Saving as PDB with 2-letter chain id gives unreadable file

[goddard@…]

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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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 <listcomp>  
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

test.pdb​

[goddard@…]

Added by email2trac

[Tom Goddard]

Jing He was trying to save individual chains of ribosome structure. She wanted mmCIF format but that requires using split command because saving mmCIF does not have "selectedOnly" flag. Thus I was trying to save selected in PDB format.

[pett]

Turns out this happens for single-character chain IDs as well. I wonder how long this has been broken.

[pett]

Doesn't seem to happen with daily builds, only development builds. So, probably PDB compilation wasn't up-to-date with atomic.