[Chimera-users] something flakey with measure buriedArea?
Tom Goddard
goddard at cgl.ucsf.edu
Tue Apr 27 18:09:43 PDT 2010
Hi Scott,
Here's some previous mailing list commentary on problems computing
buried surface area
http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-August/004195.html
As you've notice the surface calculation is pretty unstable. Lots of
warnings are common. How serious they are is hard to tell. You might
look for consistency of buried area numbers with slightly different
probe radii as a crude way to judge.
The completely erroneous values (negative buried surface area) that you
reported are related to the surface calculation partially failing for
one or more of the needed 3 surfaces (A, B, A+B). By a partial failure
I mean the code falls back to computing just one exterior surface
components and no interior components. If that happens for one of the 3
needed calculations and not the others you get completely screwed up
numbers (e.g. negative). Unfortunately the Chimera code is not
detecting this partial failure case, though you should see the
"fallback" warning in the reply log.
Chimera is not supposed to crash when mscalc (a separate stand-alone
program) crashes. I assume you mean that just mscalc crashes, Chimera
keeps running. You should not see a Mac crash report dialog if mscalc
crashes if you are using a current Chimera version (1.4, maybe even
1.3). I added some code to suppress the crash dumps on mscalc because
they happen frequently and are caused by the instability of the MSMS
code which we did not write.
Tom
> I'm seeing some very odd results coming from the measure buriedArea command
> if I use different values for probeRaduis and then grep for WARNINGs
> I get the following results:
>
> probeRadius # of WARNINGs
> 1.50 = 12
> 1.40 = 4
> 1.39 = 14
> 1.35 = 59
> 1.30 = 3
> 1.20 = 0
>
> Here are some examples of the types of warnings I'm seeing:
>
> WARNING: check_SES_edge: weird case, 1 probe full2 and not full1
> WARNING: class_arete2: warning hole in a reentrant face 1735
> WARNING: check_SES_edge: weird case, 1 probe full2 and not full1
> WARNING: check_SES_edge: weird case, 1 probe full2 and not full1
> WARNING: class_arete2: warning hole in a reentrant face 2557
> WARNING: check_SES_edge: weird case, 1 probe full2 and not full1
> WARNING: class_arete2: warning hole in a reentrant face 1836
> WARNING: check_SES_edge: weird case, 1 probe full2 and not full1
> WARNING: check_SES_edge: weird case, 1 probe full2 and not full1
> WARNING: class_arete2: warning hole in a reentrant face 2090
> WARNING: class_arete2: warning hole in a reentrant face 1925
> WARNING: compute_SES_area: ERROR: Solide angle (-1.972093) for contact face 3142 too large or too small
>
> Should I be concerned?
>
> Another unusual thing is that for certain calculations I get some crazy answers. For example the following command
>
> measure buriedArea '#0:.A,.B& #0:10.Dz<8' #0:10.D probeRadius 1.4 vertexDensity 2
>
>
> outputs:
> B1SES = -583.491, B2SES = 51.4762, BaveSES = -266.007
>
> but the same command with the probeRadius changed to 1.37
>
> measure buriedArea '#0:.A,.B& #0:10.Dz<8' #0:10.D probeRadius 1.37 vertexDensity 2
>
> outputs:
> B1SES = 53.9334, B2SES = 51.7969, BaveSES = 52.8652
>
> Why would B1SES be so radically different for these two measurements?
>
> Thanks,
> Scott
>
>
> ps When doing these calculations Chimera randomly crashes with the following mscalc crash report:
>
>
> Process: mscalc [25532]
> Path: /Applications/Chimera-1.5b.app/Contents/Resources/bin/mscalc
> Identifier: mscalc
> Version: ??? (???)
> Code Type: X86-64 (Native)
> Parent Process: python2.6 [25482]
>
> Date/Time: 2010-04-27 17:23:08.864 -0700
> OS Version: Mac OS X 10.6.3 (10D573)
> Report Version: 6
>
> Interval Since Last Report: 402 sec
> Crashes Since Last Report: 1
> Per-App Crashes Since Last Report: 1
> Anonymous UUID: D0B1026B-AD5E-454C-8E35-49CCF7598339
>
> Exception Type: EXC_CRASH (SIGABRT)
> Exception Codes: 0x0000000000000000, 0x0000000000000000
> Crashed Thread: 0 Dispatch queue: com.apple.main-thread
>
> Application Specific Information:
> abort() called
>
> Thread 0 Crashed: Dispatch queue: com.apple.main-thread
> 0 libSystem.B.dylib 0x00007fff83cc7886 __kill + 10
> 1 libSystem.B.dylib 0x00007fff83d67eae abort + 83
> 2 libSystem.B.dylib 0x00007fff83c7fa75 free + 128
> 3 mscalc 0x00000001000218e5 MS_delete_SES_face + 920
> 4 mscalc 0x00000001000361f4 MS_update_ses + 919
> 5 mscalc 0x0000000100034f68 MS_restart_from_ses + 613
> 6 mscalc 0x0000000100036963 MS_update_ses + 2822
> 7 mscalc 0x0000000100037d94 MS_restart_from_triangulation + 591
> 8 mscalc 0x0000000100046c66 MS_triangulate_SES_component + 925
> 9 mscalc 0x00000001000066f6 MS_compute_surface + 443
> 10 mscalc 0x0000000100000ea2 main + 382
> 11 mscalc 0x0000000100000d1c start + 52
>
> Thread 0 crashed with X86 Thread State (64-bit):
> rax: 0x0000000000000000 rbx: 0x0000000000000001 rcx: 0x00007fff5fbfd998 rdx: 0x0000000000000000
> rdi: 0x00000000000063bc rsi: 0x0000000000000006 rbp: 0x00007fff5fbfd9b0 rsp: 0x00007fff5fbfd998
> r8: 0x0000000000000e03 r9: 0x0000000000000000 r10: 0x00007fff83cc38ca r11: 0x0000000000000206
> r12: 0x00000001001e4000 r13: 0x0000000100200000 r14: 0x0000000000000000 r15: 0x00000001004f7c70
> rip: 0x00007fff83cc7886 rfl: 0x0000000000000206 cr2: 0x000000010022a000
>
> Binary Images:
> 0x100000000 - 0x10004eff7 +mscalc ??? (???)<AF86E566-5546-A8C8-DE97-4A16408CB1BC> /Applications/Chimera-1.5b.app/Contents/Resources/bin/mscalc
> 0x7fff5fc00000 - 0x7fff5fc3bdef dyld 132.1 (???)<B633F790-4DDB-53CD-7ACF-2A3682BCEA9F> /usr/lib/dyld
> 0x7fff83c78000 - 0x7fff83e37ff7 libSystem.B.dylib 125.0.1 (compatibility 1.0.0)<CB9A4929-61AF-DE71-5635-133E9EC95783> /usr/lib/libSystem.B.dylib
> 0x7fff885a7000 - 0x7fff885abff7 libmathCommon.A.dylib 315.0.0 (compatibility 1.0.0)<95718673-FEEE-B6ED-B127-BCDBDB60D4E5> /usr/lib/system/libmathCommon.A.dylib
> 0x7fffffe00000 - 0x7fffffe01fff libSystem.B.dylib ??? (???)<CB9A4929-61AF-DE71-5635-133E9EC95783> /usr/lib/libSystem.B.dylib
>
> Model: MacPro1,1, BootROM MP11.005C.B08, 4 processors, Dual-Core Intel Xeon, 2.66 GHz, 14 GB, SMC 1.7f10
> Graphics: ATI Radeon X1900 XT, ATY,RadeonX1900, PCIe, 512 MB
> Memory Module: global_name
> AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x87), Broadcom BCM43xx 1.0 (5.10.91.27)
> Bluetooth: Version 2.3.1f4, 2 service, 19 devices, 1 incoming serial ports
> Network Service: Built-in Ethernet 2, Ethernet, en1
> PCI Card: ATY,RadeonX1900, Display, Slot-1
> Serial ATA Device: ST3250824AS P, 232.89 GB
> Serial ATA Device: WDC WD2500JD-00HBC0, 232.89 GB
> Serial ATA Device: WDC WD1002FBYS-01A6B0, 931.51 GB
> Serial ATA Device: WDC WD1002FBYS-01A6B0, 931.51 GB
> Parallel ATA Device: SONY DVD RW DW-D150A
> USB Device: Hub, 0x05ac (Apple Inc.), 0x9131, 0xfd400000
> USB Device: iPhone, 0x05ac (Apple Inc.), 0x1292, 0xfd430000
> USB Device: Keyboard Hub, 0x05ac (Apple Inc.), 0x1005, 0xfd410000
> USB Device: Apple Keyboard, 0x05ac (Apple Inc.), 0x021d, 0xfd412000
> USB Device: Apple Cinema HD Display, 0x05ac (Apple Inc.), 0x9223, 0xfd420000
> USB Device: Hub, 0x05ac (Apple Inc.), 0x9122, 0xfd300000
> USB Device: Apple Cinema HD Display, 0x05ac (Apple Inc.), 0x921e, 0xfd320000
> USB Device: USB Receiver, 0x046d (Logitech Inc.), 0xc525, 0x1d200000
> USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8206, 0x5d200000
> USB Device: Back-UPS CS 500 FW:806.q5.D USB FW:q5, 0x051d (American Power Conversion), 0x0002, 0x5d100000
> FireWire Device: built-in_hub, Up to 800 Mb/sec
> FireWire Device: unknown_device, Unknown
>
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