Opened 6 years ago

Closed 5 years ago

#3022 closed defect (fixed)

ISOLDE used with incompatible ChimeraX

Reported by: csrobb@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc: Conrad Huang
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.1.2.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 0.91 (2019-06-14)
Description
clipper assoc #2 to #1

Does not happen with another map/model

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-06-14)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/crobb/Documents/Ribosome/Y320/6ek0_SSU-coot-17.pdb

Summary of feedback from opening /home/crobb/Documents/Ribosome/Y320/6ek0_SSU-
coot-17.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 18 18 PRO G
58 LEU G 74 1 17  
Start residue of secondary structure not found: HELIX 19 19 PRO G 77 ALA G 86
1 10  
Start residue of secondary structure not found: HELIX 20 20 ASP G 88 ARG G 103
1 16  
Start residue of secondary structure not found: HELIX 21 21 THR G 106 GLY G
124 1 19  
Start residue of secondary structure not found: HELIX 22 22 GLY G 139 LYS G
150 1 12  
6 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 29 29 SER N 16 SER N 34 1
19  
Start residue of secondary structure not found: HELIX 30 30 ARG N 44 GLY N 52
1 9  
Start residue of secondary structure not found: HELIX 31 31 LYS N 83 GLY N 88
1 6  
Start residue of secondary structure not found: HELIX 32 32 SER N 97 GLY N 111
1 15  
Start residue of secondary structure not found: HELIX 33 33 HIS N 139 ASN N
145 1 7  
Start residue of secondary structure not found: HELIX 34 34 HIS N 158 GLY N
163 1 6  
32 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 67 67 ASN W 33 LYS W 43 1
11  
Start residue of secondary structure not found: HELIX 68 68 ASN W 45 ASN W 50
1 6  
Start residue of secondary structure not found: HELIX 69 69 THR W 52 LYS W 60
1 9  
Start residue of secondary structure not found: HELIX 70 70 MET W 91 LYS W 97
1 7  
Start residue of secondary structure not found: HELIX 71 71 GLN W 104 LYS W
124 1 21  
Start residue of secondary structure not found: HELIX 72 72 ASP X 72 LYS X 78
1 7  
3 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 76 76 GLY Z 58 LYS Z 67 1
10  
Start residue of secondary structure not found: HELIX 77 77 ASN Z 76 MET Z 81
1 6  
Start residue of secondary structure not found: HELIX 78 78 ASP Z 92 ASN Z 97
1 6  
Start residue of secondary structure not found: HELIX 79 79 LYS Z 98 PRO Z 104
1 7  
Start residue of secondary structure not found: HELIX 80 80 ALA Z 105 GLY Z
125 1 21  
Start residue of secondary structure not found: HELIX 81 81 ASN Z 127 LYS Z
133 1 7  
38 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 120 120 GLY A 167 GLY A
187 1 21  
Start residue of secondary structure not found: HELIX 121 121 MET A 198 TYR A
204 1 7  
Start residue of secondary structure not found: HELIX 122 122 ASP B 23 ASP B
29 1 7  
Start residue of secondary structure not found: HELIX 123 123 ILE B 57 ARG B
65 1 9  
Start residue of secondary structure not found: HELIX 124 124 SER B 70 ASN B
76 1 7  
Start residue of secondary structure not found: HELIX 125 125 THR B 106 LYS B
115 1 10  
37 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 163 163 SER I 106 ALA I
118 1 13  
Start residue of secondary structure not found: HELIX 164 164 ILE I 145 ALA I
156 1 12  
Start residue of secondary structure not found: HELIX 165 165 SER I 159 GLY I
169 1 11  
Start residue of secondary structure not found: HELIX 166 166 GLY I 192 GLY I
207 1 16  
Start residue of secondary structure not found: HELIX 167 167 GLU J 21 GLY J
36 1 16  
Start residue of secondary structure not found: HELIX 168 168 ASN J 39 ASP J
64 1 26  
47 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 1 12 4 ALA N 35 ALA N 39 0  
Start residue of secondary structure not found: SHEET 2 12 4 GLY N 58 ARG N 67
-1 N ARG N 65 O ALA N 35  
Start residue of secondary structure not found: SHEET 3 12 4 TYR N 127 ASP N
136 -1  
Start residue of secondary structure not found: SHEET 4 12 4 LEU N 113 LEU N
116 -1 N LEU N 116 O ILE N 133  
Start residue of secondary structure not found: SHEET 1 13 2 ASN N 117 VAL N
121 0  
End residue of secondary structure not found: SHEET 2 13 2 PHE N 129 ILE N 133
-1 N ILE N 133 O ASN N 117  
Start residue of secondary structure not found: SHEET 1 14 2 VAL O 6 ASP O 10
0  
End residue of secondary structure not found: SHEET 2 14 2 LYS O 32 VAL O 36 1
N VAL O 34 O LEU O 7  
Start residue of secondary structure not found: SHEET 1 15 3 LYS P 16 SER P 20
0  
Start residue of secondary structure not found: SHEET 2 15 3 PRO P 143 LEU P
150 -1 N MET P 148 O SER P 17  
Start residue of secondary structure not found: SHEET 3 15 3 GLU P 115 ALA P
122 -1 N ALA P 122 O PRO P 143  
Start residue of secondary structure not found: SHEET 1 16 2 LYS P 124 ARG P
131 0  
Start residue of secondary structure not found: SHEET 2 16 2 ARG P 135 SER P
142 -1 N SER P 141 O MET P 125  
8 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 4 18 6 LYS V 35 ILE V 40
-1 N ILE V 39 O ALA V 24  
Start residue of secondary structure not found: SHEET 5 18 6 ASP V 59 VAL V 65
-1 N THR V 64 O TYR V 38  
Start residue of secondary structure not found: SHEET 6 18 6 VAL V 76 VAL V 81
-1 N VAL V 81 O ASP V 59  
Start residue of secondary structure not found: SHEET 1 19 2 PRO V 78 VAL V 81
0  
Start residue of secondary structure not found: SHEET 2 19 2 GLY V 103 VAL V
106 -1 N VAL V 106 O PRO V 78  
Start residue of secondary structure not found: SHEET 1 20 2 VAL W 3 CYS W 6 0  
8 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 1 24 3 LYS Z 27 ASP Z 30 0  
Start residue of secondary structure not found: SHEET 2 24 3 SER Z 39 GLY Z 45
-1 N LEU Z 42 O LYS Z 27  
Start residue of secondary structure not found: SHEET 3 24 3 PHE Z 71 VAL Z 74
-1 N LYS Z 73 O VAL Z 43  
Start residue of secondary structure not found: SHEET 1 25 2 VAL a 122 ALA a
126 0  
Start residue of secondary structure not found: SHEET 2 25 2 GLY a 142 LEU a
146 1 N ALA a 143 O VAL a 122  
Start residue of secondary structure not found: SHEET 1 26 4 LYS c 26 LEU c 29
0  
14 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 6 29 6 ILE f 101 MET f 104
-1 N MET f 104 O ARG f 46  
Start residue of secondary structure not found: SHEET 1 30 2 TRP f 6 ALA f 12
0  
Start residue of secondary structure not found: SHEET 2 30 2 GLY f 98 MET f
104 -1 N VAL f 103 O SER f 7  
Start residue of secondary structure not found: SHEET 1 31 2 THR g 20 ARG g 24
0  
Start residue of secondary structure not found: SHEET 2 31 2 ILE g 30 TYR g 34
-1 N LEU g 33 O ARG g 21  
Start residue of secondary structure not found: SHEET 1 32 5 PRO k 2 ILE k 5 0  
45 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 1 46 3 LYS E 128 VAL E 131
0  
End residue of secondary structure not found: SHEET 2 46 3 PRO E 137 THR E 141
-1 N VAL E 140 O LYS E 128  
Start residue of secondary structure not found: SHEET 3 46 3 ARG E 145 ARG E
148 -1 N ILE E 147 O LEU E 139  
Start residue of secondary structure not found: SHEET 1 47 2 LEU E 180 VAL E
183 0  
Start residue of secondary structure not found: SHEET 2 47 2 ILE E 225 ILE E
228 -1 N ILE E 228 O LEU E 180  
Start residue of secondary structure not found: SHEET 1 48 3 ASN E 197 ARG E
200 0  
Start residue of secondary structure not found: SHEET 2 48 3 ASP E 206 ASP E
212 -1 N HIS E 209 O ASN E 197  
64 messages similar to the above omitted  
  
Chain information for 6ek0_SSU-coot-17.pdb #1  
---  
Chain | Description  
2 | No description available  
5 | No description available  
8 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
x | No description available  
  

> open /home/crobb/Documents/Ribosome/Y320/SSU_410_postprocess_masked.mrc

Opened SSU_410_postprocess_masked.mrc, grid size 410,410,410, pixel 1.14,
shown at level 0.0151, step 2, values float32  

> select up

Nothing selected  

> set bgColor white

> clipper associate #2 toModel #1

Traceback (most recent call last):  
File "/home/crobb/Programs/chimerax-2019.06.14/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File "/home/crobb/Programs/chimerax-2019.06.14/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2641, in run  
result = ci.function(session, **kw_args)  
File "/home/crobb/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/cmd.py", line 108, in associate_volumes  
mgr = get_map_mgr(to_model, create=True)  
File "/home/crobb/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 166, in get_map_mgr  
sh = get_symmetry_handler(structure, create=create,
auto_add_to_session=auto_add_to_session)  
File "/home/crobb/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 151, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/home/crobb/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 162, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/home/crobb/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 529, in __init__  
spotlight_mode=spotlight_mode)  
File "/home/crobb/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 550, in add_model  
self._anisou_sanity_check(model.atoms)  
File "/home/crobb/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 583, in _anisou_sanity_check  
remove_invalid_anisou(self.session, atoms)  
File "/home/crobb/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/sanity_check.py", line 22, in remove_invalid_anisou  
with a.suppress_alt_loc_change_notifications():  
File "/home/crobb/Programs/chimerax-2019.06.14/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/home/crobb/Programs/chimerax-2019.06.14/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Atom' object has no attribute
'suppress_alt_loc_change_notifications'  
  
AttributeError: 'Atom' object has no attribute
'suppress_alt_loc_change_notifications'  
  
File "/home/crobb/Programs/chimerax-2019.06.14/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

> clipper associate #2 toModel #1

Traceback (most recent call last):  
File "/home/crobb/Programs/chimerax-2019.06.14/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File "/home/crobb/Programs/chimerax-2019.06.14/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2641, in run  
result = ci.function(session, **kw_args)  
File "/home/crobb/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/cmd.py", line 108, in associate_volumes  
mgr = get_map_mgr(to_model, create=True)  
File "/home/crobb/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 166, in get_map_mgr  
sh = get_symmetry_handler(structure, create=create,
auto_add_to_session=auto_add_to_session)  
File "/home/crobb/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 151, in get_symmetry_handler  
sh = _get_symmetry_handler(structure, create)  
File "/home/crobb/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 162, in _get_symmetry_handler  
return SymmetryManager(structure.session, model=structure)  
File "/home/crobb/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 529, in __init__  
spotlight_mode=spotlight_mode)  
File "/home/crobb/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 550, in add_model  
self._anisou_sanity_check(model.atoms)  
File "/home/crobb/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/symmetry.py", line 583, in _anisou_sanity_check  
remove_invalid_anisou(self.session, atoms)  
File "/home/crobb/.local/share/ChimeraX/0.91/site-
packages/chimerax/clipper/sanity_check.py", line 22, in remove_invalid_anisou  
with a.suppress_alt_loc_change_notifications():  
File "/home/crobb/Programs/chimerax-2019.06.14/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "/home/crobb/Programs/chimerax-2019.06.14/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Atom' object has no attribute
'suppress_alt_loc_change_notifications'  
  
AttributeError: 'Atom' object has no attribute
'suppress_alt_loc_change_notifications'  
  
File "/home/crobb/Programs/chimerax-2019.06.14/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

> addh

Summary of feedback from adding hydrogens to 6ek0_SSU-coot-17.pdb #1  
---  
warnings | Not adding hydrogens to /2 C 785 C4' because it is missing heavy-
atom bond partners  
Not adding hydrogens to /2 C 785 C3' because it is missing heavy-atom bond
partners  
Not adding hydrogens to /B LYS 294 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /B LYS 297 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /D ASP 127 CB because it is missing heavy-atom bond
partners  
2 messages similar to the above omitted  
Unknown hybridization for atom (O5') of residue type PSU; not adding hydrogens
to it  
notes | No usable SEQRES records for 6ek0_SSU-coot-17.pdb (#1) chain 2;
guessing termini instead  
No usable SEQRES records for 6ek0_SSU-coot-17.pdb (#1) chain 5; guessing
termini instead  
No usable SEQRES records for 6ek0_SSU-coot-17.pdb (#1) chain 8; guessing
termini instead  
No usable SEQRES records for 6ek0_SSU-coot-17.pdb (#1) chain A; guessing
termini instead  
No usable SEQRES records for 6ek0_SSU-coot-17.pdb (#1) chain B; guessing
termini instead  
45 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /2 U 1, /5 C 1, /8 C 1, /A
GLY 2, /B SER 2, /C VAL 54, /D LYS 26, /E GLY 2, /F GLU 3, /G TYR 4, /H SER 2,
/I GLN 17, /J SER 10, /K MET 1, /L ILE 40, /M GLY 2, /N PRO 2, /O ILE 14, /P
ASN 18, /Q ALA 2, /R SER 2, /S VAL 2, /T LEU 17, /U THR 2, /V PRO 2, /W SER 2,
/X MET 1, /Y LEU 33, /Z ALA 2, /a HIS 24, /b VAL 21, /c GLU 59, /d MET 1, /e
ALA 2, /f MET 1, /g SER 5, /h GLY 2, /i PRO 2, /j ASP 3, /k GLY 2, /l ASN 26,
/m MET 1, /n MET 1, /o VAL 2, /p GLY 2, /q ASN 2, /r THR 2, /s LEU 3, /t ARG
5, /x SER 5  
Chain-initial residues that are not actual N termini: /2 C 140, /2 U 289, /2 G
546, /2 C 730, /2 G 744, /2 C 785, /2 U 1329, /2 U 1485, /2 G 1680, /2 G 1777,
/5 A 33, /5 G 90, /5 U 287, /5 C 358, /5 U 393, /5 A 420, /5 C 1306, /5 C
1521, /5 C 1675, /5 A 2347, /5 C 3594, /5 G 4061, /5 G 4338, /5 G 4742, /5 C
4858, /K ARG 71, /L LYS 63, /N PHE 53, /N PHE 129, /g GLN 114, /h ILE 145, /j
LYS 32, /j GLN 154, /m VAL 98, /m THR 123, /s ILE 43, /s VAL 62, /x LYS 53  
Chain-final residues that are actual C termini: /2 A 1869, /5 U 5069, /8 U
156, /D GLY 266, /E ARG 204, /F VAL 203, /J ALA 140, /L ILE 156, /M PHE 136,
/N ALA 148, /R ILE 110, /V LYS 70, /W LEU 51, /Z GLN 92, /e GLY 263, /k ALA
151, /l LEU 151, /o PHE 130, /x SER 59  
Chain-final residues that are not actual C termini: /2 C 129, /2 G 225, /2 G
535, /2 G 698, /2 C 739, /2 C 753, /2 C 1213, /2 A 1388, /2 C 1488, /2 C 1752,
/5 U 13, /5 G 54, /5 A 94, /5 U 290, /5 A 376, /5 A2M 398, /5 A 435, /5 A
1334, /5 U 1652, /5 C 1678, /5 U 2900, /5 U 3950, /5 A 4205, /5 G 4740, /5 G
4776, /A THR 249, /B ALA 403, /C LYS 106, /G THR 151, /H LEU 188, /I PHE 115,
/K LYS 124, /K GLY 62, /L LEU 54, /N ARG 42, /N LYS 127, /O ARG 106, /P GLU
124, /Q LEU 129, /S LYS 115, /T LYS 66, /U LEU 67, /X SER 24, /Y ALA 60, /a
PRO 207, /b GLU 234, /c VAL 274, /d GLY 199, /f ARG 233, /g PHE 192, /g ARG
109, /h GLY 207, /h GLY 122, /i GLY 186, /j GLN 154, /j VAL 23, /j THR 151, /m
GLY 133, /m LYS 10, /m LEU 109, /n PHE 83, /p ARG 140, /q ALA 124, /r PRO 99,
/s ARG 81, /s VAL 35, /s LEU 55, /t ALA 65, /x ASN 44  
32384 hydrogen bonds  
Adding 'H' to /K ARG 71  
Adding 'H' to /L LYS 63  
Adding 'H' to /N PHE 53  
Adding 'H' to /N PHE 129  
Adding 'H' to /g GLN 114  
8 messages similar to the above omitted  
/A THR 249 is not terminus, removing H atom from 'C'  
/B ALA 403 is not terminus, removing H atom from 'C'  
/C LYS 106 is not terminus, removing H atom from 'C'  
/G THR 151 is not terminus, removing H atom from 'C'  
/H LEU 188 is not terminus, removing H atom from 'C'  
39 messages similar to the above omitted  
103814 hydrogens added  
  




OpenGL version: 3.3.0 NVIDIA 430.50
OpenGL renderer: Quadro P4200 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (4)

in reply to:  1 ; comment:1 by csrobb@…, 6 years ago 

Hi ChimeraX,


I solved this by removing the residue with an alternate conf.


Thanks

Craig

On 4/6/20 12:32 PM, ChimeraX wrote:

comment:2 by pett, 6 years ago

Cc: Conrad Huang added
Component: Unassigned → Tool Shed
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE used with incompatible ChimeraX

The "suppress_alt_loc_change_notifications" attribute of Atom was added on 2019-07-19, roughly a month after the version of ChimeraX that Craig is using here.

comment:3 by Tristan Croll, 6 years ago

If you update to ChimeraX 0.93 and the matching ISOLDE version, this problem should go away.

comment:4 by Greg Couch, 5 years ago

Resolution: → fixed
Status: assigned → closed

0.93 is out. This problem should not crop up with future versions.

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