puzzle picture
1419: Medium Monomer Design
Status: Closed

Summary

Name: 1419: Medium Monomer Design
Status: Closed
Created: 08/18/2017
Points: 100
Expired: 08/25/2017 - 23:00
Difficulty: Intermediate
Description: This puzzle challenges players to design a single-chain protein with 75-90 residues. We've adjusted the scoring function here so that alanine residues are more tolerable in loops (they are still restricted in helices and sheets!). The starting structure has 75 residues, but more can be added at a cost of 23 points per residue. See the puzzle comments for filter details. The Baker Lab will run folding predictions on your solutions for this puzzle, and those that perform well will be synthesized in the lab. Remember, you can use the Upload for Scientists button for up to 5 designs that you want us to look at, even if they are not the best-scoring solutions!
Categories: Design, Overall

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Comments

bkoep's picture
User offline. Last seen 18 hours 43 min ago. Offline
Joined: 11/15/2012
Groups: None
Filters

Residue IE Score: Monitors that all PHE, TYR, and TRP residues are scoring well.

Core Existence: Ensures that at least 30% of the residues are buried in the core of your design.

Secondary Structure: Checks that no more than 50% of residues are in helices; penalties are incurred if more than 50% of residues form helices.

Secondary Structure Design: Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets; penalizes GLY, ALA, SER, THR in helices.

Residue Count: Penalizes extra residues inserted beyond the starting 75. Players may use up to 90 residues in total.

Ideal Loops: Penalizes loops that do not conform to preferred ABEGO patterns. Use Auto Structures to see which residues count as "loops."

Joined: 06/24/2008
Groups: Void Crushers
Crashed twice

Crashed twice; taking my computer down:

com.apple.message.domain: com.apple.crashreporter.writereport.cpu_resource.diag
com.apple.message.signature: Foldit
com.apple.message.signature2: UNBUNDLED ||| ??? (1.0) ((null))
com.apple.message.signature3: cpu usage
com.apple.message.result: noop
com.apple.message.summarize: YES
SenderMachUUID: CE4C7F36-9981-3467-92E7-EA2CD33C84BC

Process: WindowServer [204]
Path: /System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/Resources/WindowServer
Identifier: WindowServer
Version: 600.00 (15)
Code Type: X86-64 (Native)
Parent Process: launchd [1]
Responsible: WindowServer [204]
User ID: 88

Date/Time: 2017-08-23 10:53:31.945 -0400
OS Version: Mac OS X 10.12.6 (16G29)
Report Version: 12
Anonymous UUID: 33EE3CDF-5594-343C-1DA0-97104E3F3B3E

Sleep/Wake UUID: 263A460C-9566-4254-9CDF-9FDF2C0DFCE6

Time Awake Since Boot: 46000 seconds
Time Since Wake: 4300 seconds

System Integrity Protection: enabled

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY

Application Specific Information:
Assertion failed: (false && "10 seconds of continuous GPU Driver unreadiness, relaunching WindowServer"), function void IMGGraphicsStackReadinessFailure(), file Server/Windows/Updater.cc, line 2864.

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fffdd9d2d42 __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fffddac0457 pthread_kill + 90
2 libsystem_c.dylib 0x00007fffdd938420 abort + 129
3 libsystem_c.dylib 0x00007fffdd8ff893 __assert_rtn + 320
4 com.apple.SkyLight 0x00007fffd9d5e5be update_display_callback(void*, double) + 796
5 com.apple.SkyLight 0x00007fffd9c97c9a run_timer_pass + 700
6 com.apple.SkyLight 0x00007fffd9bdf125 CGXRunOneServicesPass + 149
7 com.apple.SkyLight 0x00007fffd9be08cf SLXServer + 3843
8 WindowServer 0x00000001055d4dde 0x1055d4000 + 3550
9 libdyld.dylib 0x00007fffdd8a4235 start + 1

Thread 1:
0 libsystem_kernel.dylib 0x00007fffdd9cb34a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fffdd9ca797 mach_msg + 55
2 com.apple.CoreDisplay 0x00007fffc80752bc CoreDisplay::Mach::Server::Start() + 132
3 com.apple.CoreDisplay 0x00007fffc8075f41 void* std::__1::__thread_proxy >(void*) + 113
4 libsystem_pthread.dylib 0x00007fffddabd93b _pthread_body + 180
5 libsystem_pthread.dylib 0x00007fffddabd887 _pthread_start + 286
6 libsystem_pthread.dylib 0x00007fffddabd08d thread_start + 13

Thread 2:
0 libsystem_kernel.dylib 0x00007fffdd9cb34a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fffdd9ca797 mach_msg + 55
2 com.apple.CoreFoundation 0x00007fffc8125434 __CFRunLoopServiceMachPort + 212
3 com.apple.CoreFoundation 0x00007fffc81248c1 __CFRunLoopRun + 1361
4 com.apple.CoreFoundation 0x00007fffc8124114 CFRunLoopRunSpecific + 420
5 com.apple.CoreFoundation 0x00007fffc8163b91 CFRunLoopRun + 97
6 com.apple.DFRDisplay 0x00000001057744b1 DFRDisplayRunloopThread + 119
7 libsystem_pthread.dylib 0x00007fffddabd93b _pthread_body + 180
8 libsystem_pthread.dylib 0x00007fffddabd887 _pthread_start + 286
9 libsystem_pthread.dylib 0x00007fffddabd08d thread_start + 13

Thread 3:: com.apple.coreanimation.render-server
0 libsystem_kernel.dylib 0x00007fffdd9cb34a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fffdd9ca797 mach_msg + 55
2 com.apple.QuartzCore 0x00007fffcdd08bd4 CA::Render::Server::server_thread(void*) + 272
3 com.apple.QuartzCore 0x00007fffcddb93ab thread_fun + 25
4 libsystem_pthread.dylib 0x00007fffddabd93b _pthread_body + 180
5 libsystem_pthread.dylib 0x00007fffddabd887 _pthread_start + 286
6 libsystem_pthread.dylib 0x00007fffddabd08d thread_start + 13

Thread 4:
0 libsystem_kernel.dylib 0x00007fffdd9d344e __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fffddabd48e _pthread_wqthread + 1023
2 libsystem_pthread.dylib 0x00007fffddabd07d start_wqthread + 13

Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000000000006 rcx: 0x00007fff5a62b598 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x00007fff5a62b5c0 rsp: 0x00007fff5a62b598
r8: 0x0000000000000000 r9: 0x0000000000000b30 r10: 0x0000000008000000 r11: 0x0000000000000206
r12: 0x000000013d888028 r13: 0x000000013d888000 r14: 0x00007fffe67b83c0 r15: 0x00007fffd9dfcec0
rip: 0x00007fffdd9d2d42 rfl: 0x0000000000000206 cr2: 0x00007fffe679a128

Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133

Binary Images:
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0x7fffc52b3000 - 0x7fffc56a9fef libLAPACK.dylib (1185.50.4) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
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0x7fffc56c1000 - 0x7fffc56c7fff libQuadrature.dylib (3) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libQuadrature.dylib
0x7fffc56c8000 - 0x7fffc56dcff7 libSparseBLAS.dylib (1185.50.4) <67BA432E-FB59-3C78-A8BE-ED4274CBC359> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparseBLAS.dylib
0x7fffc56dd000 - 0x7fffc5864fe7 libvDSP.dylib (600.60.1) <4155F45B-41CD-3782-AE8F-7AE740FD83C3> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
0x7fffc5865000 - 0x7fffc5917fff libvMisc.dylib (600.60.1) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
0x7fffc5918000 - 0x7fffc5918fff com.apple.Accelerate.vecLib (3.11 - vecLib 3.11) <7C5733E7-0568-3E7D-AF61-160F19FED544> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
0x7fffc5bd7000 - 0x7fffc69b0ff3 com.apple.AppKit (6.9 - 1504.83.101) /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
0x7fffc69c2000 - 0x7fffc69c2fff com.apple.ApplicationServices (48 - 48) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
0x7fffc69c3000 - 0x7fffc6a31ff7 com.apple.ApplicationServices.ATS (377 - 422.2) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS
0x7fffc6acb000 - 0x7fffc6bfaff7 libFontParser.dylib (194.12) <73C3946D-EF92-3AC1-89C3-0E75B2A85325> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib
0x7fffc6bfb000 - 0x7fffc6c45fff libFontRegistry.dylib (196.4) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib
0x7fffc6d42000 - 0x7fffc6decff7 com.apple.ColorSync (4.12.0 - 502.2) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync
0x7fffc6ded000 - 0x7fffc6e3efff com.apple.HIServices (1.22 - 593) <045870A9-1D92-3FEF-8722-671E99A35E71> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
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0x7fffc70f2000 - 0x7fffc70f2fff com.apple.audio.units.AudioUnit (1.14 - 1.14) /System/Library/Frameworks/AudioUnit.framework/Versions/A/AudioUnit
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0x7fffdd8a5000 - 0x7fffdd8a5ffb libkeymgr.dylib (28) <7AA011A9-DC21-3488-BF73-3B5B14D1FDD6> /usr/lib/system/libkeymgr.dylib
0x7fffdd8a6000 - 0x7fffdd8b2fff libkxld.dylib (3789.70.16) /usr/lib/system/libkxld.dylib
0x7fffdd8b3000 - 0x7fffdd8b3fff liblaunch.dylib (972.70.1) /usr/lib/system/liblaunch.dylib
0x7fffdd8b4000 - 0x7fffdd8b9ff3 libmacho.dylib (898) <17D5D855-F6C3-3B04-B680-E9BF02EF8AED> /usr/lib/system/libmacho.dylib
0x7fffdd8ba000 - 0x7fffdd8bcff3 libquarantine.dylib (85.50.1) <12448CC2-378E-35F3-BE33-9DC395A5B970> /usr/lib/system/libquarantine.dylib
0x7fffdd8bd000 - 0x7fffdd8beffb libremovefile.dylib (45) <38D4CB9C-10CD-30D3-8B7B-A515EC75FE85> /usr/lib/system/libremovefile.dylib
0x7fffdd8bf000 - 0x7fffdd8d7ff7 libsystem_asl.dylib (349.50.5) <096E4228-3B7C-30A6-8B13-EC909A64499A> /usr/lib/system/libsystem_asl.dylib
0x7fffdd8d8000 - 0x7fffdd8d8ff7 libsystem_blocks.dylib (67) <10DC5404-73AB-35B3-A277-A8AFECB476EB> /usr/lib/system/libsystem_blocks.dylib
0x7fffdd8d9000 - 0x7fffdd966fef libsystem_c.dylib (1158.50.2) /usr/lib/system/libsystem_c.dylib
0x7fffdd967000 - 0x7fffdd96affb libsystem_configuration.dylib (888.60.2) /usr/lib/system/libsystem_configuration.dylib
0x7fffdd96b000 - 0x7fffdd96efff libsystem_coreservices.dylib (41.4) <7D26DE79-B424-3450-85E1-F7FAB32714AB> /usr/lib/system/libsystem_coreservices.dylib
0x7fffdd96f000 - 0x7fffdd987fff libsystem_coretls.dylib (121.50.4) /usr/lib/system/libsystem_coretls.dylib
0x7fffdd988000 - 0x7fffdd98efff libsystem_dnssd.dylib (765.50.9) /usr/lib/system/libsystem_dnssd.dylib
0x7fffdd98f000 - 0x7fffdd9b8ff7 libsystem_info.dylib (503.50.4) <611DB84C-BF70-3F92-8702-B9F28A900920> /usr/lib/system/libsystem_info.dylib
0x7fffdd9b9000 - 0x7fffdd9dbff7 libsystem_kernel.dylib (3789.70.16) <34B1F16C-BC9C-3C5F-9045-0CAE91CB5914> /usr/lib/system/libsystem_kernel.dylib
0x7fffdd9dc000 - 0x7fffdda23fe7 libsystem_m.dylib (3121.6) <86D499B5-BBDC-3D3B-8A4E-97AE8E6672A4> /usr/lib/system/libsystem_m.dylib
0x7fffdda24000 - 0x7fffdda42ff7 libsystem_malloc.dylib (116.50.8) /usr/lib/system/libsystem_malloc.dylib
0x7fffdda43000 - 0x7fffdda9cffb libsystem_network.dylib (856.60.1) <369D0221-56CA-3C3E-9EDE-94B41CAE77B7> /usr/lib/system/libsystem_network.dylib
0x7fffdda9d000 - 0x7fffddaa6ff3 libsystem_networkextension.dylib (563.60.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fffddaa7000 - 0x7fffddab0ff3 libsystem_notify.dylib (165.20.1) /usr/lib/system/libsystem_notify.dylib
0x7fffddab1000 - 0x7fffddab9fe7 libsystem_platform.dylib (126.50.8) <897462FD-B318-321B-A554-E61982630F7E> /usr/lib/system/libsystem_platform.dylib
0x7fffddaba000 - 0x7fffddac4ff7 libsystem_pthread.dylib (218.60.3) /usr/lib/system/libsystem_pthread.dylib
0x7fffddac5000 - 0x7fffddac8ff7 libsystem_sandbox.dylib (592.70.1) <4B92EC49-ACD0-36AE-B07A-A2B8152EAF9D> /usr/lib/system/libsystem_sandbox.dylib
0x7fffddac9000 - 0x7fffddacaff3 libsystem_secinit.dylib (24.50.4) /usr/lib/system/libsystem_secinit.dylib
0x7fffddacb000 - 0x7fffddad2ffb libsystem_symptoms.dylib (532.50.47) <3390E07C-C1CE-348F-ADBD-2C5440B45EAA> /usr/lib/system/libsystem_symptoms.dylib
0x7fffddad3000 - 0x7fffddae6ff7 libsystem_trace.dylib (518.70.1) /usr/lib/system/libsystem_trace.dylib
0x7fffddae7000 - 0x7fffddaecffb libunwind.dylib (35.3) <3D50D8A8-C460-334D-A519-2DA841102C6B> /usr/lib/system/libunwind.dylib
0x7fffddaed000 - 0x7fffddb16ff7 libxpc.dylib (972.70.1) /usr/lib/system/libxpc.dylib

External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 91
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 23997
thread_create: 0
thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=273.9M resident=0K(0%) swapped_out_or_unallocated=273.9M(100%)
Writable regions: Total=1.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.1G(100%)

VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Activity Tracing 256K 2
CG backing stores 51.7M 131
CG framebuffers 775.0M 7
CG framebuffers (reserved) 35.0M 6 reserved VM address space (unallocated)
CG image 1188K 19
CoreAnimation 75.1M 247
CoreUI image data 244K 8
Dispatch continuations 16.0M 2
Image IO 1508K 22
Kernel Alloc Once 8K 2
MALLOC 240.3M 57
MALLOC guard page 48K 10
Memory Tag 252 20.0M 3
OpenGL GLSL 256K 4
STACK GUARD 56.0M 6
Stack 10.0M 6
VM_ALLOCATE 968K 55
__CGSERVER 4K 2
__DATA 30.9M 210
__GLSLBUILTINS 2588K 2
__IMAGE 528K 2
__LINKEDIT 116.3M 13
__TEXT 157.6M 212
__UNICODE 556K 2
mapped file 24.7M 2
shared memory 172K 16
=========== ======= =======
TOTAL 1.6G 1022
TOTAL, minus reserved VM space 1.5G 1022

Susume's picture
User offline. Last seen 4 hours 13 min ago. Offline
Joined: 10/02/2011
Might be graphics problem

I think this may be the pertinent error message in that Mac output: "10 seconds of continuous GPU Driver unreadiness, relaunching WindowServer".

There are numerous reports around the web from 2016 of this mac error message relating to various apps under Sierra, although I don't find any reports from 2017. Are you up to date on OS updates? Have you recently changed anything about your graphics or monitor(s)?

toshiue's picture
User offline. Last seen 1 hour 40 min ago. Offline
Joined: 01/31/2016
Groups: Go Science
Rank and scoring

Rank and scoring in the client is wrong.

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