I'm mistaken. The documentation is mistaken; there is no bug. I'll fix
the documentation.
Bob Hanson wrote:
it's a bug. I think a new version will be coming out tomorrow or Monday.
I'll get this fix into it.
measure (atomID1) (atomID2)
just like
measure (X*) (Y*)
only measures the distance between the FIRST matching atom in the entire
model in each set.
Thus, to measure a distance BETWEEN two models, you need to specify the
two atoms explicitly:
measure (atomno=3 and */1) (atomno=6 and */3)
Otherwise atomno=3 and atomno=6 in model 1 will be measured.
Then:
measure all (X*) (Y*)
measures all possible (X*) (Y*) distances, but restricts the
measurements to within individual frames.
measure allconnected (X*) (Y*)
does the same, but only if X-Y are connected.
The documenation now reads:
Renders a measurement between the specified atoms. See also {#.set
measurement~}. Two general syntaxes are available. In the older syntax,
a series of two to four atom numbers are given, and the appropriate
measure (distance, angle, or dihedral angle) is then displayed. The
newer, more general syntax is as follows: <br /> <br />measure RANGE
<minValue> <maxValue> ALL|ALLCONNECTED|DELETE (<atom
expression>) (<atom expression>) ... <br /> <br />Using this syntax
one can specify a <i>set</i> of measurements to define all at once. Note
that these sets are embedded {#.atom expressions~atom expressions} that
must be enclosed in parentheses. By default, only the first atom in each
specified set is used for the measurement. Using ALL or ALLCONNECTED,
all matching criteria in all frames are generated, thus allowing for
"animated" measures. In general, this syntax restricts measurements to
within the same model. However, measures can also be between two atoms
in different frames (different models) as long as <b> frame all </b> has
been specified so that the two models are visible and each atom
expression evaluates to a single, specific atom. (To specify a
particular model, use "AND */n", where n is a model number, "ATOMNO=3"
by itself, for example, will indicate the third atom in each
model/frame). If none of the keywords ALL, ALLCONNECTED, or DELETE are
present only the <i>first matching</i> atom in the entire model set (all
frames, so probably the first frame) is used for the measurement. For
the applet, using {#.getProperty~getProperty measurementInfo} will then
deliver full information relating to all measurements.
Bob
Bob
> Angel Herraez wrote:
>
>> Hi Craig
>>
>> Try
>> monitor all (atomID1) (atomID2)
>>
>> I find the documentation for this at
>> http://www.stolaf.edu/academics/chemapps/jmol/docs/?ver=11.0#measure
>> to be confusing, if not plain wrong. It says that by default "all
>> matching criteria in all frames are generated". I understand this to
>> mean what Craig wants, but what I get is that measurements are
>> generated only on the first frame/model.
>> Moreover, documentation for ALL says that it will create measurements
>> from first atomSet to all atoms in the others; however, this is
>> restricted to atoms in the same frame.
>>
>>
>>
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