id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5469 Request for help in debugging Tristan Croll Greg Couch "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.3rc202110222254 (2021-10-22 22:54:52 UTC) Description Not a ChimeraX bug, but an appeal for suggestions. Offender is a PyBind11-wrapped function taking (amongst other arguments) a vector of doubles, provided to it by Python as a list of floats. Has been working fine on all three platforms, but now breaks in Windows. Usually returns `ValueError: vector too long`, sometimes `MemoryError: bad allocation`, and *extremely* rarely seems to get past it. Very worrying. I added some logging in the wrapped function that never gets hit, so the exception is thrown in the bindings. Possibilities: - this is a new (to me) PC, and it came to me with Visual Studio Community 2019 installed so I've been using that to compile Clipper and ISOLDE. I've uninstalled that and am currently installing 2015, in case there's some subtle ABI problem. It's clear there are at least some differences to the underlying libraries - I used to have to add some Microsoft-specific code to define std::basic_string::npos, but with 2019 that now raises a compile-time error. - a bug in PyBind11 - I just recently bumped the version I'm using up to 2.7.1. Seems unlikely, since casting of Python lists to vectors will be used all over the place. - something a bit funky about this particular machine. Not impossible, if I'm being honest - it generally seems a little flaky and prone to multi-second hang-ups, so I'm not ruling out some memory fault. Any ideas? Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.3rc202110222254 (2021-10-22) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1un9 structureFactors true Summary of feedback from opening 1un9 fetched from pdb --- warning | No free flags detected in this dataset! Automatically generated a new random set with 1291 free from 25746 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. notes | Fetching compressed mmCIF 1un9 from http://files.rcsb.org/download/1un9.cif Fetching CCD ANP from http://ligand-expo.rcsb.org/reports/A/ANP/ANP.cif Fetching compressed 1un9 structure factors from http://files.rcsb.org/download/1un9-sf.cif Resolution: 3.1000607613626228 Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 26,28,26, pixel 1.01,0.976,0.986, shown at level 0.153, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 26,28,26, pixel 1.01,0.976,0.986, shown at level -0.0887,0.0887, step 1, values float32 Opened (LIVE) 2mFo-DFc_sharp_32 as #1.1.1.4, grid size 26,28,26, pixel 1.01,0.976,0.986, shown at level 0.337, step 1, values float32 1un9 title: Crystal structure of the dihydroxyacetone kinase from C. freundii in complex with AMP-PNP and Mg2+ [more info...] Chain information for 1un9 --- Chain | Description | UniProt 1.2/A 1.2/B | dihydroxyacetone kinase | DAK_CITFR Non-standard residues in 1un9 #1.2 --- 2HA — dihydroxyacetone ANP — phosphoaminophosphonic acid-adenylate ester MG — magnesium ion > close #1 Deleting Crystallographic maps (1un9-sf.cif) Deleting (LIVE) 2mFo-DFc Deleting (LIVE) mFo-DFc Deleting (LIVE) 2mFo-DFc_sharp_32 > open 3u9q structureFactors true Summary of feedback from opening 3u9q fetched from pdb --- notes | Fetching compressed mmCIF 3u9q from http://files.rcsb.org/download/3u9q.cif Fetching CCD DKA from http://ligand-expo.rcsb.org/reports/D/DKA/DKA.cif Fetching compressed 3u9q structure factors from http://files.rcsb.org/download/3u9q-sf.cif Resolution: 1.522 Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 68,50,50, pixel 0.486,0.503,0.506, shown at level 1.03, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 68,50,50, pixel 0.486,0.503,0.506, shown at level -0.233,0.233, step 1, values float32 Opened (LIVE) 2mFo-DFc_smooth_22 as #1.1.1.4, grid size 68,50,50, pixel 0.486,0.503,0.506, shown at level 0.614, step 1, values float32 3u9q title: Ligand binding domain of PPARgamma complexed with Decanoic Acid and PGC-1a peptide [more info...] Chain information for 3u9q --- Chain | Description | UniProt 1.2/A | Peroxisome proliferator-activated receptor γ | PPARG_HUMAN 1.2/B | PGC-1a peptide | PRGC1_HUMAN Non-standard residues in 3u9q #1.2 --- DKA — decanoic acid > close #1 Deleting Crystallographic maps (3u9q-sf.cif) Deleting (LIVE) 2mFo-DFc Deleting (LIVE) mFo-DFc Deleting (LIVE) 2mFo-DFc_smooth_22 > open 1zgy structureFactors true Summary of feedback from opening 1zgy fetched from pdb --- notes | Fetching compressed mmCIF 1zgy from http://files.rcsb.org/download/1zgy.cif Fetching CCD BRL from http://ligand-expo.rcsb.org/reports/B/BRL/BRL.cif Fetching compressed 1zgy structure factors from http://files.rcsb.org/download/1zgy-sf.cif Resolution: 1.8034515382614822 Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 50,46,42, pixel 0.57,0.568,0.594, shown at level 0.499, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 50,46,42, pixel 0.57,0.568,0.594, shown at level -0.149,0.149, step 1, values float32 Opened (LIVE) 2mFo-DFc_smooth_18 as #1.1.1.4, grid size 50,46,42, pixel 0.57,0.568,0.594, shown at level 0.376, step 1, values float32 1zgy title: Structural and Biochemical Basis for Selective Repression of the Orphan Nuclear Receptor LRH-1 by SHP [more info...] Chain information for 1zgy --- Chain | Description | UniProt 1.2/A | Peroxisome proliferator activated receptor γ | PPAT_HUMAN 1.2/B | Nuclear receptor subfamily 0, group B, member 2 | P97947_RAT Non-standard residues in 1zgy #1.2 --- BRL — 2,4-thiazolidiinedione, 5-[[4-[2-(methyl-2-pyridinylamino)ethoxy]phenyl]methyl]-(9CL) (BRL49653; rosiglitazone) > close #1 Deleting Crystallographic maps (1zgy-sf.cif) Deleting (LIVE) 2mFo-DFc Deleting (LIVE) mFo-DFc Deleting (LIVE) 2mFo-DFc_smooth_18 > open 4prg structureFactors true Summary of feedback from opening 4prg fetched from pdb --- warning | No free flags detected in this dataset! Automatically generated a new random set with 1540 free from 30801 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. notes | Fetching compressed mmCIF 4prg from http://files.rcsb.org/download/4prg.cif Fetching CCD 072 from http://ligand-expo.rcsb.org/reports/0/072/072.cif Fetching compressed 4prg structure factors from http://files.rcsb.org/download/4prg-sf.cif Resolution: 2.5906391632025545 Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 151, in provider_open models, status = collated_open(session, database_name, ident, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 432, in collated_open return remember_data_format() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 403, in remember_data_format models, status = func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mmcif\\__init__.py"", line 75, in fetch return fetcher(session, ident, ignore_cache=ignore_cache, **kw) File ""src\mmcif.pyx"", line 349, in chimerax.mmcif.mmcif.fetch_mmcif File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\map_mgr.py"", line 306, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 187, in __init__ self.init_maps(use_static_maps, use_live_maps, File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) ValueError: vector too long ValueError: vector too long File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) See log for complete Python traceback. > open 4prg structureFactors true Summary of feedback from opening 4prg fetched from pdb --- warning | No free flags detected in this dataset! Automatically generated a new random set with 1550 free from 30801 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. notes | Resolution: 2.5906391632025545 Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 151, in provider_open models, status = collated_open(session, database_name, ident, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 432, in collated_open return remember_data_format() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 403, in remember_data_format models, status = func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mmcif\\__init__.py"", line 75, in fetch return fetcher(session, ident, ignore_cache=ignore_cache, **kw) File ""src\mmcif.pyx"", line 349, in chimerax.mmcif.mmcif.fetch_mmcif File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\map_mgr.py"", line 306, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 187, in __init__ self.init_maps(use_static_maps, use_live_maps, File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) ValueError: vector too long ValueError: vector too long File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) See log for complete Python traceback. > open 4prg structureFactors true Summary of feedback from opening 4prg fetched from pdb --- warning | No free flags detected in this dataset! Automatically generated a new random set with 1549 free from 30801 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. notes | Resolution: 2.5906391632025545 Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 151, in provider_open models, status = collated_open(session, database_name, ident, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 432, in collated_open return remember_data_format() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 403, in remember_data_format models, status = func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mmcif\\__init__.py"", line 75, in fetch return fetcher(session, ident, ignore_cache=ignore_cache, **kw) File ""src\mmcif.pyx"", line 349, in chimerax.mmcif.mmcif.fetch_mmcif File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\map_mgr.py"", line 306, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 187, in __init__ self.init_maps(use_static_maps, use_live_maps, File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) ValueError: vector too long ValueError: vector too long File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) See log for complete Python traceback. > open 4prg structureFactors true Summary of feedback from opening 4prg fetched from pdb --- warning | No free flags detected in this dataset! Automatically generated a new random set with 1509 free from 30801 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. notes | Resolution: 2.5906391632025545 Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 151, in provider_open models, status = collated_open(session, database_name, ident, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 432, in collated_open return remember_data_format() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 403, in remember_data_format models, status = func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mmcif\\__init__.py"", line 75, in fetch return fetcher(session, ident, ignore_cache=ignore_cache, **kw) File ""src\mmcif.pyx"", line 349, in chimerax.mmcif.mmcif.fetch_mmcif File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\map_mgr.py"", line 306, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 187, in __init__ self.init_maps(use_static_maps, use_live_maps, File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) ValueError: vector too long ValueError: vector too long File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) See log for complete Python traceback. > open 4prg structureFactors true Summary of feedback from opening 4prg fetched from pdb --- warning | No free flags detected in this dataset! Automatically generated a new random set with 1547 free from 30801 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. notes | Resolution: 2.5906391632025545 Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 151, in provider_open models, status = collated_open(session, database_name, ident, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 432, in collated_open return remember_data_format() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 403, in remember_data_format models, status = func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mmcif\\__init__.py"", line 75, in fetch return fetcher(session, ident, ignore_cache=ignore_cache, **kw) File ""src\mmcif.pyx"", line 349, in chimerax.mmcif.mmcif.fetch_mmcif File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\map_mgr.py"", line 306, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 187, in __init__ self.init_maps(use_static_maps, use_live_maps, File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) ValueError: vector too long ValueError: vector too long File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) See log for complete Python traceback. > open 4prg structureFactors true Summary of feedback from opening 4prg fetched from pdb --- warning | No free flags detected in this dataset! Automatically generated a new random set with 1560 free from 30801 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. notes | Resolution: 2.5906391632025545 Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 151, in provider_open models, status = collated_open(session, database_name, ident, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 432, in collated_open return remember_data_format() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 403, in remember_data_format models, status = func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mmcif\\__init__.py"", line 75, in fetch return fetcher(session, ident, ignore_cache=ignore_cache, **kw) File ""src\mmcif.pyx"", line 349, in chimerax.mmcif.mmcif.fetch_mmcif File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\map_mgr.py"", line 306, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 187, in __init__ self.init_maps(use_static_maps, use_live_maps, File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) ValueError: vector too long ValueError: vector too long File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) See log for complete Python traceback. > open 4prg structureFactors true Summary of feedback from opening 4prg fetched from pdb --- warning | No free flags detected in this dataset! Automatically generated a new random set with 1560 free from 30801 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. notes | Resolution: 2.5906391632025545 Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 151, in provider_open models, status = collated_open(session, database_name, ident, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 432, in collated_open return remember_data_format() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 403, in remember_data_format models, status = func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mmcif\\__init__.py"", line 75, in fetch return fetcher(session, ident, ignore_cache=ignore_cache, **kw) File ""src\mmcif.pyx"", line 349, in chimerax.mmcif.mmcif.fetch_mmcif File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\map_mgr.py"", line 306, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 187, in __init__ self.init_maps(use_static_maps, use_live_maps, File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) ValueError: vector too long ValueError: vector too long File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) See log for complete Python traceback. > open 4prg structureFactors true Summary of feedback from opening 4prg fetched from pdb --- warning | No free flags detected in this dataset! Automatically generated a new random set with 1558 free from 30801 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. notes | Resolution: 2.5906391632025545 Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 151, in provider_open models, status = collated_open(session, database_name, ident, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 432, in collated_open return remember_data_format() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 403, in remember_data_format models, status = func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mmcif\\__init__.py"", line 75, in fetch return fetcher(session, ident, ignore_cache=ignore_cache, **kw) File ""src\mmcif.pyx"", line 349, in chimerax.mmcif.mmcif.fetch_mmcif File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\map_mgr.py"", line 306, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 187, in __init__ self.init_maps(use_static_maps, use_live_maps, File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) ValueError: vector too long ValueError: vector too long File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) See log for complete Python traceback. > open 4prg structureFactors true Summary of feedback from opening 4prg fetched from pdb --- warning | No free flags detected in this dataset! Automatically generated a new random set with 1549 free from 30801 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. notes | Resolution: 2.5906391632025545 Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 151, in provider_open models, status = collated_open(session, database_name, ident, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 432, in collated_open return remember_data_format() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 403, in remember_data_format models, status = func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mmcif\\__init__.py"", line 75, in fetch return fetcher(session, ident, ignore_cache=ignore_cache, **kw) File ""src\mmcif.pyx"", line 349, in chimerax.mmcif.mmcif.fetch_mmcif File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\map_mgr.py"", line 306, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 187, in __init__ self.init_maps(use_static_maps, use_live_maps, File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) ValueError: vector too long ValueError: vector too long File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) See log for complete Python traceback. > open 4prg structureFactors true Summary of feedback from opening 4prg fetched from pdb --- warning | No free flags detected in this dataset! Automatically generated a new random set with 1550 free from 30801 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. notes | Resolution: 2.5906391632025545 Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 151, in provider_open models, status = collated_open(session, database_name, ident, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 432, in collated_open return remember_data_format() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 403, in remember_data_format models, status = func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mmcif\\__init__.py"", line 75, in fetch return fetcher(session, ident, ignore_cache=ignore_cache, **kw) File ""src\mmcif.pyx"", line 349, in chimerax.mmcif.mmcif.fetch_mmcif File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\map_mgr.py"", line 306, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 187, in __init__ self.init_maps(use_static_maps, use_live_maps, File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) ValueError: vector too long ValueError: vector too long File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) See log for complete Python traceback. > open 4prg structureFactors true Summary of feedback from opening 4prg fetched from pdb --- warning | No free flags detected in this dataset! Automatically generated a new random set with 1533 free from 30801 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. notes | Resolution: 2.5906391632025545 Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 151, in provider_open models, status = collated_open(session, database_name, ident, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 432, in collated_open return remember_data_format() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 403, in remember_data_format models, status = func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mmcif\\__init__.py"", line 75, in fetch return fetcher(session, ident, ignore_cache=ignore_cache, **kw) File ""src\mmcif.pyx"", line 349, in chimerax.mmcif.mmcif.fetch_mmcif File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\map_mgr.py"", line 306, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 187, in __init__ self.init_maps(use_static_maps, use_live_maps, File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) ValueError: vector too long ValueError: vector too long File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) See log for complete Python traceback. > open 4prg structureFactors true Summary of feedback from opening 4prg fetched from pdb --- warning | No free flags detected in this dataset! Automatically generated a new random set with 1522 free from 30801 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. notes | Resolution: 2.5906391632025545 Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 151, in provider_open models, status = collated_open(session, database_name, ident, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 432, in collated_open return remember_data_format() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 403, in remember_data_format models, status = func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mmcif\\__init__.py"", line 75, in fetch return fetcher(session, ident, ignore_cache=ignore_cache, **kw) File ""src\mmcif.pyx"", line 349, in chimerax.mmcif.mmcif.fetch_mmcif File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\map_mgr.py"", line 306, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 187, in __init__ self.init_maps(use_static_maps, use_live_maps, File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) ValueError: vector too long ValueError: vector too long File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) See log for complete Python traceback. > open 4prg structureFactors true Summary of feedback from opening 4prg fetched from pdb --- warning | No free flags detected in this dataset! Automatically generated a new random set with 1518 free from 30801 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. notes | Resolution: 2.5906391632025545 Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 297, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 151, in provider_open models, status = collated_open(session, database_name, ident, File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 432, in collated_open return remember_data_format() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 403, in remember_data_format models, status = func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\mmcif\\__init__.py"", line 75, in fetch return fetcher(session, ident, ignore_cache=ignore_cache, **kw) File ""src\mmcif.pyx"", line 349, in chimerax.mmcif.mmcif.fetch_mmcif File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\map_mgr.py"", line 306, in add_xmapset_from_file return XmapSet(self, mtzdata) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 187, in __init__ self.init_maps(use_static_maps, use_live_maps, File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\maps\xmapset.py"", line 245, in init_maps fsigf_data = french_wilson_analytical(fsigf.data) File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) MemoryError: bad allocation MemoryError: bad allocation File ""C:\Users\tristan\AppData\Local\UCSF\ChimeraX\1.3\site- packages\chimerax\clipper\reflection_tools\french_wilson.py"", line 80, in french_wilson_analytical rfn = ResolutionFn(hkls, basisfn, target, params) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 471.11 OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Notebook Model: P7xxTM1 OS: Microsoft Windows 10 Education (Build 19041) Memory: 68,654,501,888 MaxProcessMemory: 137,438,953,344 CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz OSLanguage: en-GB Locale: ('en_GB', 'cp1252') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.10.8 cftime: 1.5.1 charset-normalizer: 2.0.7 ChimeraX-AddCharge: 1.1.4 ChimeraX-AddH: 2.1.10 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.30.2 ChimeraX-AtomicLibrary: 4.1.5 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1.1 ChimeraX-Clipper: 0.17.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3rc202110222254 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.3.dev32 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.2 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.4 ChimeraX-ModelPanel: 1.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.4 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.5 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.6 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 comtypes: 1.1.10 cxservices: 1.1 cycler: 0.10.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.5.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.2.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.8.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.7.3 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.2 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.21 psutil: 5.8.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 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