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Hi Thomas<br>
<br>
Could you try something for us? Simply turn off the real time
contact mode by adding this to the cmview.cfg file:<br>
<br>
SHOW_CONTACTS_IN_REALTIME=false<br>
<br>
Then restart cmview and try a few selections and keep using it for a
couple of minutes as you say to see if it still crashes.<br>
<br>
The real-time feature was introduced quite late and might have
issues as it produces a lot of pymol requests.<br>
<br>
Cheers<br>
<br>
Jose<br>
<br>
PS: I'm copying to the list just to keep everyone informed<br>
<br>
<br>
<br>
On 11/04/2011 01:50 PM, Thomas Hopf wrote:
<blockquote cite="mid:4EB3DF8C.6090002@gmail.com" type="cite">Hi
Jose,
<br>
<br>
yes, I tried it a couple of times and the bug was reproducible in
a sense that it always happened after a couple of minutes, after
performing the following actions for some time: I did nothing but
select some of the contacts in CMView and rotate the protein in
MacPymol. At some point, when selecting other contacts in CMView,
Pymol crashes.
<br>
<br>
Unfortunately, I can't link it to anything more specific like
selecting a particular contact at the moment, but I will also try
whether I can find out if there is a more specific pattern to it.
<br>
<br>
Best,
<br>
Thomas
<br>
<br>
Am 04.11.11 12:40, schrieb Jose Duarte:
<br>
<blockquote type="cite">Hi Thomas
<br>
<br>
Thanks a lot for the quick reply!
<br>
<br>
Below is your email... I think the problem is that the mailing
list server we are using has some kind of misconfiguration issue
at the moment. It uses <a class="moz-txt-link-abbreviated" href="mailto:cmview-devel@www.bioinformatics.org">cmview-devel@www.bioinformatics.org</a>
rather than <a class="moz-txt-link-abbreviated" href="mailto:cmview-devel@bioinformatics.org">cmview-devel@bioinformatics.org</a> when you hit the
"reply to" button (it seems to depend on mail client anyway). We
have reported the problem and hope it will be solve soon. In the
meantime please use the address <a class="moz-txt-link-abbreviated" href="mailto:cmview-devel@bioinformatics.org">cmview-devel@bioinformatics.org</a>
<br>
<br>
Anyway thanks for the bug report, I'll try to have a look at it
at some point. Whenever you test from Linux it would be good to
have the outcome too. Also it would be good to know what exactly
you were doing to get the program to crash. You say it's
reproducible isn't it?
<br>
<br>
Cheers
<br>
<br>
Jose
<br>
<br>
</blockquote>
<br>
</blockquote>
Hi Jose and all,
<br>
<br>
here are both the console output and the crash log. I'll try and see
whether I can reproduce the bug in a Linux and Windows environment
in the next days.
<br>
<br>
Best,
<br>
Thomas
<br>
<br>
******************************
<br>
CMView console ouput
<br>
******************************
<br>
Starting CMView 1.1.1
<br>
Loading configuration file cmview.cfg
<br>
Using temporary directory <i class="moz-txt-slash"><span
class="moz-txt-tag">/</span>var/folders/QW/QW00CdXLFnqZDuc5zJ5fBU+++TI<span
class="moz-txt-tag">/</span></i>-Tmp-/
<br>
Connecting to PyMol...
<br>
Starting PyMol...
<br>
Connected.
<br>
Using DSSP executable ./DSSP_MAC.EXE
<br>
Mon Sep 26 12:15:20 Thomas-Hopfs-MacBook-Pro.local java[14704]
<Error>: kCGErrorIllegalArgument: CGSOrderWindowList
<br>
Mon Sep 26 12:15:20 Thomas-Hopfs-MacBook-Pro.local java[14704]
<Error>: kCGErrorFailure: Set a breakpoint @
CGErrorBreakpoint() to catch errors as they are logged.
<br>
Loading from online PDB
<br>
PDB code: 1hzx
<br>
Model serial: 1
<br>
Chain code: A
<br>
Contact type: Ca
<br>
Dist. cutoff: 8.0
<br>
Min. Seq. Sep.: 6
<br>
Max. Seq. Sep.: none
<br>
(Re)assigning secondary structure using DSSP
<br>
Warning: 9 unobserved or non-standard residues
<br>
Contact map 1hzxA loaded.
<br>
Shutting down
<br>
<br>
<br>
******************************
<br>
Mac OS crash log
<br>
******************************
<br>
<br>
Process: MacPyMOL [14705]
<br>
Path: /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL
<br>
Identifier: com.schrodinger.macpymol
<br>
Version: 1.3 (1.3)
<br>
Code Type: X86 (Native)
<br>
Parent Process: java [14704]
<br>
<br>
Date/Time: 2011-09-26 12:18:35.517 -0400
<br>
OS Version: Mac OS X 10.6.8 (10K549)
<br>
Report Version: 6
<br>
<br>
Interval Since Last Report: 2118983 sec
<br>
Crashes Since Last Report: 30
<br>
Per-App Interval Since Last Report: 788771 sec
<br>
Per-App Crashes Since Last Report: 6
<br>
Anonymous UUID:
725F98BC-E768-4B0C-BD4C-88C9203C02CE
<br>
<br>
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
<br>
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000044656d3c
<br>
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
<br>
<br>
Thread 0 Crashed: Dispatch queue: com.apple.main-thread
<br>
0 com.schrodinger.macpymol 0x000edfa6 SettingGet_i + 54
<br>
1 com.schrodinger.macpymol 0x0022f07e
ExecutiveUpdateSceneMembers + 718
<br>
2 com.schrodinger.macpymol 0x0022f347 ExecutiveDrawNow +
215
<br>
3 com.schrodinger.macpymol 0x002d21cd PyMOL_Draw + 573
<br>
4 com.schrodinger.macpymol 0x003ba204 -[PyMOLOpenGLView
drawRect:] + 148
<br>
5 com.apple.AppKit 0x9150e61e -[NSView
_drawRect:clip:] + 3510
<br>
6 com.apple.AppKit 0x9150d2bc -[NSView
_recursiveDisplayAllDirtyWithLockFocus:visRect:] + 1600
<br>
7 com.apple.AppKit 0x9150b7db -[NSView
_recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:]
+ 711
<br>
8 com.apple.AppKit 0x9150c750 -[NSView
_recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:]
+ 4668
<br>
9 com.apple.AppKit 0x9150c750 -[NSView
_recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:]
+ 4668
<br>
10 com.apple.AppKit 0x9150c750 -[NSView
_recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:]
+ 4668
<br>
11 com.apple.AppKit 0x9150b34f -[NSThemeFrame
_recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:]
+ 265
<br>
12 com.apple.AppKit 0x91507c96 -[NSView
_displayRectIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:]
+ 3309
<br>
13 com.apple.AppKit 0x9146884b -[NSView
displayIfNeeded] + 818
<br>
14 com.apple.AppKit 0x91431b64 -[NSWindow
displayIfNeeded] + 204
<br>
15 com.apple.AppKit 0x9146307e
_handleWindowNeedsDisplay + 696
<br>
16 com.apple.CoreFoundation 0x959f1e02
__CFRunLoopDoObservers + 1186
<br>
17 com.apple.CoreFoundation 0x959add1d __CFRunLoopRun +
557
<br>
18 com.apple.CoreFoundation 0x959ad3f4
CFRunLoopRunSpecific + 452
<br>
19 com.apple.CoreFoundation 0x959ad221 CFRunLoopRunInMode
+ 97
<br>
20 com.apple.HIToolbox 0x94551d60
RunCurrentEventLoopInMode + 392
<br>
21 com.apple.HIToolbox 0x94551b17
ReceiveNextEventCommon + 354
<br>
22 com.apple.HIToolbox 0x9455199c
BlockUntilNextEventMatchingListInMode + 81
<br>
23 com.apple.AppKit 0x91439595 _DPSNextEvent + 847
<br>
24 com.apple.AppKit 0x91438dd6 -[NSApplication
nextEventMatchingMask:untilDate:inMode:dequeue:] + 156
<br>
25 com.apple.AppKit 0x913fb1f3 -[NSApplication
run] + 821
<br>
26 com.schrodinger.macpymol 0x003bbd7b main + 4139
<br>
27 com.schrodinger.macpymol 0x00002b72 start + 54
<br>
<br>
Thread 1: Dispatch queue: com.apple.libdispatch-manager
<br>
0 libSystem.B.dylib 0x90175382 kevent + 10
<br>
1 libSystem.B.dylib 0x90175a9c
_dispatch_mgr_invoke + 215
<br>
2 libSystem.B.dylib 0x90174f59
_dispatch_queue_invoke + 163
<br>
3 libSystem.B.dylib 0x90174cfe
_dispatch_worker_thread2 + 240
<br>
4 libSystem.B.dylib 0x90174781 _pthread_wqthread +
390
<br>
5 libSystem.B.dylib 0x901745c6 start_wqthread + 30
<br>
<br>
Thread 2:
<br>
0 libSystem.B.dylib 0x9014ee26 read + 10
<br>
1 libSystem.B.dylib 0x901798fd _sread + 41
<br>
2 libSystem.B.dylib 0x9017977e __srefill + 48
<br>
3 libSystem.B.dylib 0x901802e0 __srget + 18
<br>
4 org.python.python 0x00a0a577 PyFile_AsFile + 407
<br>
5 org.python.python 0x00a0bd6a PyFile_SetBufSize +
2080
<br>
6 org.python.python 0x00a65d4d PyEval_EvalFrameEx
+ 16241
<br>
7 org.python.python 0x00a67ac6 PyEval_EvalCodeEx +
1734
<br>
8 org.python.python 0x00a12461 PyClassMethod_New +
2104
<br>
9 org.python.python 0x009f72a8 PyObject_Call + 50
<br>
10 org.python.python 0x00a67363 PyEval_EvalFrameEx
+ 21895
<br>
11 org.python.python 0x00a65edc PyEval_EvalFrameEx
+ 16640
<br>
12 org.python.python 0x00a65edc PyEval_EvalFrameEx
+ 16640
<br>
13 org.python.python 0x00a67ac6 PyEval_EvalCodeEx +
1734
<br>
14 org.python.python 0x00a124ce PyClassMethod_New +
2213
<br>
15 org.python.python 0x009f72a8 PyObject_Call + 50
<br>
16 org.python.python 0x00a00db7 PyClass_New + 1710
<br>
17 org.python.python 0x009f72a8 PyObject_Call + 50
<br>
18 org.python.python 0x00a61130
PyEval_CallObjectWithKeywords + 211
<br>
19 org.python.python 0x00a8eedf initthread + 1756
<br>
20 libSystem.B.dylib 0x9017c259 _pthread_start +
345
<br>
21 libSystem.B.dylib 0x9017c0de thread_start + 34
<br>
<br>
Thread 0 crashed with X86 Thread State (32-bit):
<br>
eax: 0x00002d3c ebx: 0x000edf84 ecx: 0x44656d3c edx: 0x01c27a50
<br>
edi: 0x00000243 esi: 0x00000000 ebp: 0xbfffb808 esp: 0xbfffb6d0
<br>
ss: 0x00000023 efl: 0x00010206 eip: 0x000edfa6 cs: 0x0000001b
<br>
ds: 0x00000023 es: 0x00000023 fs: 0x00000000 gs: 0x0000000f
<br>
cr2: 0x44656d3c
<br>
<br>
Binary Images:
<br>
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<br>
0x9f0000 - 0xac3fff org.python.python 2.5.4 (2.5)
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<br>
0xbbf000 - 0xbc0ff3 +time.so ??? (???)
/Applications/MacPyMOL.app/pymol/ext/lib/python2.5/lib-dynload/time.so
<br>
0xbcb000 - 0xbcefff +strop.so ??? (???)
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<br>
0xf0c000 - 0xf30fe7 GLRendererFloat ??? (???)
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<2DCD13E3-1BD1-6F25-119A-3863A3848B90>
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<br>
<br>
Model: MacBookPro8,1, BootROM MBP81.0047.B1E, 2 processors, Intel
Core i5, 2.3 GHz, 4 GB, SMC 1.68f96
<br>
Graphics: Intel HD Graphics 3000, Intel HD Graphics 3000, Built-In,
384 MB
<br>
Memory Module: global_name
<br>
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4,
0xD6), Broadcom BCM43xx 1.0 5.100.198.104.5)
<br>
Bluetooth: Version 2.4.5f3, 2 service, 19 devices, 1 incoming serial
ports
<br>
Network Service: Ethernet, Ethernet, en0
<br>
Network Service: AirPort, AirPort, en1
<br>
Serial ATA Device: Hitachi HTS545032B9A302, 298.09 GB
<br>
Serial ATA Device: HL-DT-ST DVDRW GS31N
<br>
USB Device: FaceTime HD Camera (Built-in), 0x05ac (Apple Inc.),
0x8509, 0xfa200000 / 3
<br>
USB Device: Hub, 0x0424 (SMSC), 0x2513, 0xfa100000 / 2
<br>
USB Device: BRCM2070 Hub, 0x0a5c (Broadcom Corp.), 0x4500,
0xfa110000 / 5
<br>
USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.),
0x821a, 0xfa113000 / 8
<br>
USB Device: Apple Internal Keyboard / Trackpad, 0x05ac (Apple
Inc.), 0x0246, 0xfa120000 / 4
<br>
USB Device: Hub, 0x0424 (SMSC), 0x2513, 0xfd100000 / 2
<br>
USB Device: Dell QuietKey Keyboard, 0x413c (Dell Inc.), 0x2106,
0xfd120000 / 4
<br>
USB Device: IR Receiver, 0x05ac (Apple Inc.), 0x8242, 0xfd110000 /
3
<br>
</body>
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