[Jmol-users] Jmol 11.5.38

[Bob H. <ha...@st...>]

Nico has released 11.5.38. A few additional items got included, some of 
which might be of use in general:

--Math functions: random(), cross(), sin(), cos()

--User measurements can now include points created with DRAW, mixed with 
atom positions. Use

  set drawPicking TRUE

to enable this feature.

--CIF reading of thermal B factors (as well as U factors). Untested.

--wildcards for draw, pmesh, and isosurface on/off/delete (specifically)

You can now turn on or off or delete these objects using * as a 
wildcard. For example,

  draw pt* off

might hide all the points, but leave the lines in place, if the lines 
had names like "line1", "line2" and the points had names like "pt1", "pt2".

[Maybe you can tell that I'm working on automated scripts that create 
loads of drawn vectors, which I need to measure using sines and cosines 
and take cross products. (Dot product in Jmol math is v1 * v2).
The list of bug fixes includes:

# bug fix: pm rounding to integer value
# bug fix: select n-m:c  chain selection inappropriately case sensitive
# bug fix: lcaoCartoon naming for multiple centers
# bug fix: scaling of draw object for multimodel environment can cause 
null pointer exception
# bug fix: scaling of VECTOR was from center, not origin
# bug fix: draw ARROW {atom center} {xyz}  draws arrow the wrong way
# bug fix: draw CIRCLE for multiple models
# bug fix: application -- "make crystal..." menu item does nothing -- 
removed
# bug fix: zap of quaternion also zaps model inappropriately
# bug fix: zap to one model assigns -1 to currentModelIndex instead of 0

11.5.39 adds some Chime features that were never implemented in Jmol, 
but which are needed if we are ever to get Protein Explorer up and 
running using Jmol:

  show info
  show residue(s)
  show chain(s)
  show sequence

and

  set messageStyleChime TRUE/FALSE  [ default FALSE ]

Examples:

$ load data/1crn.pdb
Script completed
$ show info
Molecule name ....... MOL_ID: 1; MOLECULE: CRAMBIN; CHAIN: A; 
ENGINEERED: YES
Secondary Structure . PDB Data Records
Brookhaven Code ..... 1CRN
Number of Chains .... 1
Number of Groups .... 46
Number of Atoms ..... 327
Number of Bonds ..... 337
Number of Models ...... 1
Number of Helices ... 2
Number of Strands ... 2
Number of Turns ..... 1


$ select ala;show residues
25 atoms selected
[ALA]9:A
[ALA]9:A
[ALA]24:A
[ALA]27:A
[ALA]38:A
[ALA]45:A

$ select atomno < 50;show sequence
49 atoms selected

Model 1
Chain A:
[THR]1    [THR]2    [CYS]3    [CYS]4    [PRO]5   
[SER]6    [ILE]7    [VAL]8   

$ load data/1hf4.cif; show chain

A
B
Y
Z


Note that you can operate on these lists using the script() function:

$print script("show chain").split()[2]

B



Bob



-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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