- phenixbb - phenix-online.org

Thresholding for N/Q/H errors in phenix.refine?
by Nicholas Gao 15 Nov '21

15 Nov '21

Hi, For the correction of N/Q/H errors in phenix.refine: is this option binary (that is, can it only be turned on or off)? Or can it be adjusted to be on but its stringency adjusted to an arbitrary scale? https://phenix-online.org/documentation/reference/refinement.html#id19 <--suggests its binary, but asking here for thoroughness. Sincerely, Nicholas Gao

2 1

superpose mrc maps (and also mtz files)
by Georg Mlynek 15 Nov '21

15 Nov '21

Dear Scientific community, I got a few .mrc maps from collaborators. Is there a way in phenix to superpose models and corresponding mrc maps. Using superpose maps I get the error:" This file format CCP4 map is not supported as input for this field; only files of type 'Reflections' are allowed. Also the program Structure comparison does not recognize .mrc files. On top there are also a few mtz files I would like to superpose on the .mrc files. Many thanks, br Georg.

3 3

Phenix bug report [[email protected] - Mon Jun 22 19:42:79 2021]
by Robert Munoz 15 Nov '21

15 Nov '21

User name: Robert Munoz E-mail address: robertm(a)lbl.gov Version: 1.18.2-3874 Platform: mac-intel-osx-x86_64 Comments: Trying to refinement using locscale out map Traceback: RuntimeError : cctbx Internal Error: /Users/builder/slave/phenix-nightly-mac-intel-osx-x86_64/modules/cctbx_project/cctbx/maptbx/resolution.h(38): CCTBX_ASSERT(sum_all != 0.) failure. Traceback: File "/Applications/phenix-1.18.2-3874/modules/cctbx_project/libtbx/runtime_utils.py", line 181, in run return_value = self.target() File "/Applications/phenix-1.18.2-3874/modules/cctbx_project/libtbx/runtime_utils.py", line 76, in __call__ result = self.run() File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 908, in run self.result = run(args=self.args, validated=True, log=sys.stdout) File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 581, in __init__ self.caller(func = self.initialize, prefix="Initialize") File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 619, in caller status = func(prefix=prefix, **kwargs) File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 696, in initialize self.inputs = self.process_inputs() File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 675, in process_inputs return process_inputs_stage_1(process_inputs_stage_0_object=pis_0, log=self.log) File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 403, in process_inputs_stage_1 crystal_symmetry = model.crystal_symmetry()).result.d99 File "/Applications/phenix-1.18.2-3874/modules/cctbx_project/cctbx/maptbx/__init__.py", line 117, in __init__ d_max = self.d_max) Platform info: __FILE__ = /Users/builder/slave/phenix-nightly-mac-intel-osx-x86_64/modules/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = May 17 2020 __TIME__ = 22:35:27 __TIMESTAMP__ = Thu Feb 27 10:57:04 2020 __x86_64__ __APPLE_CC__ = 6000 __GNUC__ = 4 __GNUC_MINOR__ = 2 __GNUC_PATCHLEVEL__ = 1 __clang__ __clang_major__ = 11 __clang_minor__ = 0 __clang_patchlevel__ = 0 __clang_version__ = 11.0.0 (clang-1100.0.33.17) __llvm__ __GXX_WEAK__ = 1 __LP64__ = 1 __VERSION__ = 4.2.1 Compatible Apple LLVM 11.0.0 (clang-1100.0.33.17) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 63 __SSE2__ = 1 BOOST_LIB_VERSION = 1_63 PY_VERSION = 2.7.15 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 8 sizeof(std::size_t) = 8 sizeof(void*) = 8 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 16 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG boost/TAG: None os.name: posix sys.platform: darwin sys.byteorder: little platform.platform(): Darwin-17.7.0-x86_64-i386-64bit platform.architecture(): ('64bit', '') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 4 Memory total: 17,179,869,184 Memory free: unknown import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = Å

2 1

Double difference anomalous maps
by Mark Saper 09 Nov '21

09 Nov '21

I tried the "Isomorphous difference map” action and specified a file for input 1 containing F1+, F1– at one wavelength, and the file input 2 containing F2+,F2– at another wavelength. I selected the appropriate Labels for the columns containing the anomalous data. I then specified in "Advanced Options” to use anomalous differences instead of amplitudes. Will this procedure use the following coefficients for the difference Fourier? ( F1(+) – F1(–) ) – ( F2(+) – F2(–) ), alpha(calc) Can someone confirm if this is indeed what is calculated? Many thanks, Mark Saper __________________ Mark A. Saper, Ph.D. Visiting Professor at the Faculty of Medicine Hebrew University of Jerusalem Ein Kerem Jerusalem ISRAEL saper(a)umich.edu mobile +972 52 815-0480‬ Powered by Mailbutler <https://www.mailbutler.io/?utm_source=watermark&utm_medium=email&utm_campai…>, the email extension that does it all

2 1

Parameters in "reference_model" during "real space refinement"
by Coudray, Nicolas 08 Nov '21

08 Nov '21

Hi, I would be interested in understanding more the exact meaning of the options related to "reference model" when doing "real space refinement" (in https://phenix-online.org/documentation/reference/real_space_refine.html): * hydrogens = False * main_chain = True * side_chain = True * fix_outliers = True * strict_rotamer_matching = False * auto_shutoff_for_ncs = False * secondary_structure_only = False It is a bit unclear what setting each of them to "True" would exactly imply or what the difference between them are. Does anyone have more information? Thanks, Best, Nicolas ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

2 2

eLBOW crashes Phenix
by Xavier Brazzolotto 03 Nov '21

03 Nov '21

Hi, I am using the latest stable Phenix release (1.19.2-4158) on macOS (v12.0.1) and I do have an odd bug with Phenix eLBOW. The program by it self runs and generates the expected cif files. If I open REEL to check the models, I do see them but as soon as I exit REEL, it crashes the whole Phenix process. Is it a know bug ? I paste the crash report below if this helps. ------------------------------------- Translated Report (Full Report Below) ------------------------------------- Process: python [57745] Path: /Applications/phenix-1.19.2-4158/*/python.app/Contents/MacOS/python Identifier: com.continuum.python Version: ??? Code Type: X86-64 (Native) Parent Process: launchd [1] User ID: 501 Date/Time: 2021-11-03 18:05:27.1449 +0100 OS Version: macOS 12.0.1 (21A559) Report Version: 12 Bridge OS Version: 6.0 (19P548) Anonymous UUID: 461A1FA5-1FFE-CC49-2057-0C0BB25A7143 Sleep/Wake UUID: 335CBE5C-1D37-4713-B3EA-80B0E830794F Time Awake Since Boot: 300000 seconds Time Since Wake: 13706 seconds System Integrity Protection: enabled Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000020 Exception Codes: 0x0000000000000001, 0x0000000000000020 Exception Note: EXC_CORPSE_NOTIFY Termination Reason: Namespace SIGNAL, Code 11 Segmentation fault: 11 Terminating Process: exc handler [57745] VM Region Info: 0x20 is not in any region. Bytes before following region: 4480602080 REGION TYPE START - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL UNUSED SPACE AT START ---> __TEXT 10b109000-10b10a000 [ 4K] r-x/rwx SM=COW .../MacOS/python Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libobjc.A.dylib 0x7ff81e00bc4f objc_release + 31 1 Foundation 0x7ff81f1ecde8 empty + 58 2 Foundation 0x7ff81f094dd9 dealloc + 38 3 Foundation 0x7ff81f094d64 -[NSConcreteMapTable dealloc] + 54 4 libobjc.A.dylib 0x7ff81e0290fe objc_object::sidetable_release(bool, bool) + 232 5 AppKit 0x7ff8212d8c4c ___NSTouchBarFinderSetNeedsUpdateOnMain_block_invoke_2 + 2233 6 AppKit 0x7ff820d3130c NSDisplayCycleObserverInvoke + 155 7 AppKit 0x7ff820d30e97 NSDisplayCycleFlush + 952 8 QuartzCore 0x7ff8252a5434 CA::Transaction::run_commit_handlers(CATransactionPhase) + 98 9 QuartzCore 0x7ff8252a41b2 CA::Transaction::commit() + 376 10 AppKit 0x7ff820dd24e2 __62+[CATransaction(NSCATransaction) NS_setFlushesWithDisplayLink]_block_invoke + 285 11 AppKit 0x7ff821518724 ___NSRunLoopObserverCreateWithHandler_block_invoke + 41 12 CoreFoundation 0x7ff81e23bc07 __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ + 23 13 CoreFoundation 0x7ff81e23baa4 __CFRunLoopDoObservers + 543 14 CoreFoundation 0x7ff81e23af37 __CFRunLoopRun + 841 15 CoreFoundation 0x7ff81e23a52d CFRunLoopRunSpecific + 563 16 HIToolbox 0x7ff826e583e1 RunCurrentEventLoopInMode + 292 17 HIToolbox 0x7ff826e58008 ReceiveNextEventCommon + 284 18 HIToolbox 0x7ff826e57ed5 _BlockUntilNextEventMatchingListInModeWithFilter + 70 19 AppKit 0x7ff820c658f0 _DPSNextEvent + 886 20 AppKit 0x7ff820c63f5c -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1411 21 AppKit 0x7ff820c56359 -[NSApplication run] + 586 22 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d2b0a23 wxGUIEventLoop::OSXDoRun() + 115 23 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d192ce4 wxCFEventLoop::DoRun() + 52 24 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d0c2885 wxEventLoopBase::Run() + 165 25 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d087521 wxAppConsoleBase::MainLoop() + 209 26 _core_.so 0x10bd94114 wxPyApp::MainLoop() + 84 27 _core_.so 0x10bdf7902 _wrap_PyApp_MainLoop(_object*, _object*) + 82 28 libpython2.7.dylib 0x10b4967ee PyEval_EvalFrameEx + 30382 29 libpython2.7.dylib 0x10b48eeb3 PyEval_EvalCodeEx + 2147 30 libpython2.7.dylib 0x10b409a84 function_call + 388 31 libpython2.7.dylib 0x10b3dcce1 PyObject_Call + 97 32 libpython2.7.dylib 0x10b3ee5d4 instancemethod_call + 180 33 libpython2.7.dylib 0x10b3dcce1 PyObject_Call + 97 34 libpython2.7.dylib 0x10b4957b6 PyEval_EvalFrameEx + 26230 35 libpython2.7.dylib 0x10b49c631 fast_function + 337 36 libpython2.7.dylib 0x10b495889 PyEval_EvalFrameEx + 26441 37 libpython2.7.dylib 0x10b48eeb3 PyEval_EvalCodeEx + 2147 38 libpython2.7.dylib 0x10b49c54a fast_function + 106 39 libpython2.7.dylib 0x10b495889 PyEval_EvalFrameEx + 26441 40 libpython2.7.dylib 0x10b48eeb3 PyEval_EvalCodeEx + 2147 41 libpython2.7.dylib 0x10b48e642 PyEval_EvalCode + 34 42 libpython2.7.dylib 0x10b4c0901 PyRun_FileExFlags + 161 43 libpython2.7.dylib 0x10b4c035f PyRun_SimpleFileExFlags + 847 44 libpython2.7.dylib 0x10b4d8dfb Py_Main + 3483 45 dyld 0x11609f4fe start + 462 Thread 1:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x7ff81e138aba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x7ff81e138e2b mach_msg + 59 2 CoreFoundation 0x7ff81e23ca42 __CFRunLoopServiceMachPort + 319 3 CoreFoundation 0x7ff81e23b11b __CFRunLoopRun + 1325 4 CoreFoundation 0x7ff81e23a52d CFRunLoopRunSpecific + 563 5 AppKit 0x7ff820dd3cec _NSEventThread + 132 6 libsystem_pthread.dylib 0x7ff81e175514 _pthread_start + 125 7 libsystem_pthread.dylib 0x7ff81e17102f thread_start + 15 Thread 2: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 3: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 4:: Dispatch queue: com.apple.NSXPCConnection.user.endpoint.NSRemoteView.IMKTextInputFunctionRowItemServiceViewController 0 CoreFoundation 0x7ff81e1c5746 CFHash + 134 1 CoreFoundation 0x7ff81e1e49fb CFBasicHashAddValue + 223 2 CoreFoundation 0x7ff81e22e09c CFSetCreate + 66 3 CoreFoundation 0x7ff81e223179 CFRunLoopPerformBlock + 288 4 ViewBridge 0x7ff82572020d deferBlockOntoMainThread + 280 5 ViewBridge 0x7ff82572d4d5 deferNSXPCInvocationOntoMainThread + 130 6 Foundation 0x7ff81f0acc12 -[NSXPCConnection _decodeAndInvokeMessageWithEvent:flags:] + 1576 7 Foundation 0x7ff81f063f1a message_handler + 206 8 libxpc.dylib 0x7ff81deba530 _xpc_connection_call_event_handler + 56 9 libxpc.dylib 0x7ff81deb928c _xpc_connection_mach_event + 1387 10 libdispatch.dylib 0x7ff81dfbed63 _dispatch_client_callout4 + 9 11 libdispatch.dylib 0x7ff81dfd78b7 _dispatch_mach_msg_invoke + 452 12 libdispatch.dylib 0x7ff81dfc4b85 _dispatch_lane_serial_drain + 335 13 libdispatch.dylib 0x7ff81dfd83fb _dispatch_mach_invoke + 484 14 libdispatch.dylib 0x7ff81dfc4b85 _dispatch_lane_serial_drain + 335 15 libdispatch.dylib 0x7ff81dfc57c8 _dispatch_lane_invoke + 366 16 libdispatch.dylib 0x7ff81dfcf7e1 _dispatch_workloop_worker_thread + 758 17 libsystem_pthread.dylib 0x7ff81e17208f _pthread_wqthread + 326 18 libsystem_pthread.dylib 0x7ff81e17101b start_wqthread + 15 Thread 5: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 6: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 7: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 8: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 9: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 10: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 11: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 12: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x6000000000000000 rbx: 0x0000000000000018 rcx: 0x0000000000000000 rdx: 0x00007f8ec5973a00 rdi: 0x00007f8ea57830d0 rsi: 0x0000000000000000 rbp: 0x00007ff7b4df3260 rsp: 0x00007ff7b4df3238 r8: 0x0000000000000200 r9: 0x00007f8ec5972d20 r10: 0x00007ff85f8105d0 r11: 0x00007ff81f094d2e r12: 0x00007f8f01f8e7c0 r13: 0x00007ff85f966a01 r14: 0x00007f8f01f8e7c8 r15: 0x000000000000000d rip: 0x00007ff81e00bc4f rfl: 0x0000000000010246 cr2: 0x0000000000000020 Logical CPU: 0 Error Code: 0x00000004 (no mapping for user data read) Trap Number: 14 Thread 0 instruction stream: 34 48 89 c2 48 01 ca 72-12 f0 48 0f b1 17 74 25 4H..H..r..H...t% a8 01 75 e4 31 f6 e9 7c-d7 01 00 31 f6 e9 eb 86 ..u.1..|...1.... 00 00 48 b9 f8 ff ff ff-ff 7f 00 00 48 21 c8 f6 ..H.........H!.. 40 1c 01 74 df 48 89 f8-c3 90 90 90 90 90 90 90 @..t.H.......... 90 48 85 ff 74 76 89 f8-83 e0 01 48 85 c0 75 6c .H..tv.....H..ul 48 8b 07 48 b9 f8 ff ff-ff ff 7f 00 00 48 21 c1 H..H.........H!. [48]8b 51 20 f6 c2 04 74-54 a8 01 74 6f 48 b9 00 H.Q ...tT..toH.. <== 00 00 00 00 00 80 00 48-ba 00 00 00 00 00 00 00 .......H........ 01 48 39 c8 72 36 48 89-c6 48 29 d6 72 17 f0 48 .H9.r6H..H).r..H 0f b1 37 74 22 a8 01 75-e8 31 f6 ba 01 00 00 00 ..7t"..u.1...... e9 82 d3 01 00 48 85 c8-75 3a 48 8b 35 18 f5 99 .....H..u:H.5... 41 ff 25 f2 d2 e6 3f 48-39 ce 72 ee c3 f6 c2 02 A.%...?H9.r..... 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(*) <00000000-0000-0000-0000-000000000000> ??? 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1 0

Phenix 1.20 release candidates
by Billy Poon 02 Nov '21

02 Nov '21

Hi everyone, We are doing a final Python 2.7 release of Phenix and the first release candidate is available from https://phenix-online.org/download/nightly_builds.cgi This release will contain several new features, such as tools for using AlphaFold models. The release after that is planned to be in Python 3.7. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 27 Oct '21

27 Oct '21

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 11 DEC 2021. Please consider writing an article of general interest to the community. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template is attached to this email. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

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Re: [phenixbb] Restricting real-space refinement and weights to specific atom selections
by Josh Cofsky 19 Oct '21

19 Oct '21

Thanks for that suggestion, Phil. After several weeks, I've finally found solid answers to all my questions, which I'll write here in case anyone reading this message is curious: Q1: Is there any way to apply different map weights to different pieces of the structure during refinement? A1: Pavel tells me the answer is no—this feature is not available in Phenix yet. The way I was able to accomplish something to a similar effect was by performing full-model refinements at different weights. Then, in a final refinement job, use torsion restraints from each of those output models (as reference models) across the desired stretches of residues. Clunky, but it solved a few problems for me. Q2: How is the generic "weight" parameter at the bottom of the Phenix GUI applied to the refinement? A2: The target function is T = Tmap * weight + Trestraints. At the time of writing this message, there is a typo in the Phenix Real-Space Refine documentation, which incorrectly reports the target function as "T = Tmap + weight * Trestraints" (Pavel confirmed). Q3: Why is the PDB validation telling me I have geometric issues that were not acknowledged by Phenix? A3: Phil is right. The ESD for several nucleic acid bond lengths and angles is wide as compared to the sigma tolerated by wwPDB. To fix this, I went into the CIF files within the geostd folder and made the following changes to the troublesome RNA and DNA nucleotide files: *data_AD.cif, data_TD.cif, data_CD.cif, data_GD.cif:* length: C1'-N1, ESD=0.020 C3'-O3', ESD=0.020 angles: O4'-C1'-N9/N1, ESD=0.30 *data_U.cif* angles: C5-C6-N1, ESD=0.5 C6-N1-C2, ESD=0.5 *data_C.cif* angles: C6-N1-C2, ESD=0.5 *data_A.cif* angles: N7-C8-N9, ESD=0.5 Best, Josh On Mon, Sep 13, 2021 at 7:23 AM Philip D. Jeffrey <pjeffrey(a)princeton.edu> wrote: > :: most of the outliers are not acknowledged as such (by Phenix), and I > only become > :: aware of them when the wwPDB validation tells me they are there. > > Check that the equilibrium values that PDB are using and the ones that > Phenix are using are the same. If they're not (or if the sigmas are way > different) you're not going to be able to change the outcome just by > changing weights. > > Phil Jeffrey > Princeton > > ------------------------------ > *From:* phenixbb-bounces(a)phenix-online.org < > phenixbb-bounces(a)phenix-online.org> on behalf of Josh Cofsky < > josh.cofsky(a)gmail.com> > *Sent:* Sunday, September 12, 2021 9:42 PM > *To:* phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org> > *Subject:* Re: [phenixbb] Restricting real-space refinement and weights > to specific atom selections > > I now realize that I am confused as to what the mentioned "weight" > parameter refers to. The Phenix RSR documentation contains a line that > reads "T = Tmap + weight * Trestraints"—if I'm understanding correctly > (?), this means a larger "weight" value should yield greater conformity to > geometric restraints at the expense of model/map fit. In reality, I observe > the opposite trend in my refinements (which is why I assumed it was a "map > weight"). Can someone clarify what "weight" (Refinement Settings > "Other > Options") refers to? > > The reason I am exploring these questions is that Phenix RSR is > introducing bond angle outliers into a low-resolution area of a DNA > molecule in my model—most of the outliers are not acknowledged as such (by > Phenix), and I only become aware of them when the wwPDB validation tells me > they are there. I assumed this was the result of overfitting to the map > because setting "weight" to 0.0 prevented these outliers from appearing, > but at the expense of map-model fit in the remainder of the structure > (which is why I wanted to apply different weights to different segments of > the model). > > Thanks, > Josh > > On Sun, Sep 12, 2021 at 12:21 PM Josh Cofsky <josh.cofsky(a)gmail.com> > wrote: > > Hi all, > > I'm using phenix.real_space_refine to refine a model into a cryo-EM map. > My local map resolution is highly variable across the molecule, and using a > single map weight (the parameter shown in the Refinement Settings > "Other > Options" in the GUI) on the whole model leads to poor map-to-model fit in > some locations and overfitting in others. Potential solutions could be to: > 1. assign different map weights to different segments of the model (based > on a user-specified atom selection) > OR > 2. perform iterative refinements with different weight settings, holding > different (user-specified) segments of the model fixed during each > iteration (I suspect this isn't possible based on Pavel's message here: > http://phenix-online.org/pipermail/phenixbb/2021-May/025037.html) > > Is either of these approaches (or another one that accomplishes the same > goal) possible? I am using the Phenix GUI, but if this is only possible in > command line, and you're willing to share an example command that > accomplishes either of these tasks, please let me know. > > Thanks! > -Josh > > (also, apologies if this is a duplicate message...still trying to figure > out the phenixbb listserv) > >

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Job opening: Scientist/Sr. Scientist, Structural Biology at Plexxikon Inc, South San Francisco, CA, USA
by Ying Zhang 15 Oct '21

15 Oct '21

Dear all, This post is to bring your attention to a job opportunity of a scientist/Sr. Sicentist position at Plexxikon Inc. We are looking for a highly motivated, structural biologist with expertise in crystallography. Plexxikon (https://www.plexxikon.com/) is located in South San Francisco at CA, USA. We only consider candidates based in US. This Scientist will be a critical member of the Structural Chemistry team. This is an exceptional opportunity to gain experience in structure-guided drug discovery in a successful biotech company. Plexxikon utilizes its proprietary discovery platform to successfully develop a portfolio of competitively differentiated clinical and preclinical stage compounds in a number of therapeutic areas, including two marketed drug. Zelboraf(tm) (vemurafenib) was the first precision medicine to be approved for the treatment of BRAF-mutant metastatic melanoma; Turalio(tm) (pexidartinib) was the first FDA-approved therapy for tenosynovial giant cell tumor. You can find details about this position at https://careers.jobscore.com/careers/plexxikon/jobs/scientist-structural-bi… Please apply through the link. Best Regards, Ying Zhang, Ph.D Sr Director, Research Planning Plexxikon Inc

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