I have tried to use 12.0.RC4 with Firstglance running from local
files (not from a server). This mode works OK with Safari/OS X and
Jmol 11.8.22 unsigned applet. With 12.0.RC4, I get no errors in the
javascript console, no molecule, and the java null pointer exception
below in the java console. The same exception occurs in Firefox on OS X.
Below the failed java console log, I have pasted a successful one
from Jmol 11.8.22 for comparison.
-Eric
------------------
Java Plug-in 1.5.0
Using JRE version 1.5.0_22 Java HotSpot(TM) Client VM
User home directory = /Users/emartz
----------------------------------------------------
c: clear console window
f: finalize objects on finalization queue
g: garbage collect
h: display this help message
l: dump classloader list
m: print memory usage
o: trigger logging
p: reload proxy configuration
q: hide console
r: reload policy configuration
s: dump system and deployment properties
t: dump thread list
v: dump thread stack
x: clear classloader cache
0-5: set trace level to <n>
----------------------------------------------------
urlImage=jar:file:/Volumes/FGIJ/JmolApplet0.jar!/jmol75x29x8.gif
Jmol applet jmolApplet0__null__ initializing
AppletRegistry.checkIn(jmolApplet0__null__)
1604 script command tokens
applet context: -applet
appletDocumentBase=file:/Volumes/FGIJ/fg.htm?mol=1d66
appletCodeBase=file:/Volumes/FGIJ/
(C) 2009 Jmol Development
Jmol Version 12.0.RC4 2010-04-05 15:10
java.vendor:Apple Inc.
java.version:1.5.0_22
os.name:Mac OS X
memory:2.9/4.0
useCommandThread: false
appletId:jmolApplet0__null__
defaults = "Jmol"
backgroundColor = "black"
loadStructCallback = "jmolLoadStructCallback"
messageCallback = "jmolMessageCallback"
pickCallback = "jmolPickCallback"
language=en_US
Note -- Presence of message callback disables disable translation; to
enable message translation use jmolSetTranslation(true) prior to jmolApplet()
Note -- language translation disabled
FileManager.getAtomSetCollectionFromFile(1atom.pdb)
FileManager opening file:/Volumes/FGIJ/1atom.pdb
The Resolver thinks Pdb
openFile(1atom.pdb): 65 ms
reading 1 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or
getProperty "auxiliaryInfo" to inspect them.
Default Van der Waal type for model set to Babel
ModelSet: autobonding; use autobond=false to not generate bonds automatically
Jmol applet loading completed.
Now loading the molecule ...
FileManager.getAtomSetCollectionFromFile(localTestPDBFiles/1d66.pdb)
FileManager opening file:/Volumes/FGIJ/localTestPDBFiles/1d66.pdb
The Resolver thinks Pdb
Setting space group name to P 43 21 2
openFile(localTestPDBFiles/1d66.pdb): 160 ms
reading 1762 atoms
ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or
getProperty "auxiliaryInfo" to inspect them.
Default Van der Waal type for model set to Jmol
ModelSet: autobonding; use autobond=false to not generate bonds automatically
spinY = 5
hermiteLevel = 0
Exception in thread "QueueThread0" java.lang.NullPointerException
at org.jmol.shapespecial.Dots.setSize(Unknown Source)
at org.jmol.shape.AtomShape.setSize(Unknown Source)
at org.jmol.shape.Shape.setShapeSize(Unknown Source)
at org.jmol.modelset.ModelSet.setShapeSize(Unknown Source)
at org.jmol.viewer.Viewer.setShapeSize(Unknown Source)
at org.jmol.script.ScriptEvaluator.setShapeSize(Unknown Source)
at org.jmol.script.ScriptEvaluator.restrictSelected(Unknown Source)
at org.jmol.script.ScriptEvaluator.restrict(Unknown Source)
at org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown
Source)
at org.jmol.script.ScriptEvaluator.evaluateCompiledScript(Unknown
Source)
at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown
Source)
at
org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown Source)
at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown Source)
at java.lang.Thread.run(Thread.java:613)
-------------------
START SUCCESSFUL JAVA CONSOLE LOG FOR JMOL 11.8.22:
Java Plug-in 1.5.0
Using JRE version 1.5.0_22 Java HotSpot(TM) Client VM
User home directory = /Users/emartz
----------------------------------------------------
c: clear console window
f: finalize objects on finalization queue
g: garbage collect
h: display this help message
l: dump classloader list
m: print memory usage
o: trigger logging
p: reload proxy configuration
q: hide console
r: reload policy configuration
s: dump system and deployment properties
t: dump thread list
v: dump thread stack
x: clear classloader cache
0-5: set trace level to <n>
----------------------------------------------------
urlImage=jar:file:/Volumes/FGIJ/JmolApplet0.jar!/jmol75x29x8.gif
Jmol applet jmolApplet0__null__ initializing
AppletRegistry.checkIn(jmolApplet0__null__)
applet context: -applet
appletDocumentBase=file:/Volumes/FGIJ/fg.htm?mol=1d66
appletCodeBase=file:/Volumes/FGIJ/
(C) 2009 Jmol Development
Jmol Version 11.8.22 2010-02-28 19:28
java.vendor:Apple Inc.
java.version:1.5.0_22
os.name:Mac OS X
memory:2.7/4.0
useCommandThread: false
appletId:jmolApplet0__null__
defaults = "Jmol"
backgroundColor = "black"
loadStructCallback = "jmolLoadStructCallback"
messageCallback = "jmolMessageCallback"
pickCallback = "jmolPickCallback"
language=en_US
Note -- Presence of message callback disables disable translation; to
enable message translation use jmolSetTranslation(true) prior to jmolApplet()
Note -- language translation disabled
FileManager.getAtomSetCollectionFromFile(1atom.pdb) //1atom.pdb
FileManager opening file:/Volumes/FGIJ/1atom.pdb
The Resolver thinks Pdb
openFile(1atom.pdb): 81 ms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or
getProperty "auxiliaryInfo" to inspect them.
ModelSet: autobonding; use autobond=false to not generate bonds automatically
Jmol applet loading completed.
Now loading the molecule ...
FileManager.getAtomSetCollectionFromFile(localTestPDBFiles/1d66.pdb)
//localTestPDBFiles/1d66.pdb
FileManager opening file:/Volumes/FGIJ/localTestPDBFiles/1d66.pdb
The Resolver thinks Pdb
openFile(localTestPDBFiles/1d66.pdb): 147 ms
ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or
getProperty "auxiliaryInfo" to inspect them.
ModelSet: autobonding; use autobond=false to not generate bonds automatically
hermitelevel = 0
hermitelevel = 0
cartoonrockets = false
hermitelevel = 0
1D66
mark_end_firstview
mark_begin_show_pdbheader
FileManager opening file:/Volumes/FGIJ/localTestPDBFiles/1d66.pdb
HEADER TRANSCRIPTION
REGULATION 06-MAR-92 1D66 1D66 2
COMPND GAL4 (RESIDUES 1 - 65) COMPLEX WITH 19MER
DNA 1D66 3
SOURCE (SACCHAROMYCES $CEREVISIAE) OVEREXPRESSED IN
(ESCHERICHIA 1D66 4
SOURCE 2
$COLI) 1D66 5
AUTHOR R.MARMORSTEIN,S.HARRISON
1D66 6
REVDAT 1 15-APR-93
1D66 0 1D66 7
JRNL AUTH R.MARMORSTEIN,M.CAREY,M.PTASHNE,S.C.HARRISON
1D66 8
JRNL TITL /DNA$ RECOGNITION BY /GAL4$: STRUCTURE OF
A 1D66 9
JRNL TITL 2 PROTEIN(SLASH)/DNA$
COMPLEX 1D66 10
JRNL REF NATURE V. 356 408
1992 1D66 11
JRNL REFN ASTM NATUAS UK ISSN
0028-0836 006 1D66 12
REMARK 1
1D66 13
REMARK 2
1D66 14
REMARK 2 RESOLUTION.
2.7 ANGSTROMS. 1D66 15
REMARK 3
1D66 16
REMARK 3
REFINEMENT. 1D66 17
REMARK 3 PROGRAM CORELS;TNT;XPLOR
1D66 18
REMARK 3 AUTHORS J.SUSSMAN;D.TRONRUD;A.BRUNGER
1D66 19
REMARK 3 R
VALUE 0.230 1D66 20
REMARK 3 RMSD BOND
DISTANCES 0.015 ANGSTROMS 1D66 21
REMARK 3 RMSD BOND
ANGLES 2.9 DEGREES 1D66 22
REMARK 4
1D66 23
REMARK 4 THERE ARE TWO DNA CHAINS WHICH HAVE BEEN ASSIGNED
CHAIN 1D66 24
REMARK 4 INDICATORS *D* AND *E*. THERE ARE TWO PROTEIN
CHAINS 1D66 25
REMARK 4 WHICH HAVE BEEN ASSIGNED CHAIN INDICATORS *A* AND
*B*. 1D66 26
REMARK 4 EACH PROTEIN - DNA COMPLEX CONTAINS FOUR BOUND CD
IONS. 1D66 27
REMARK 5
1D66 28
REMARK 5 THE PROTEIN CONTAINS THE N-TERMINAL 65 RESIDUES OF
GAL4 1D66 29
REMARK 5 PLUS A C-TERMINAL PHE DERIVED FROM THE CLONING
CONSTRUCT. 1D66 30
REMARK 6
1D66 31
REMARK 6 RESIDUES LEU A 19 - LYS A 27 AND LEU B 19 - LYS B 27
FORM 1D66 32
REMARK 6 TIGHT TURNS WHICH CONNECT HELICES. RESIDUES TRP A 39
- 1D66 33
REMARK 6 LEU A 49 AND TRP B 39 - LEU B 49 FORM EXTENDED
CHAINS 1D66 34
REMARK 6 WHICH CONNECT
HELICES. 1D66 35
REMARK 7
1D66 36
REMARK 7 RESIDUES LYS A 18, ASN A 35, LYS B 18, AND ASN B 35
HAVE 1D66 37
REMARK 7 POSITIVE PHI
ANGLES. 1D66 38
REMARK 8
1D66 39
REMARK 8 THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW
WILL 1D66 40
REMARK 8 YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED
TO 1D66 41
REMARK 8 CHAIN
*A*. 1D66 42
REMARK 9
1D66 43
REMARK 9 THE HYDROGEN BONDS BETWEEN BASE PAIRS IN THIS ENTRY
FOLLOW 1D66 44
REMARK 9 THE CONVENTIONAL WATSON-CRICK HYDROGEN BONDING
PATTERN. 1D66 45
REMARK 9 THEY HAVE NOT BEEN PRESENTED ON *CONECT* RECORDS IN
THIS 1D66 46
REMARK 9
ENTRY. 1D66 47
SEQRES 1
D 19 C C G G A G G A C A G T C 1D66 48
SEQRES 2
D 19 C T C C G G 1D66 49
SEQRES 1
E 19 C C G G A G G A C T G T C 1D66 50
SEQRES 2
E 19 C T C C G G 1D66 51
SEQRES 1 A 66 MET LYS LEU LEU SER SER ILE GLU GLN ALA CYS ASP
ILE 1D66 52
SEQRES 2 A 66 CYS ARG LEU LYS LYS LEU LYS CYS SER LYS GLU LYS
PRO 1D66 53
SEQRES 3 A 66 LYS CYS ALA LYS CYS LEU LYS ASN ASN TRP GLU CYS
ARG 1D66 54
SEQRES 4 A 66 TYR SER PRO LYS THR LYS ARG SER PRO LEU THR ARG
ALA 1D66 55
SEQRES 5 A 66 HIS LEU THR GLU VAL GLU SER ARG LEU GLU ARG LEU
GLU 1D66 56
SEQRES 6
A 66 PHE 1D66 57
SEQRES 1 B 66 MET LYS LEU LEU SER SER ILE GLU GLN ALA CYS ASP
ILE 1D66 58
SEQRES 2 B 66 CYS ARG LEU LYS LYS LEU LYS CYS SER LYS GLU LYS
PRO 1D66 59
SEQRES 3 B 66 LYS CYS ALA LYS CYS LEU LYS ASN ASN TRP GLU CYS
ARG 1D66 60
SEQRES 4 B 66 TYR SER PRO LYS THR LYS ARG SER PRO LEU THR ARG
ALA 1D66 61
SEQRES 5 B 66 HIS LEU THR GLU VAL GLU SER ARG LEU GLU ARG LEU
GLU 1D66 62
SEQRES 6
B 66 PHE 1D66 63
FTNOTE 1
1D66 64
FTNOTE 1 RESIDUES PRO A 26 AND PRO B 26 ARE
CIS-PROLINES. 1D66 65
HET CD 39 1 CADMIUM
1D66 66
HET CD 40 1 CADMIUM
1D66 67
HET CD 41 1 CADMIUM
1D66 68
HET CD 42 1 CADMIUM
1D66 69
FORMUL 5 CD 4(CD1)
1D66 70
FORMUL 6 HOH *51(H2
O1) 1D66 71
HELIX 1 H1A CYS A 11 LYS A 18 1 RESIDUE 18 HAS POSITIVE
PHI 1D66 72
HELIX 2 H2A CYS A 28 ASN A 35 1 RESIDUE 35 HAS POSITIVE
PHI 1D66 73
HELIX 3 H3A THR A 50 LEU
A 64 1 1D66 74
HELIX 4 H1B CYS B 11 LYS B 18 1 RESIDUE 18 HAS POSITIVE
PHI 1D66 75
HELIX 5 H2B CYS B 28 ASN B 35 1 RESIDUE 35 HAS POSITIVE
PHI 1D66 76
HELIX 6 H3B THR B 50 LEU
B 64 1 1D66 77
CRYST1 80.850 80.850 73.700 90.00 90.00 90.00 P 43 21
2 8 1D66 78
ORIGX1 1.000000 0.000000 0.000000 0.00000
1D66 79
ORIGX2 0.000000 1.000000 0.000000 0.00000
1D66 80
ORIGX3 0.000000 0.000000 1.000000 0.00000
1D66 81
SCALE1 0.012369 0.000000 0.000000 0.00000
1D66 82
SCALE2 0.000000 0.012369 0.000000 0.00000
1D66 83
SCALE3 0.000000 0.000000 0.013569 0.00000
1D66 84
MTRIX1 1 0.969990 0.014680
-0.242700 7.19246 1 1D66 85
MTRIX2 1 0.014290 -0.999900
-0.003900 83.38941 1 1D66 86
MTRIX3 1 -0.242710 -0.000190
-0.970100 62.87497 1 1D66 87
mark_end_pdbheader_listing
--------------------
------------------------------------------------------------------------------
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