Cursory look at this release on Mac (OS 10.9.2) using Safari (7.0.3) and
Firefox (28.0) using test2:
Firefox works well except for the Flexible Fit animation. While it works, at
the end of the animation no other link works. You have to reload the page. It
might need a quit signal??
Things are not so good in Safari. The same issue as above with the flexible
fit. But many of the links below that in the second column give the
"synchronous binary file transfer" alert followed by an “unrecognized file
error”. This occurs both in local and served modes.
Phil
P.S. For reasons I do not understand, I never see the messages I post, though
I do get the notice that I have posted. I normally see the replies, I think,
but can’t be sure I see them all. I have checked my preferences and they seem
correct.
On Apr 25, 2014, at 11:58 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> 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
>
> ------------------------------------------------------------------------------
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Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu
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