A few comments on 10.00.52:

ZOOM
The zoom with perspective depth turned off is nothing short of amazing. Great work! With perspective depth ON, zoom still stops short of what might be desired in certain circumstances, but I think it is improved, and the complete lack of distortion at high zoom levels is lovely. Go, Jmol team!


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This is a bit of an aside, NOT specific to 10.00.52: With perspective depth on, centering an atom or a subset of atoms that are toward the "front" of a structure (i.e., closer to the user) automatically makes them appear smaller (they move farther away from the user). Zooming in all the way on that centered set may or may not go as close as one wants - but if you do zoom in as far as possible, and then rotate the structure 180 degrees in the y axis, wow, are the atoms on the other side ever close! I assume this is because the centered set is the center of rotation and so there has to be space for the opposite end of the structure to swing around into view. So in a way, this is what is limiting zoom on the centered set... centering it! It is ironic, since that set is what you want to examine most closely. It is tantalizing to look at the atoms on the 'other side' but without being able to rotate around them it does not provide a good view of interactions. The solution is to turn perspective depth off for close examinations of small regions in large structures.
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HBONDS and RESTRICT - BUG?
Issuing a restrict command causes hbonds to appear. For example
'restrict protein'
turns on h-bonds, as does
'restrict not water'

The restrict command does not turn hbonds on if they have been explicitly turned off prior to the restrict command. So,
'hbonds off; restrict protein'
does not turn on hbonds.

[In 10.00.52, when a protein loads, hbonds are not shown by default in the 2 pdb files I am using at present. I think this is as expected for this release, although I am a little lost on whether the current discussion of having hbonds come on by default was meant for this release or the next.]

OTHER
Is there a sense of what is going to happen to the new spin-related commands that were removed? Are they still slated for implementation in Jmol (I hope)?

Also, with the 10.1 release...
-could 'set windowCentered on/off' be implemented? This command would be very useful to have in place
-will the planned smoother translations be implemented?

With thanks to the Jmol development team,
Frieda


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Frieda Reichsman, PhD

Molecules in Motion

Interactive Molecular Structures

http://www.moleculesinmotion.com


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