>>> Q: What scaling factor would you expect to be applied?
>>the same 1A =3D 1A
> I agree with Jan.
Certainly 1A is always 1A.
The question is ... how many pixels per angstrom?
Q: If I load a large molecule followed by a small one, does the small one=
just 'fit in' without changing the scaling of the large one?
Q: If I load a small molecule followed by a large one, what happens?
>>> Regarding centering ...
>>> The first model gets centered on the screen.
>>> Q: I assume that you do not want the second model centered on the
>>> screen ... please confirm.
>>the same operation, which had been automatically applied to the first
>>molecule should be repeated to the second
> I don't understand this, but I think I we are saying the same thing: h=
> does Jmol determine placement of a single molecule? it should do the s=
> for each molecule IMO.
If it does the same thing for each molecule then every molecule will get
I fear that I may not have adequately explained the issue.
Let us assume that we load up a molecule. We take the mean of the
coordinates of the atoms. (Some call it 'unweighted center of gravity',
but that is simply the mean.) Let's say that the mean is 10,20,30. Then
all points have 10,20,30 subtracted from their coordinates so that
everything is translated to a 0,0,0 center.
Now you want to load another molecule. Let's say that mean of the points
in that file is 200,200,200.
Q: What do you want to do?
>>> If not, and if it is necessary to manipulate each model
>>> independently, then it is a *lot* of work.
>>independent manipulation (rotation, translation) like in RasMol2.7.2
>>would be nice
> I would go so far as to say independent rotation and translation are
> necessary. OTOH I don't think zoom or slab need to be independent.
I think that zoom needs to be wired together, otherwise the scaling will
be different for different molecules and things will get messed up.
If we need independent rotation and translation then we can probably
terminate the discussion ... it is a *lot* of work and will not happen in=