id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5822 ISOLDE: .cif does not appear to contain any valid residue templates kirk.n@… Tristan Croll "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description Attempted to load mmcif of AIB monomer from ccp4 library. Previously saved as mmCIF from monomer import in coot. Log: > alias mapPrep volume #1-100 step 1 level 0.05 ; set bgColor white ; lighting > simple > alias cartoons select all ; hide target a ; show target c > alias isoPrep addh ; hide @hc UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > ""/Users/kirk.n/Desktop/Work/EliLilly_Project/maps/cryosparc_P18_J732_005_volume_map_sharp > (1).mrc"" format mrc Opened cryosparc_P18_J732_005_volume_map_sharp (1).mrc as #1, grid size 400,400,400, pixel 1.06, shown at level 0.0145, step 2, values float32 > open > /Users/kirk.n/Desktop/Work/EliLilly_Project/Phenix/RealSpaceRefine_50/IM459_Final_noH_real_space_refined_050.pdb Chain information for IM459_Final_noH_real_space_refined_050.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available > mapPrep > isoPrep Summary of feedback from adding hydrogens to IM459_Final_noH_real_space_refined_050.pdb #2 --- notes | No usable SEQRES records for IM459_Final_noH_real_space_refined_050.pdb (#2) chain A; guessing termini instead No usable SEQRES records for IM459_Final_noH_real_space_refined_050.pdb (#2) chain B; guessing termini instead No usable SEQRES records for IM459_Final_noH_real_space_refined_050.pdb (#2) chain C; guessing termini instead Chain-initial residues that are actual N termini: /A SER 1, /B CYS 304, /C GLY 5 Chain-initial residues that are not actual N termini: /C GLU 154, /C ASN 168, /C PHE 178, /C TYR 277, /C LEU 299 Chain-final residues that are actual C termini: /C ASN 594 Chain-final residues that are not actual C termini: /A LEU 31, /B ALA 592, /C ASP 150, /C CYS 159, /C VAL 173, /C LYS 265, /C SER 296 664 hydrogen bonds Adding 'H' to /C GLU 154 Adding 'H' to /C ASN 168 Adding 'H' to /C PHE 178 Adding 'H' to /C TYR 277 Adding 'H' to /C LEU 299 /A LEU 31 is not terminus, removing H atom from 'C' /B ALA 592 is not terminus, removing H atom from 'C' 6989 hydrogens added > cartoons 14138 atoms, 14327 bonds, 5 pseudobonds, 882 residues, 4 models selected /Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/simtk/openmm/app/desmonddmsfile.py:411: SyntaxWarning: ""is"" with a literal. Did you mean ""==""? if implicitSolvent is 'AGBNP3': /Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/simtk/openmm/app/desmonddmsfile.py:433: SyntaxWarning: ""is"" with a literal. Did you mean ""==""? if implicitSolvent is 'GVolSA': /Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/simtk/openmm/app/desmonddmsfile.py:440: SyntaxWarning: ""is"" with a literal. Did you mean ""==""? if implicitSolvent is 'AGBNP': > isolde start > set selectionWidth 4 Chain information for IM459_Final_noH_real_space_refined_050.pdb --- Chain | Description 2.2/A | No description available 2.2/B | No description available 2.2/C | No description available Done loading forcefield Opened cryosparc_P18_J732_005_volume_map_sharp (1).mrc as #2.1.1.1, grid size 400,400,400, pixel 1.06, shown at step 1, values float32 File /Users/kirk.n/Desktop/monomer-AIB.cif does not appear to contain any valid residue templates. Traceback (most recent call last): File ""/Users/kirk.n/Library/Application Support/ChimeraX/1.2/site- packages/chimerax/isolde/isolde.py"", line 1222, in _add_cif_template_files_gui load_cif_templates(self.session, files) File ""/Users/kirk.n/Library/Application Support/ChimeraX/1.2/site- packages/chimerax/isolde/atomic/template_utils.py"", line 604, in load_cif_templates raise RuntimeError('No files successfully loaded.') RuntimeError: No files successfully loaded. RuntimeError: No files successfully loaded. File ""/Users/kirk.n/Library/Application Support/ChimeraX/1.2/site- packages/chimerax/isolde/atomic/template_utils.py"", line 604, in load_cif_templates raise RuntimeError('No files successfully loaded.') See log for complete Python traceback. OpenGL version: 4.1 INTEL-14.7.20 OpenGL renderer: Intel Iris Pro OpenGL Engine OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro11,4 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB Boot ROM Version: 428.40.10.0.0 SMC Version (system): 2.29f24 Software: System Software Overview: System Version: macOS 10.15.7 (19H1519) Kernel Version: Darwin 19.6.0 Time since boot: 4 days 23:28 Graphics/Displays: Intel Iris Pro: Chipset Model: Intel Iris Pro Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x0d26 Revision ID: 0x0008 Metal: Supported, feature set macOS GPUFamily1 v4 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically 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snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 }}} " defect closed normal Third Party fixed Greg Couch all ChimeraX