Thanks, Oliver
On Sat, Oct 1, 2011 at 9:59 PM, Oliver Stueker <
revilo2...@users.sourceforge.net> wrote:
> 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)
>
>
Wow. Didn't take long for someone to notice that! We're actively working on
it. Probably this week we can get it completed. I decided we needed to get
the documentation out without detailed explanation of the CONTACT command.
It's really rather complicated, and we want to get it right.
> 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"
>
>
Suggestion? How does this sound?
Isosurfaces can be created in Jmol using external file-based "volume" or
"polygon" data. Note that any of the formats that are volume data (APBS,
CUBE, Chem3D, DSN6/OMAP, MRC/CCP4, XPLOR/CNS) can all be used either to
generate the surface itself or (after the MAP keyword) to color a surface.
I've reorganized the isosurface description a bit.
> 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.
>
"color absolute" changed to "color range" somewhere along the way; "color
absolute" is still there for compatibility, but the documentation refers to
"color range" instead. I don't remember why I thought that was a good idea.
Maybe because there is no "color relative"?
Bob
>
> 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
>
--
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
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