id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6955 Cannot allocate Clipper array 352884536@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""E:/D1R LE300/PF/postprocess.mrc"" Opened postprocess.mrc, grid size 256,256,256, pixel 0.824, shown at level 0.0145, step 1, values float32 > open ""E:/D1R LE300/PF/D1R-all.pdb"" Summary of feedback from opening E:/D1R LE300/PF/D1R-all.pdb --- warning | Ignored bad PDB record found on line 13065 END Chain information for D1R-all.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > show cartoons > show atoms > style stick Changed 12940 atom styles > hide #!1 models > select :0@C02 1 atom, 1 model selected > select up 27 atoms, 31 bonds, 1 model selected > select up 12940 atoms, 13177 bonds, 1 model selected > select down 27 atoms, 31 bonds, 1 model selected > delete sel > addh Summary of feedback from adding hydrogens to D1R-all.pdb #2 --- warnings | Not adding hydrogens to /B HIS 476 CB because it is missing heavy- atom bond partners Not adding hydrogens to /B HIS 477 CB because it is missing heavy-atom bond partners notes | No usable SEQRES records for D1R-all.pdb (#2) chain A; guessing termini instead No usable SEQRES records for D1R-all.pdb (#2) chain B; guessing termini instead No usable SEQRES records for D1R-all.pdb (#2) chain C; guessing termini instead No usable SEQRES records for D1R-all.pdb (#2) chain D; guessing termini instead No usable SEQRES records for D1R-all.pdb (#2) chain E; guessing termini instead Chain-initial residues that are actual N termini: /A LEU 28, /B GLN 353, /C SER 11 Chain-initial residues that are not actual N termini: /C ASP 174, /C PHE 254, /C PHE 296, /D ASP 20, /E MET 23 Chain-final residues that are actual C termini: /B HIS 477 Chain-final residues that are not actual C termini: /A PRO 428, /C ARG 339, /C LYS 157, /C ALA 228, /C CYS 288, /D PRO 242, /E GLU 238 1149 hydrogen bonds Adding 'H' to /C ASP 174 Adding 'H' to /C PHE 254 Adding 'H' to /C PHE 296 /A PRO 428 is not terminus, removing H atom from 'C' /C ARG 339 is not terminus, removing H atom from 'C' /C LYS 157 is not terminus, removing H atom from 'C' /C ALA 228 is not terminus, removing H atom from 'C' /C CYS 288 is not terminus, removing H atom from 'C' 2 messages similar to the above omitted 6332 hydrogens added > clipper associate #1 toModel #2 Chain information for D1R-all.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available > isolde start > set selectionWidth 4 Done loading forcefield > clipper spotlight radius 120.00 > clipper spotlight radius 120.00 > isolde start > set bgColor white Traceback (most recent call last): File ""D:\chimeraX\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""D:\chimeraX\ChimeraX 1.0\bin\lib\site-packages\chimerax\map\volume.py"", line 3947, in _update_drawings v.update_drawings() File ""D:\chimeraX\ChimeraX 1.0\bin\lib\site-packages\chimerax\map\volume.py"", line 740, in update_drawings self._update_surfaces() File ""D:\chimeraX\ChimeraX 1.0\bin\lib\site-packages\chimerax\map\volume.py"", line 763, in _update_surfaces s.update_surface(ro) File ""C:\Users\Admin\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\clipper\maps\map_handler_base.py"", line 195, in update_surface sct.start_compute, (numpy.asfortranarray(v.matrix()), level, det, vertex_transform.matrix, normal_transform.matrix, False, True), File ""D:\chimeraX\ChimeraX 1.0\bin\lib\site-packages\numpy\core\\_asarray.py"", line 220, in asfortranarray return array(a, dtype, copy=False, order='F', ndmin=1) MemoryError: Unable to allocate 64.0 MiB for an array with shape (256, 256, 256) and data type float32 Error processing trigger ""graphics update"": MemoryError: Unable to allocate 64.0 MiB for an array with shape (256, 256, 256) and data type float32 File ""D:\chimeraX\ChimeraX 1.0\bin\lib\site-packages\numpy\core\\_asarray.py"", line 220, in asfortranarray return array(a, dtype, copy=False, order='F', ndmin=1) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 456.71 OpenGL renderer: GeForce GTX 1650 SUPER/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: IPASON Model: OS: Microsoft Windows 10 家庭中文版 (Build 19044) Memory: 17,130,639,360 MaxProcessMemory: 137,438,953,344 CPU: 6 AMD Ryzen 5 3500X 6-Core Processor "" PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 }}} " defect closed normal Third Party can't reproduce Tom Goddard all ChimeraX