Jmol 12.0.17 has been released. This includes an important fix for 12.0.16,
which was released earlier today, so if you happen to have downloaded that,
please replace it with 12.0.17. While I don't generally make it a practice
to add new features to a released version, I did add two simple ones:
# new feature: load reports model count and overall number and model number
for MOs
Thus:
$ load c6h6.smol
31 models
66 molecular obitals in model 1.1
(oops -- I see that typo now..."obitals" -- well, that will be fixed for
12.0.18)
# new feature: new 5th parameter for measureCallback is actual, unrounded
value
The measureCallback function now adds a 5th parameter that is the unrounded
value, in case you want that sort of precision.
In addition:
#version=12.0.17/12.0.16
SCRIPTING:
# bug fix: s = x[i] list variables all broken in 12.0.16
# bug fix: arrays of hashtables and other more complex variables not being
saved or created in usable form
# bug fix: //comments not searched properly for GOTO operation
PDB ALTERNATIVE LOCATIONS
# bug fix: load FILTER does not include %x for PDB files
You should be able to select just a specific alternative-location based
configuration at load time for a PDB or mmCIF file.
# bug fix: conformation n definition changed for PDB files to be consistent
with DSSP
Jmol was misinterpreting what exactly is meant by an alternative location.
In PDB files, "A" and "B" alternative locations for one residue may not have
anything at all with those for another residue, which could very easily bhe
"D" "E" and "F". The DSSP program does it right; now so does Jmol. If you
use
CONFIGURATION (aka CONFORMATION) 2
then Jmol will, for each residue, select the 2nd listed alternative
location, perhaps B for one residue and E for another. For most case, this
is no change, since A and B are listed together for each appropriate
residue. But there are a few cases in the PDB that that is not true for, and
now Jmol will handle them properly.
# bug fix: conformation not working when an alternate location is for key
atoms such as N, C, O, CA
This got broken in 12.0.1
FILE LOADING
# bug fix: hetero group protein check should not care about C CA N O file
order (1YC5)
Wow, this was a bug that went back to Jmol 10.0. Jmol should not care about
the order of groups in a PDB file residue listing.
# bug fix: loading a multi-structure PDB file with CONECT bonding may not
autobond (2q3t)
There's a bug that goes way back that Jmol fails to autobond some
multi-structure files.
# bug fix: GAMESS reader (US) not reading full atom name such as
"MOLYBDENUM"
# bug fix: load append after calculating structure recalculates structure
for other models
# bug fix: load '@x' not saved properly in state
SAVE STRUCTURE
# bug fix: undocumented save STRUCTURE not working for initial structure
state
I guess I forgot to document this, and it was not working properly anyway.
MEASURE
# bug fix: measure search("...{X}....{X}...") does not work
You can now specify the two atoms to connect using a SMARTS search. Just put
{...} around the two (or three, or four) atoms to be selected from the
search. Works like a charm (now).
# bug fix: %8.4VALUE still truncating in set defaultdistancelabel
CALCULATE STRUCTURE
# bug fix: calculate structure only works with last model loaded
# bug fix: calculate structure after zap x.y fails
# bug fix: calculate structure does not target selected model
# bug fix: bioshapes not clearing automatically after calculate STRUCTURE
LABEL
# bug fix: label %1 will cause exception
ISOSURFACE
# bug fix: isosurface MEP with multiple frames fails on second isosurface
CONNECT
# bug fix: data "connect_atoms" does not update bond diameter, order, or
energy
--
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
------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.
Spend less time writing and rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
