id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3535 Nucleotides: asking for distance from None mks131@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 0.93 (2020-04-03) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Downloading bundle ChimeraX_ISOLDE-1.0b5-cp37-cp37m-win_amd64.whl Downloading bundle ChimeraX_ISOLDE-1.0b5-cp37-cp37m-win_amd64.whl Downloading bundle ChimeraX_ISOLDE-1.0b5-cp37-cp37m-win_amd64.whl > help help:quickstart Successfully installed ChimeraX-Clipper-0.12.1 ChimeraX-ISOLDE-1.0b5 Installed ChimeraX-Clipper (0.12.1) Installed ChimeraX-ISOLDE (1.0b5) Bundle installation canceled Bundle installation canceled > open2 > C:/Users/Manoj/Downloads/relion_postprocess_job126_masked_refined_pixelsize.ccp4 > format ccp4 Opened relion_postprocess_job126_masked_refined_pixelsize.ccp4, grid size 376,376,376, pixel 0.649, shown at level 0.00472, step 2, values float32 > toolshed show ISOLDE > set selectionWidth 4 Forcefield cache not found or out of date. Regenerating from ffXML files. This is normal if running ISOLDE for the first time, or after upgrading OpenMM. Done loading forcefield > open2 > C:/Users/Manoj/Downloads/Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb Summary of feedback from opening <_io.textiowrapper name=""C:/Users/Manoj/Downloads/Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb"" mode=""rt"" encoding=""utf-8""> --- warnings | Ignored bad PDB record found on line 20 Ignored bad PDB record found on line 21 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 22 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 23 BOND : 0.006 0.070 12495 Ignored bad PDB record found on line 24 ANGLE : 0.827 8.410 18038 18 messages similar to the above omitted Chain information for Lin28B-NCP_truncated_DNA_P1_real_space_refined.pdb #2 --- Chain | Description A E | No description available B | No description available C G | No description available D H | No description available F | No description available I | No description available J | No description available > volume #1 style image region 0,0,186,375,375,186 step 1 showOutlineBox true > graphics silhouettes true > nucleotides ladder > nucleotides atoms > style nucleic stick Changed 5614 atom styles > nucleotides fill > style nucleic stick Changed 5614 atom styles > nucleotides tube/slab shape muffler > nucleotides tube/slab shape ellipsoid > nucleotides tube/slab shape box > color bynucleotide QWindowsNativeFileDialogBase::shellItem : Unhandled scheme: ""data"" > open2 C:/Users/Manoj/Phenix/phenix-installer-1.13-2998-intel- > windows-x86_64/base/MapToModel_15/Lin28_maptomodel_0.pdb Summary of feedback from opening <_io.textiowrapper name=""C:/Users/Manoj/Phenix/phenix-installer-1.13-2998-intel- windows-x86_64/base/MapToModel_15/Lin28_maptomodel_0.pdb"" mode=""rt"" encoding=""utf-8""> --- warning | Ignored bad PDB record found on line 2301 END Chain information for Lin28_maptomodel_0.pdb #3 --- Chain | Description U | No description available Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\nucleotides\\_data.py"", line 525, in rebuild _rebuild_molecule('internal', mol) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\nucleotides\\_data.py"", line 652, in _rebuild_molecule hide_residues = make_ladder(nd, residues, mol._ladder_params) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\nucleotides\\_data.py"", line 1237, in make_ladder va, na, ta = get_cylinder(params.rung_radius, ep0, ep1) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\nucleotides\\_data.py"", line 733, in get_cylinder h = distance(p0, p1) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\geometry\vector.py"", line 71, in distance return sqrt(distance_squared(p, q)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\geometry\vector.py"", line 63, in distance_squared if len(p) == 3: TypeError: object of type 'NoneType' has no len() Error processing trigger ""new frame"": TypeError: object of type 'NoneType' has no len() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\geometry\vector.py"", line 63, in distance_squared if len(p) == 3: See log for complete Python traceback. OpenGL version: 3.3.0 - Build 20.19.15.4531 OpenGL renderer: Intel(R) HD Graphics 5500 OpenGL vendor: Intel Manufacturer: Dell Inc. Model: Inspiron 7348 OS: Microsoft Windows 10 Home (Build 18362) Memory: 8,501,149,696 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i7-5500U CPU @ 2.40GHz"" }}} " defect closed normal Depiction fixed Greg Couch all ChimeraX