Hi Bob,
and yet again you have managed to make a great piece of Software even
much greater!
I just recently noticed two things that haven't found their way into
the online docs:
1) the new CONTACT command
(but luckily that has a good section on the examples-12/new.htm
page - if you know where to look)
2) that ISOSURFACE MAP can take an "apbs.dx" file as an argument
e.g. ISOSURFACE iso1 COLORSCHEME "rwb" COLOR absolute -5 5
SASURFACE MAP "apbs.dx.gz"
well if someone sees that data can be passed as a variable someone
could also try to load the file directly there,
but I had to look at the PDB2PQR / APBS server at the NBCR to
figure that out.
2b) I believe "ISOSURFACE COLOR absolute -n n" isn't mentioned in the
ISOSURFACE section as well.
And it would be a real pity if those features would be forgotten.
Oliver
On Sat, Oct 1, 2011 at 16:57, Robert Hanson <hans...@stolaf.edu> wrote:
> version=12.2.0
>
> Documentation is pretty much all there:
> http://chemapps.stolaf.edu/jmol/docs/
>
> # 224 new features (see
> http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/viewer/Jmol.properties?view=markup)
>
> # summary of feature changes between Jmol 12.0 and 12.2:
>
> # FEATURE CHANGE: "ligand" definition changed to
> # !(protein,nucleic,water,UREA)"
> # instead of "hetero and not solvent"
> # FEATURE CHANGE: default zShadePower set to 3
> # FEATURE CHANGE: undocumented a[13] = 3 (where a is a matrix, for a[1][3])
> removed
> # FEATURE CHANGE: DSSP default for "calculate structure"
> # -- old way is now "calculate structure RAMACHANDRAN"
> # FEATURE CHANGE: DSSP default for LOAD of PDB file with no header.
> # in previous versions, Jmol used a ramachandran-angle-based calculation
> # for secondary structure determination when a PDB file had no HELIX or
> SHEET records.
> # It just seems reasonable to use the industry-standard DSSP method
> instead.
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2dcopy2
> _______________________________________________
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>
------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2dcopy2
_______________________________________________
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers
