> In the category of wish lists, may I propose the following?
>
> Currently "monitor" ("measure") uses AtomNo for each of its parameters.
>
> As I develop a single page to service an Applet that
> can dynamically load different, related structures,
> the monitor command, of course, is less useful.
Yes. I understand the problem. This is an issue that has bothered me for
some time.
> The S on Cys35, chain B has different atom numbers
> in the two structures. Most of my other commands work fine in
> this context.
>
> Might I suggest that the Monitor/Measure algorithm optionally take a
> unique atom descriptor for each of its arguments?
>
> Example: monitor 184:A.CA 367:A.CA
Your *protein* bias is showing ... we need to have a format that would
work for all file types ;-)
Here are the thoughts that I have had on this subject in the past:
'measure' should take a set of atoms, where the set is defined using the
normal 'atom expression' syntax. Unfortunately, this will only work for
distance measurements. Angles and torsions must be ordered, and sets are
unordered collections of atoms.
The first solution I tried to come up with was to try and maintain an
order within small sets. That is, if the set size is small then remember
the order in which the atoms were selected. The boolean set operators
(and, or, not) would make a 'best efforts' attempt to maintain some type
of order that made sense.
However, I think I concluded that this would be error-prone and would
break down as people tried to work with more complicated atom expressions.
The other solutions I came up with was:
Allow multiple sets to be passed to the 'measure' command. The scripting
language grammer is rather poorly defined. To enable accurate parsing each
set would have to be fully enclosed in parentheses. (note that the
polyhedra command takes an optional parenthesized atom set)
In the general case, the atoms sets would be required to have exactly one
atom each. Using your example from above:
measure (184:A.CA) (367:A.CA);
In the special case of two atoms, we might choose to allow the following:
monitor (184:A.CA,367:A.CA);
which could also be written as:
select 184:A.CA,367:A.CA;
monitor selected;
Having the extra parentheses seems somewhat verbose, but given the grammar
that we started with, I don't see much other choice.
Tell me what you think.
Miguel
-
Open Source Molecular Visualization
www.jmol.org
[EMAIL PROTECTED]
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