I have just posted Jmol10pre2 on:
http://jmol.sf.net/betatest
The text from the website is:
----------------------------
Jmol10pre2
Jmol version 10 pre-release 2 is now released. This release includes the
following enhancements:
* has updated/improved/correct nucleotide set definitions
* properly supports PickCallBack
* respects CONECT records in .pdb files
* offers preliminary/rudimentary cartoon support
* chooses conformation A when alternate locations are present
* renders 'ribbons' as strands
* supports 'color monitors'
* Note application name change jmol.jar -> Jmol.jar
This release continues to have the following functional limitations:
* Only supports .xyz, .mol, and .pdb files
* Does not handle animations
* Does not handle crystal cells
* Will not automatically recognize protein secondary structures
* Will not render isosurfaces
* Does not handle nucleotide shapes
--------------------
Some more detail on some of these things:
Nucleotide set definitions
--------------------------
Thanks to those who participated in the discussions regarding nucleotide
definitions (and apologies to those who got their mailboxes filled up :-)
Tim Driscoll updated/corrected/*implemented* the nucleotide related
predefined sets; nucleic, a, g, c, t, purine, pyrimidine, etc. With the
input of others, he believes that these sets are 'better than
RasMol/Chime'. (Since this is way beyond my area of expertise I have no
way to verify this extravagent claim :-)
.pdb CONECT records
-------------------
CONECT records from .pdb files are now read and applied. Multiple-bonds
also work.
There is still work to be done in this area. Most importantly, the proper
criteria for determining when to apply 'auto-bonding' still need to be
established. The current criterion that I implemented is:
if (number-of-CONECT-bonds < number-of-atoms/2)
apply auto-bond to determine rest of connectivity
else
assume that all connectivity was defined by CONECT records
The 'set connect' commands are not implemented.
Several people have reported that they experienced problems with
RasMol/Chime auto-bonding behavior in the past. If you have the time,
please try out the models which gave you problems in the past and let us
know if they continue to be problematic.
ribbons hooked up to strands
----------------------------
The ribbons command is *not* implemented.
However, it is now hooked up to 'strands'. That allows existing scripts to
continue execution rather than crash.
rudimentary cartoon
-------------------
Similarly, the cartoon command is *not* implemented.
However, a rudimentary form of 'cartoon' is implemented. It is not
compatible with the RasMol/Chime 'cartoon' that you may know and love.
Again, the primary purpose is to allow existing scripts to continue
execution rather than die.
It has a number of problems, including the fact that the helix axis is not
calculated properly. It only works if the HELIX and SHEET records are
present in the .pdb file ... we have not yet implemented an algorithm to
detect these structures.
A handful of other bugs were also fixed.
Miguel
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