)
>
>>>- show chain, show model, show information, show pdbheader, show
>>> sequence, show view, send a message back to the user via this
>>> method.
>>>
>>As I recall, none of the 'show' commands are currently implemented. It
>> won't be difficult to do, but it hasn't happened yet.
>>Is the output of these commands in Chime the same as in RasMol?
> better
One of the main reasons that the 'picking' and 'show' commands are not
implemented is because the RasMol documentation doesn't say very
much about them. (To date I have been working from RasMol v2.6 doc)
I have never written a Chime app and I have only tinkered with RasMol
when I didn't understand the documentation, so I don't really know what
the behavior should be.
We need to develop a little more formal specification of what the behavior
& parameter values/format should be for:
MessageCallBack
PickCallBack
show ?
set picking ?
Jan & Paul, your messages have been *very* helpful in getting this started.
>>>
> I hope we don't need an extra dummy frame:-)
I assume that the 'extra dummy frame' is related to some quirk in Chime
web app development ... what is it?
Miguel
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