id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2228 Saving as PDB with 2-letter chain id gives unreadable file goddard@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-18.6.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-07-16) Description Saving selected atoms in PDB format for chain AP (two-letter chain id) writes the file without complaint, but puts a non-ascii character in the chain id columns, and reading that PDB file gives this unicode error. I tried it a few times and it gave a different chain id character in the file each time (sometimes even an ascii character). Log: UCSF ChimeraX version: 0.91 (2019-07-16) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 4v68 format mmCIF fromDatabase pdb Summary of feedback from opening 4v68 fetched from pdb --- warning | Unable to infer polymer connectivity due to unspecified label_seq_id for residue ""PHA"" near line 170882 4v68 title: T. thermophilus 70S ribosome in complex with mRNA, tRNAs and EF- Tu.GDP.kirromycin ternary complex, fitted to a 6.4 A Cryo-EM map. [more info...] Chain information for 4v68 #1 --- Chain | Description A0 | MRNA codon AA | 16S rRNA AB | 30S ribosomal protein S2 AC | 30S ribosomal protein S3 AD | 30S ribosomal protein S4 AE | 30S ribosomal protein S5 AF | 30S ribosomal protein S6 AG | 30S ribosomal protein S7 AH | 30S ribosomal protein S8 AI | 30S ribosomal protein S9 AJ | 30S ribosomal protein S10 AK | 30S ribosomal protein S11 AL | 30S ribosomal protein S12 AM | 30S ribosomal protein S13 AN | 30S ribosomal protein S14 AO | 30S ribosomal protein S15 AP | 30S ribosomal protein S16 AQ | 30S ribosomal protein S17 AR | 30S ribosomal protein S18 AS | 30S ribosomal protein S19 AT | 30S ribosomal protein S20 AU | 30S ribosomal protein Thx AV | P-site TRNA AW | E-site TRNA AX | synthetic MRNA AY | At-site TRNA AZ | Elongation factor Tu-A B0 | 50S ribosomal protein L27 B1 | 50S ribosomal protein L28 B2 | 50S ribosomal protein L29 B3 | 50S ribosomal protein L30 B4 | 50S ribosomal protein L31 B5 | 50S ribosomal protein L32 B6 | 50S ribosomal protein L33 B7 | 50S ribosomal protein L34 B8 | 50S ribosomal protein L35 B9 | 50S ribosomal protein L36 BA | 23S rRNA BB | 5S rRNA BC | 50S ribosomal protein L1 BD | 50S ribosomal protein L2 BE | 50S ribosomal protein L3 BF | 50S ribosomal protein L4 BG | 50S ribosomal protein L5 BH | 50S ribosomal protein L6 BI | 50S ribosomal protein L9 BL | 50S ribosomal protein L11 BN | 50S ribosomal protein L13 BO | 50S ribosomal protein L14 BP | 50S ribosomal protein L15 BQ | 50S ribosomal protein L16 BR | 50S ribosomal protein L17 BS | 50S ribosomal protein L18 BT | 50S ribosomal protein L19 BU | 50S ribosomal protein L20 BV | 50S ribosomal protein L21 BW | 50S ribosomal protein L22 BX | 50S ribosomal protein L23 BY | 50S ribosomal protein L24 BZ | 50S ribosomal protein L25 Non-standard residues in 4v68 #1 --- BME — β-mercaptoethanol MAU — N-methyl kirromycin (aurodox; 1-methylmocimycin; antibiotic X-5108; goldinodox; goldinomycin) > select /AP 701 atoms, 717 bonds, 1 model selected > save /Users/goddard/Desktop/test.pdb models #1 selectedOnly true > open /Users/goddard/Desktop/test.pdb Summary of feedback from opening /Users/goddard/Desktop/test.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 VAL ? 7 HIS ? 16 1 10 Start residue of secondary structure not found: HELIX 2 2 ASN ? 25 TYR ? 31 1 7 Start residue of secondary structure not found: HELIX 3 3 ASP ? 43 MET ? 63 1 21 Start residue of secondary structure not found: HELIX 4 4 LYS ? 74 GLN ? 76 1 3 End residue of secondary structure not found: HELIX 5 5 ALA ? 77 ARG ? 87 1 11 Start residue of secondary structure not found: HELIX 6 6 MET ? 101 THR ? 103 1 3 Start residue of secondary structure not found: HELIX 7 7 ASN ? 104 ALA ? 123 1 20 Start residue of secondary structure not found: HELIX 8 8 SER ? 124 GLU ? 129 1 6 Start residue of secondary structure not found: HELIX 9 9 PRO ? 131 SER ? 150 1 20 Start residue of secondary structure not found: HELIX 10 10 PRO ? 167 LYS ? 169 1 3 16 messages similar to the above omitted End residue of secondary structure not found: HELIX 27 27 ARG ? 71 ILE ? 81 1 11 Start residue of secondary structure not found: HELIX 28 28 ASP ? 4 TYR ? 20 1 17 Start residue of secondary structure not found: HELIX 29 29 SER ? 29 GLU ? 42 1 14 Start residue of secondary structure not found: HELIX 30 30 ARG ? 102 LEU ? 107 1 6 Start residue of secondary structure not found: HELIX 31 31 ARG ? 122 GLY ? 128 1 7 Start residue of secondary structure not found: HELIX 32 32 GLY ? 46 ILE ? 48 1 3 10 messages similar to the above omitted End residue of secondary structure not found: HELIX 45 45 ARG ? 81 TYR ? 95 1 15 Start residue of secondary structure not found: HELIX 46 46 GLU ? 96 SER ? 99 1 4 Start residue of secondary structure not found: HELIX 47 47 LYS ? 21 LEU ? 26 1 6 Start residue of secondary structure not found: HELIX 48 48 ASN ? 36 ARG ? 42 1 7 Start residue of secondary structure not found: HELIX 49 49 PRO ? 52 GLY ? 57 1 6 Start residue of secondary structure not found: HELIX 50 50 SER ? 59 LEU ? 76 1 18 13 messages similar to the above omitted End residue of secondary structure not found: HELIX 64 64 LYS ? 35 LYS ? 48 1 14 Start residue of secondary structure not found: HELIX 65 65 GLU ? 57 ASN ? 68 1 12 Start residue of secondary structure not found: HELIX 66 66 SER ? 92 ARG ? 111 1 20 Start residue of secondary structure not found: HELIX 67 67 ARG ? 115 GLY ? 130 1 16 Start residue of secondary structure not found: HELIX 68 68 GLY ? 132 ASN ? 148 1 17 Start residue of secondary structure not found: HELIX 69 69 ARG ? 149 HIS ? 153 1 5 1 messages similar to the above omitted End residue of secondary structure not found: HELIX 71 71 ARG ? 42 ALA ? 46 1 5 Start residue of secondary structure not found: HELIX 72 72 PRO ? 49 VAL ? 53 1 5 Start residue of secondary structure not found: HELIX 73 73 GLY ? 69 TYR ? 88 1 20 Start residue of secondary structure not found: HELIX 74 74 TYR ? 92 LYS ? 97 1 6 Start residue of secondary structure not found: HELIX 75 75 ASP ? 12 ALA ? 26 1 15 Start residue of secondary structure not found: HELIX 76 76 ASN ? 78 LEU ? 88 1 11 Start residue of secondary structure not found: HELIX 77 77 ARG ? 14 LEU ? 19 1 6 1 messages similar to the above omitted End residue of secondary structure not found: HELIX 79 79 LYS ? 27 GLU ? 32 1 6 Start residue of secondary structure not found: HELIX 80 80 THR ? 49 TRP ? 64 1 16 Start residue of secondary structure not found: HELIX 81 81 LEU ? 70 ASP ? 83 1 14 Start residue of secondary structure not found: HELIX 82 82 ARG ? 3 ARG ? 12 1 10 Start residue of secondary structure not found: HELIX 83 83 PHE ? 16 ALA ? 20 1 5 Start residue of secondary structure not found: HELIX 84 84 CYS ? 40 GLY ? 51 1 12 42 messages similar to the above omitted End residue of secondary structure not found: HELIX 127 127 GLU ? 54 GLY ? 65 1 12 Start residue of secondary structure not found: HELIX 128 128 ARG ? 96 LEU ? 107 1 12 Start residue of secondary structure not found: HELIX 129 129 THR ? 165 LEU ? 176 1 12 Start residue of secondary structure not found: HELIX 130 130 GLU ? 58 SER ? 80 1 23 Start residue of secondary structure not found: HELIX 131 131 GLY ? 142 ALA ? 150 1 9 Start residue of secondary structure not found: HELIX 132 132 LYS ? 22 TYR ? 29 1 8 Start residue of secondary structure not found: HELIX 133 133 THR ? 40 LEU ? 58 1 19 Start residue of secondary structure not found: HELIX 134 134 ALA ? 65 GLU ? 73 1 9 16 messages similar to the above omitted End residue of secondary structure not found: HELIX 151 151 HIS ? 13 HIS ? 31 1 19 Start residue of secondary structure not found: HELIX 152 152 VAL ? 38 ARG ? 57 1 20 Start residue of secondary structure not found: HELIX 153 153 ASP ? 59 ARG ? 68 1 10 Start residue of secondary structure not found: HELIX 154 154 ASP ? 72 ASP ? 81 1 10 Start residue of secondary structure not found: HELIX 155 155 ASN ? 61 LEU ? 80 1 20 Start residue of secondary structure not found: HELIX 156 156 ARG ? 3 SER ? 12 1 10 8 messages similar to the above omitted End residue of secondary structure not found: HELIX 165 165 VAL ? 51 ALA ? 55 1 5 Start residue of secondary structure not found: HELIX 166 166 SER ? 13 LEU ? 23 1 11 Start residue of secondary structure not found: HELIX 167 167 SER ? 28 TYR ? 38 1 11 End residue of secondary structure not found: HELIX 168 168 ARG ? 42 ASN ? 61 1 20 Start residue of secondary structure not found: HELIX 169 169 LEU ? 65 ASP ? 67 1 3 Start residue of secondary structure not found: HELIX 170 170 SER ? 14 ALA ? 22 1 9 Start residue of secondary structure not found: HELIX 171 171 ILE ? 39 GLU ? 44 1 6 Start residue of secondary structure not found: HELIX 172 172 HIS ? 68 VAL ? 72 1 5 Start residue of secondary structure not found: HELIX 173 173 LYS ? 14 GLY ? 22 1 9 End residue of secondary structure not found: HELIX 174 174 ASP ? 40 SER ? 52 1 13 Start residue of secondary structure not found: SHEET 1 1 1 ALA ? 34 ARG ? 36 0 Start residue of secondary structure not found: SHEET 2 2 1 ILE ? 39 ILE ? 41 0 Start residue of secondary structure not found: SHEET 3 3 1 LEU ? 69 VAL ? 71 0 Start residue of secondary structure not found: SHEET 4 4 1 TYR ? 92 VAL ? 93 0 Start residue of secondary structure not found: SHEET 5 5 1 ILE ? 162 VAL ? 164 0 20 messages similar to the above omitted End residue of secondary structure not found: SHEET 26 26 1 TYR ? 58 LEU ? 63 0 Start residue of secondary structure not found: SHEET 27 27 1 HIS ? 82 ARG ? 85 0 Start residue of secondary structure not found: SHEET 28 28 1 TYR ? 94 VAL ? 95 0 Start residue of secondary structure not found: SHEET 29 29 1 LEU ? 112 THR ? 114 0 Start residue of secondary structure not found: SHEET 30 30 1 GLY ? 117 LEU ? 119 0 Start residue of secondary structure not found: SHEET 31 31 1 GLY ? 131 GLU ? 132 0 31 messages similar to the above omitted End residue of secondary structure not found: SHEET 67 67 1 ILE ? 4 LYS ? 7 0 Start residue of secondary structure not found: SHEET 68 68 1 VAL ? 34 ILE ? 38 0 Start residue of secondary structure not found: SHEET 69 69 1 PHE ? 47 VAL ? 49 0 Start residue of secondary structure not found: SHEET 70 70 1 GLU ? 61 PHE ? 63 0 Start residue of secondary structure not found: SHEET 71 71 1 LEU ? 71 ILE ? 74 0 Start residue of secondary structure not found: SHEET 72 72 1 ILE ? 98 LYS ? 99 0 28 messages similar to the above omitted End residue of secondary structure not found: SHEET 101 101 1 ILE ? 36 ARG ? 39 0 Start residue of secondary structure not found: SHEET 102 102 1 LYS ? 46 PRO ? 47 0 End residue of secondary structure not found: SHEET 103 103 1 VAL ? 51 MET ? 53 0 Start residue of secondary structure not found: SHEET 104 104 1 LEU ? 59 ALA ? 61 0 Start residue of secondary structure not found: SHEET 105 105 1 GLY ? 65 ASP ? 71 0 Start residue of secondary structure not found: SHEET 106 106 1 ARG ? 77 ARG ? 82 0 Start residue of secondary structure not found: SHEET 107 107 1 LYS ? 23 LYS ? 25 0 Start residue of secondary structure not found: SHEET 108 108 1 THR ? 35 SER ? 38 0 11 messages similar to the above omitted End residue of secondary structure not found: SHEET 121 121 1 ALA ? 77 ALA ? 81 0 Start residue of secondary structure not found: SHEET 122 122 1 ILE ? 92 TYR ? 97 0 Start residue of secondary structure not found: SHEET 123 123 1 LYS ? 102 ILE ? 106 0 Start residue of secondary structure not found: SHEET 124 124 1 GLN ? 116 VAL ? 117 0 Start residue of secondary structure not found: SHEET 125 125 1 ALA ? 130 PRO ? 132 0 Start residue of secondary structure not found: SHEET 126 126 1 VAL ? 141 HIS ? 143 0 40 messages similar to the above omitted End residue of secondary structure not found: SHEET 167 167 1 VAL ? 53 TYR ? 60 0 Start residue of secondary structure not found: SHEET 168 168 1 SER ? 64 THR ? 69 0 Start residue of secondary structure not found: SHEET 169 169 1 GLY ? 97 ILE ? 99 0 Start residue of secondary structure not found: SHEET 170 170 1 VAL ? 136 VAL ? 138 0 Start residue of secondary structure not found: SHEET 171 171 1 LEU ? 15 ILE ? 16 0 End residue of secondary structure not found: SHEET 172 172 1 VAL ? 53 VAL ? 54 0 Start residue of secondary structure not found: SHEET 173 173 1 LYS ? 121 VAL ? 122 0 Start residue of secondary structure not found: SHEET 174 174 1 TYR ? 7 VAL ? 10 0 Start residue of secondary structure not found: SHEET 175 175 1 LYS ? 18 VAL ? 24 0 Start residue of secondary structure not found: SHEET 176 176 1 VAL ? 38 GLU ? 45 0 Start residue of secondary structure not found: SHEET 177 177 1 VAL ? 57 ARG ? 64 0 15 messages similar to the above omitted End residue of secondary structure not found: SHEET 193 193 1 ARG ? 25 SER ? 27 0 Start residue of secondary structure not found: SHEET 194 194 1 ALA ? 37 ASP ? 41 0 Start residue of secondary structure not found: SHEET 195 195 1 VAL ? 46 ALA ? 51 0 Start residue of secondary structure not found: SHEET 196 196 1 ILE ? 48 ARG ? 53 0 Start residue of secondary structure not found: SHEET 197 197 1 THR ? 60 SER ? 67 0 Start residue of secondary structure not found: SHEET 198 198 1 VAL ? 70 PHE ? 76 0 End residue of secondary structure not found: SHEET 199 199 1 ILE ? 4 THR ? 7 0 Start residue of secondary structure not found: SHEET 200 200 1 LYS ? 10 ARG ? 13 0 Start residue of secondary structure not found: SHEET 201 201 1 LEU ? 62 GLY ? 63 0 End residue of secondary structure not found: SHEET 202 202 1 ALA ? 77 LYS ? 78 0 Start residue of secondary structure not found: SHEET 203 203 1 ARG ? 83 LYS ? 84 0 Start residue of secondary structure not found: SHEET 204 204 1 LYS ? 97 GLU ? 98 0 Start residue of secondary structure not found: SHEET 205 205 1 LEU ? 69 GLU ? 78 0 Start residue of secondary structure not found: SHEET 206 206 1 LEU ? 82 LEU ? 86 0 Start residue of secondary structure not found: SHEET 207 207 1 ASP ? 94 LYS ? 98 0 20 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (9 ) Cannot find LINK/SSBOND residue CYS (12 ) Cannot find LINK/SSBOND residue CYS (12 ) Cannot find LINK/SSBOND residue CYS (11 ) Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 254, in execute cmd.run(cmd_text) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2646, in run result = ci.function(session, **kw_args) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py"", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 628, in open self.add(models) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 481, in add m.added_to_session(session) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2286, in added_to_session self._report_chain_descriptions(session) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2531, in _report_chain_descriptions self._report_chain_summary(session, descripts, chain_text, False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2578, in _report_chain_summary summary += ' '.join([chain_text(chain) for chain in chains]) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2578, in summary += ' '.join([chain_text(chain) for chain in chains]) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2530, in chain_text chain_res_range(chain), chain.chain_id) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2629, in chain_res_range return ""%s-%s"" % (first.string(style=""command""), last.string(residue_only=True, style=""command"")[1:]) File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2677, in _update_graphics_if_needed s[i]._update_graphics_if_needed() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data Error processing trigger ""graphics update"": 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data: UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command ""graphics restart"" after changing the settings that caused the error. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 72, in draw_new_frame view.draw(check_for_changes = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 164, in draw self._draw_scene(camera, drawings) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 207, in _draw_scene self._update_projection(camera, vnum) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 796, in _update_projection near_far = self.near_far_distances(camera, view_num) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. Traceback (most recent call last): File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 129, in _redraw_timer_callback s.ui.mouse_modes.mouse_pause_tracking() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 349, in mouse_pause_tracking self._mouse_pause() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 443, in _mouse_pause m.pause(self._mouse_pause_position) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/std_modes.py"", line 431, in pause p = picked_object(x, y, self.view) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py"", line 581, in picked_object xyz1, xyz2 = view.clip_plane_points(window_x, window_y) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 850, in clip_plane_points near, far = self.near_far_distances(c, view_num, include_clipping = False) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 811, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 824, in _near_far_bounds b = self.drawing_bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 579, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 906, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 1691, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 309, in _update_graphics_if_needed self._create_ribbon_graphics() File ""/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 611, in _create_ribbon_graphics rp = RibbonDrawing(self.name + "" "" + str(residues[0]) + "" ribbons"") File ""cymol.pyx"", line 851, in chimerax.atomic.cymol.CyResidue.__str__ File ""cymol.pyx"", line 1464, in chimerax.atomic.cymol.CyResidue.string File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd8 in position 0: unexpected end of data File ""cymol.pyx"", line 887, in chimerax.atomic.cymol.CyResidue.chain_id.__get__ See log for complete Python traceback. OpenGL version: 4.1 ATI-2.9.26 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc. File attachment: test.pdb }}} [attachment:""test.pdb""] " defect closed major Input/Output can't reproduce all ChimeraX