We'll have to experiment. You could add some but not all -- just select the
atoms you want to add the hydrogens to. As implemented, Jmol will not add
MORE hydrogens to any atom already bearing hydrogens.
-- oh, the latest has formal charge added. I don't know about radicals.....
Mostly we need to keep this very simple. Let's see what people can do with
it and then tweak it later. It would be nice if we just had a list of PDB
atom types and their number of H atoms to add. Someone must have that.
Angel, I'm starting to think the "Jmol 12.0" idea is a good one. A few
"quantum leaps" here, I think, since 11.0:
-- loads of cyrstallography-related features
-- full support for electron microscopy data (EfVET, CCP4, MRC, XPLOR)
-- new vertex/triangle-based surface readers
-- XML-based JVXL file format "XJVXL"
-- vertex/triangle compression in XJVXL
-- WebExport functionality in application
-- PovRAY, UDTF, X3D, VRML export
-- "live" JPG and PNG images with embedded Jmol state scripts
-- calculate AROMATIC
-- calculate HBONDS
-- calculate HYROGEN
-- calcuate POINTGROUP
-- calculate SURFACEDISTANCE
-- minimize (UFF calculation)
-- minimize addHydrogens
-- atom and model deletion
-- customizable boundbox, measures, and unit cells
-- scalable label and echo fonts
-- customizable Van der Waals radius
-- cube file subset reading
-- draw CIRCLE, LINE, VECTOR, POLYGON, and LINEDATA options
-- draw RAMACHANDRAN, FRAME, BOUNDBOX, UNITCELL options
-- draw INTERSECTION
-- isosurface CONTOURS
-- isosurface SCALE3D ("terrain" maps)
-- show/draw SYMOP
-- multifeatured anisotropic ellipsoid rendering
-- echo/background IMAGE
-- load TRAJECTORY
-- load FILTER
-- load FILTER "BIOMOLECULE..."
-- load support for filtered AMBER trajectories
-- load ZIP files as directory sets
-- select {atom expression} (boolean property expression)
-- loads of new SET parameters
-- script APPLET appletName "some script"
for direct applet-applet communication
-- script LOCALPATH/REMOTEPATH/SCRIPTPATH options
-- write LOCALPATH/REMOTEPATH options
-- RAMACHANDRAN and QUATERNION commands
-- Java/JavaScript-like feel to scripting language
-- user-definable functions
-- easily settable atom properties
-- math support for points, planes, quaternions,
atom sets, bond sets, matrices, arrays
-- user-definable color schemes
-- fully customizable menu
-- popup file dialog for signed applet
-- fully customizable mouse/action bindings
-- several new applet callbacks
-- applet synchronization
-- multi-touch
-- Chinese translation
This is a partial list, of course! Won't be any time soon, mind you.
2010/1/15 Angel Herráez <angel.herr...@uah.es>
> Robert Hanson escribió:
>
> > calculate hydrogen # adds the hydrogen atoms to C,N,O,and S atoms,
> > respecting bonding but not considering formal charge (for now).
>
> This sounds exciting, Bob!
>
>
> > minimize addHydrogens # minimizes and then adds H atoms at the end
>
>
> I have one wonder here. In my experience with 2D models, Jmol often
> minimizes non-H models badly (I was guessing if didn't have enough
> info*), but behaves well when I add the Hs (in another program)
> before minimizing.
> So, is it reasonable to add Hs after the minimization, or maybe
> before it?
>
> (*) for example, a cyclohexane remains hexagonal flat unless it has
> the Hs --an extreme case, but representative of others
>
>
>
>
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--
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
------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
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