http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.1/Jmol%2014.1.14/
-- new array capabilities
-- new LIKE operator
-- new SQL search for properties
-- new DSSR RNA/DNA structure analysis
___JmolVersion="14.1.14"
new feature: select x = [array or array variable]
-- implied OR
-- operators other than equals use implied AND
new feature: array.keys.all
-- drills down in sequential or associative arrays
-- gives all keys as well as number of array elements:
load files "=1d66/dssr"
x=getProperty("auxiliaryInfo.models.1.dssr")
print x.keys.all
basePairs
basePairs.19.DSSR
basePairs.19.LW
basePairs.19.Saenger
basePairs.19.bp
basePairs.19.bpBuckle
basePairs.19.bpChi1
basePairs.19.bpChi2
basePairs.19.bpDistC1C1
basePairs.19.bpDistC6C8
basePairs.19.bpDistNN
basePairs.19.bpLambda1
basePairs.19.bpLambda2
basePairs.19.bpOpening
basePairs.19.bpPropeller
basePairs.19.bpShear
basePairs.19.bpStagger
basePairs.19.bpStretch
basePairs.19.bpTorCNNC
basePairs.19.g1
basePairs.19.g2
basePairs.19.helixId
basePairs.19.id
basePairs.19.info
basePairs.19.key
basePairs.19.name
basePairs.19.nt1
basePairs.19.nt2
basePairs.19.res1
basePairs.19.res2
basePairs.19.stemId
coaxialStacks
coaxialStacks.1.basePairs
coaxialStacks.1.basePairs.4.5.DSSR
...
coaxialStacks.1.helix
coaxialStacks.1.stemCount
coaxialStacks.1.stems
dbn
hBonds
hBonds.188.atno1
hBonds.188.atno2
hBonds.188.atom1
hBonds.188.atom2
hBonds.188.distAng
hBonds.188.energy
hBonds.188.hbType
hBonds.188.id
hBonds.188.label
helices
helices.1.basePairs
helices.1.basePairs.19.DSSR
...
new feature: array.join()
-- creates a flat array from an array of arrays:
-- example:
$x = [1,2,[3,4,5],[6,[7,8,9]]].join()
$show x
x = [ 1,2,3,4,5,6,7,8,9 ]
new feature: LIKE operator extended to atom expressions
--as for other atom expressions, is not case-sensitive
--examples:
load =1crn
select group like "G*"
new feature: "like" operator, strings only:
a LIKE "x" a equals x
a LIKE "*x" a ends with x
a LIKE "x*" a starts with x
a LIKE "*x*" a contains x
new feature: getProperty(x, SQL_query)
-- Full SQL for any Jmol associative array.
-- Result is an array if x is an array.
-- example:
x = [ 1,2,3,{ "testing":"here","val":33 } ]
y = getProperty(x, "SELECT val WHERE testing LIKE 'here'")
show y
[ 33 ]
z = x[4]
show z
z = { "testing":"here","val":33 }
y = getProperty(z, "SELECT val WHERE testing LIKE 'here'")
show y
33
new feature: rich SQL logic in GETPROPERTY, getProperty(), and
within(dssr,"xxxx.yyy..."):
-- syntax: [SELECT keys WHERE expression]
-- keys indicating only one key, such as "nt1", return just the value
-- keys may be a LIKE wildcard such as "nt*" or "*nt" or "*nt*"
also return just the value(s)
-- keys * or */* means "return all values as an associative array"
-- keys */nt1,nt2 means "return a new associative array including only
keys nt1 and nt2"
-- keys */nt* means "return a new associative array including all keys
starting with nt"
-- if drilling to this associative array from a list, * or */... returns
an array of key/value pairs
-- expression may be any standard Jmol expression that does not involve
actual Jmol variables
(instead, the variable names should all be the keys, and their values
will be that given in the key:value pair)
-- example:
load files "=1ehz/dssr"
x = getProperty("auxiliaryInfo.models.1.dssr.basepairs");
print getProperty(x,"[SELECT nt* WHERE bp='C-G']")
print getProperty(x, "[SELECT */nt* WHERE Saenger LIKE '19*']")
-- keys may be "dotted" -- modelProperties.FreqValue -- but in this case
the dotted key (FreqValue here) must be exact case.
"modelProperties.freqvalue" would not work.
-- example:
load C6H6.smol
x = getProperty("modelInfo.models[select _ipt where
modelProperties.PATH='Frequencies' and modelProperties.FreqValue > 3000]")
select modelIndex = x // 6 models selected
new feature: JANA2006 reader adds M40 molecular group support
-- no TLS modulation
-- no local axes (third header line of pos# record)
new feature: calculate structure dssr
-- fetches
http://x3dna.bio.columbia.edu/dssr/?POST?opts=--hl%20--more&model=[pdb data]
-- builds auxiliaryInfo.models.n.dssr
-- displays summary report
-- complements calculate structure dssp, except it is done by the x3dna
server at Columbia, not Jmol
new feature: (application only) -a --autoAnimationDelay
-- delay time in seconds for press-and-hold operation of
toolbar animation buttons (default 0.2; set to 0 to disable)
new feature: calculate hbonds structure
-- now includes DSSR-calculated bonds for nucleic acids
TRANSCRIPTION/DNA 06-MAR-92 1D66
DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX
found biomolecule 1: D, E, A, B
DSSR: a software program for Defining the Secondary
Structures of RNA from three-dimensional coordinates
v1.0.6-2014apr04, Xiang-Jun Lu (xiang...@x3dna.org)
List of 19 base pairs
List of 1 helix
List of 4 stems
List of 1 coaxial stack
List of 3 internal loops
new feature: load =1msy/dssr
-- very simple RCSB/DSSR connection
-- loads both files:
FileManager opening 1 http://www.rcsb.org/pdb/files/1msy.pdb.gz
FileManager opening 1 http://x3dna.bio.columbia.edu/dssr?id=1msy
load =1msy/dssr
set backboneSteps
backbone -0.2
select within(dssr,"helices")
color blue
select within(dssr,"stems")
color red
select within (dssr,"singleStranded")
color white
select within (dssr,"multiplets")
color green
select within (dssr,"lonePairs")
color orange
select leadatom
spacefill 1.5
label %[group1]
font label 24 bold
set labeloffset 0 0
color label grey
new feature: select within(dssr,"subset")
-- subsets include
aMinorMotifs
basePairs
bulges
coaxialStacks
hairpinLoops
helices
internalLoops
junctions
kinkTurns
kissingLoops
lonePairs
multiplets
riboseZippers
singleStranded
stems
-- optionally followed by ".n" where n is a number starting with 1
-- optionally followed by ".linkedBy" for loops, bulges, and junctions
-- optionally followed by ".res1" or ".res2"
-- can accommodate SQL
-- results are cached for individual models
-- example:
select within(dssr,"multiplets")
select within(dssr,"bulges.3")
select within(dssr,"bulges.3.linkedBy")
select within(dssr,"basePairs[SELECT res* WHERE twist > 1]")
new feature: DSSR server
-- load files "=1d66" + "=dssr/1d66"
DSSR: a software program for Defining the Secondary
Structures of RNA from three-dimensional coordinates
v1.0.6-2014apr04, Xiang-Jun Lu (xiang...@x3dna.org)
-- uses new "concatenate" notation to combine data from two sources
-- after loading, try
print getProperty("auxiliaryInfo.models.1.dssr")
new feature: DSSR output reading
-- Defining the (Secondary) Structures of RNA
-- see
http://forum.x3dna.org/rna-structures/dssr-software-for-defining-the-%28secondary%29-structures-of-rna/
-- brain-child of Xiang-Jun Lu (3dna...@gmail.com; Columbia University)
-- use system command x3d-dssr.exe --input=xxxx.pdb > xxxx.out
-- then in Jmol:
load files "xxxx.pdb" + "xxxx.out"
-- all DSSR information will be in auxiliaryInfo.models.dssr with the
following keys:
aMinorMotifs
basePairs
bulges
coaxialStacks
hairpinLoops
helices
internalLoops
junctions
kinkTurns
kissingLoops
lonePairs
multiplets
riboseZippers
singleStrandedSegments
stems
-- all entries are lists.
-- most of these list entries have "nt" entries, and those
are nucleotide residue identifiers, so Jmol's
getProperty() "drill-down" capabilities allow for:
x = getProperty("auxiliaryInfo.models.1.dssr.basepairs.nt")
select @{x}
bug fix: halos ON fails for small vdw radii
bug fix: CIF reader with bsModels fails
-- example:
load maleic.cif [3 5 7]
bug fix: reading concatenated files from PNGJ with model selected
bug fix: reading gzip files from PNGJ fails when concatenated
bug fix: group1 codes for nonstandard residues not read from mmCIF
(_struct_ref_seq_dif.db_mon_id) or PDB (SEQADV)
bug fix: select group="ALA" fails due to select group ..... option
bug fix: getProperty("auxiliaryInfo") fails for JavaScript
bug fix: Gaussian FCHK file reader fails when no SP coefficients
bug fix: set defaultVDW not working
bug fix: color isosurface range broken (Lucy Cusinato)
bug fix: script compiler error: x.x*x.x requiring space: x.x * x.x
(Alexander Rose)
bug fix: lost H atoms of PDB-designated water
bug fix: mouse rotation can cause loss of model
bug fix: Jana2006 reader not reading groups correctly (still work TODO)
bug fix: functions called in script defined by script called by this script
must be lower case.
bug fix: clickable atoms may not be considered visible for hover
bug fix: select color=red should be color="red" to allow
for variable after "color="
code: upgrade of Apache Commons CLI (Command Line Interface) to 1.2 from 1.0
code: T4 generalized as extending T3, allowing 4D mesh reading.
code: implementation of Andrew Hanson's 3D Ball Roll mouse algorithm
-- no significant practical improvement, but nicer mathematics
-- a bit more involved, but this is once per mouse move. Doesn't
matter.
--
Robert M. Hanson
Larson-Anderson 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
------------------------------------------------------------------------------
Start Your Social Network Today - Download eXo Platform
Build your Enterprise Intranet with eXo Platform Software
Java Based Open Source Intranet - Social, Extensible, Cloud Ready
Get Started Now And Turn Your Intranet Into A Collaboration Platform
http://p.sf.net/sfu/ExoPlatform
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
