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Opened 5 years ago
Closed 5 years ago
#3557 closed defect (duplicate)
Open DICOM via icon: 'MainWindow' object has no attribute 'folder_open_cb'
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.4.0-42-generic-x86_64-with-debian-bullseye-sid
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Errors
---
error | Bundle 'ChimeraX-Registration' custom initialization failed
warning | Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 342, in initialize
api._api_caller.initialize(api, session, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1599, in initialize
return cls._get_func(api, "initialize")(session, bi)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/__init__.py", line 41, in initialize
nag(session)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 28, in nag
if not check_registration(logger=session.logger):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 49, in check_registration
return _check_expiration(param, logger)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 130, in _check_expiration
expires = _expiration_time(param)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 162, in _expiration_time
locale.setlocale(locale.LC_TIME, save)
File "/usr/lib/ucsf-chimerax/lib/python3.7/locale.py", line 608, in setlocale
return _setlocale(category, locale)
locale.Error: unsupported locale setting
UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/jitesh/Desktop/mds_lig/3lbk.pdb format pdb
3lbk.pdb title:
Structure of human MDM2 protein In complex with A small molecule inhibitor
[more info...]
Chain information for 3lbk.pdb #1
---
Chain | Description
A | E3 ubiquitin-protein ligase MDM2
Non-standard residues in 3lbk.pdb #1
---
K23 —
6-chloro-3-[1-(4-chlorobenzyl)-4-phenyl-1H-imidazol-5-yl]-1H-indole-2-carboxylic
acid
SO4 — sulfate ion
> ui tool show "Command Line Interface"
> addh H
No structures specified
> addh 3lbk.pdb
Expected a keyword
> addh all
Summary of feedback from adding hydrogens to 3lbk.pdb #1
---
warnings | Not adding hydrogens to /A GLN 44 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /A GLN 72 CG because it is missing heavy-atom bond
partners
Not adding hydrogens to /A VAL 110 CB because it is missing heavy-atom bond
partners
notes | Termini for 3lbk.pdb (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A THR 26
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A VAL 110
100 hydrogen bonds
Adding 'H' to /A THR 26
/A VAL 110 is not terminus, removing H atom from 'C'
777 hydrogens added
Alignment identifier is 1.A
> show sel target ab
> hide sel target a
> select clear
> ui tool show Rotamers
> ui tool show "Build Structure"
> show sel target ab
> hide sel target a
> ui tool show Rotamers
> swapaa interactive sel GLN rotLib Dunbrack
/A GLN 44: phi -103.1, psi -16.7 trans
Changed 648 bond radii
> hbonds #!1 & ~#1/A:44 & ~solvent reveal true restrict #1.1 & ~@c,ca,n
11 hydrogen bonds found
> hbonds #!1 & ~#1/A:44 & ~solvent reveal true restrict #1.1 & ~@c,ca,n
11 hydrogen bonds found
No rotamers selected
> swapaa #1/A:44 GLN criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
3lbk.pdb #1/A GLN 44: phi -103.1, psi -16.7 trans
Applying GLN rotamer (chi angles: -61.3 -61.6 -54.2) to 3lbk.pdb #1/A GLN 44
> show sel target ab
> show sel target ab
> ui tool show Rotamers
> swapaa interactive sel GLN rotLib Dunbrack
/A GLN 72: phi 78.6, psi -26.1 trans
Changed 648 bond radii
> swapaa #1/A:72 GLN criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
3lbk.pdb #1/A GLN 72: phi 78.6, psi -26.1 trans
Applying GLN rotamer (chi angles: -63.9 -64.6 -52.4) to 3lbk.pdb #1/A GLN 72
> ui tool show Rotamers
> swapaa interactive sel VAL rotLib Dunbrack
/A VAL 110: phi -54.3, psi none trans
Changed 12 bond radii
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.
> swapaa #1/A:110 VAL criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
3lbk.pdb #1/A VAL 110: phi -54.3, psi none trans
Applying VAL rotamer (chi angles: 175.9) to 3lbk.pdb #1/A VAL 110
> swapaa interactive sel VAL rotLib Dunbrack
/A VAL 110: phi -54.3, psi none trans
Changed 12 bond radii
> swapaa #1/A:110 VAL criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
3lbk.pdb #1/A VAL 110: phi -54.3, psi none trans
Applying VAL rotamer (chi angles: 175.9) to 3lbk.pdb #1/A VAL 110
> select clear
> addh all
Summary of feedback from adding hydrogens to 3lbk.pdb #1
---
notes | Termini for 3lbk.pdb (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A THR 26
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A VAL 110
95 hydrogen bonds
/A VAL 110 is not terminus, removing H atom from 'C'
19 hydrogens added
> minimize
Unknown command: minimize
> select protein
1443 atoms, 1457 bonds, 1 model selected
> hide sel target a
> select ::name="HOH"
60 atoms, 40 bonds, 1 model selected
> show sel target ab
> select ::name="K23"
47 atoms, 51 bonds, 1 model selected
> style sel ringFill thick
Changed 1 residue ring style
> style sel ringFill thin
Changed 1 residue ring style
> style sel ringFill off
Changed 1 residue ring style
> style sel ball
Changed 47 atom styles
> style sel sphere
Changed 47 atom styles
> style sel ball
Changed 47 atom styles
> select ::name="HOH"
60 atoms, 40 bonds, 1 model selected
> style sel sphere
Changed 60 atom styles
> style sel stick
Changed 60 atom styles
> select protein
1443 atoms, 1457 bonds, 1 model selected
> surface sel
> mlp sel
Map values for surface "3lbk.pdb_A SES surface": minimum -25, mean -1.985,
maximum 23.28
> transparency (#!1 & sel) 80
> transparency (#!1 & sel) 60
> select ::name="K23"
47 atoms, 51 bonds, 1 model selected
> ui tool show H-Bonds
> hbonds sel showDist true reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 3lbk.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A HOH 4 O /A K23 1 O11 /A HOH 4 H1 2.573 1.843
/A HOH 1007 O /A K23 1 O12 /A HOH 1007 H1 3.346 2.388
2 hydrogen bonds found
> hbonds sel showDist true reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 3lbk.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A HOH 4 O /A K23 1 O11 /A HOH 4 H1 2.573 1.843
/A HOH 1007 O /A K23 1 O12 /A HOH 1007 H1 3.346 2.388
2 hydrogen bonds found
> select protein
1443 atoms, 1457 bonds, 1 model selected
> cartoon hide (#!1 & sel)
> select protein
1443 atoms, 1457 bonds, 1 model selected
> ui tool show H-Bonds
> hbonds sel showDist true reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 3lbk.pdb
90 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A HOH 4 O /A PHE 55 O /A HOH 4 H2 2.708 2.010
/A HOH 8 O /A GLY 42 O /A HOH 8 H1 2.688 1.730
/A HOH 9 O /A SER 90 O /A HOH 9 H1 3.023 2.066
/A HOH 11 O /A THR 63 O /A HOH 11 H1 3.612 2.655
/A HOH 14 O /A ASP 46 OD1 /A HOH 14 H1 2.494 1.536
/A HOH 15 O /A VAL 110 O /A HOH 15 H1 3.484 2.527
/A VAL 28 N /A TYR 48 O /A VAL 28 H 2.589 1.627
/A ARG 29 N /A VAL 108 O /A ARG 29 H 2.871 1.912
/A LYS 31 N /A ASN 106 O /A LYS 31 H 2.686 1.702
/A LYS 31 NZ /A ARG 105 O /A LYS 31 HZ1 2.613 1.820
/A LEU 35 N /A LYS 31 O /A LEU 35 H 2.955 1.949
/A LYS 36 N /A PRO 32 O /A LYS 36 H 2.856 1.906
/A LYS 36 NZ /A GLU 33 OE2 /A LYS 36 HZ1 3.517 2.721
/A LEU 37 N /A GLU 33 O /A LEU 37 H 3.059 2.072
/A LEU 38 N /A LEU 34 O /A LEU 38 H 2.619 1.641
/A LYS 39 N /A LEU 35 O /A LYS 39 H 2.808 1.855
/A SER 40 N /A LYS 36 O /A SER 40 H 2.897 2.016
/A SER 40 OG /A LEU 37 O /A SER 40 HG 2.513 1.786
/A VAL 41 N /A LEU 38 O /A VAL 41 H 3.321 2.573
/A GLY 42 N /A LYS 39 O /A GLY 42 H 2.756 1.852
/A ALA 43 N /A LEU 38 O /A ALA 43 H 3.144 2.251
/A GLN 44 NE2 /A GLY 42 O /A GLN 44 HE21 3.465 2.464
/A LYS 45 NZ /A THR 47 O /A LYS 45 HZ1 2.549 1.640
/A LYS 45 NZ /A GLU 52 OE1 /A LYS 45 HZ2 3.330 2.507
/A LYS 45 NZ /A GLU 52 OE2 /A LYS 45 HZ2 3.177 2.199
/A TYR 48 N /A VAL 28 O /A TYR 48 H 2.728 1.786
/A TYR 48 OH /A LYS 45 O /A TYR 48 HH 2.644 1.825
/A THR 49 N /A GLU 52 OE1 /A THR 49 H 3.068 2.070
/A THR 49 OG1 /A GLU 52 OE1 /A THR 49 HG1 2.330 1.569
/A VAL 53 N /A THR 49 O /A VAL 53 H 3.017 2.129
/A LEU 54 N /A MET 50 O /A LEU 54 H 2.471 1.478
/A PHE 55 N /A LYS 51 O /A PHE 55 H 2.819 1.844
/A TYR 56 N /A GLU 52 O /A TYR 56 H 3.164 2.155
/A LEU 57 N /A VAL 53 O /A LEU 57 H 2.936 1.987
/A GLY 58 N /A LEU 54 O /A GLY 58 H 3.036 2.029
/A GLN 59 N /A PHE 55 O /A GLN 59 H 3.107 2.149
/A TYR 60 N /A TYR 56 O /A TYR 60 H 2.819 1.892
/A TYR 60 OH /A ASP 80 OD2 /A TYR 60 HH 2.452 1.505
/A ILE 61 N /A LEU 57 O /A ILE 61 H 2.762 1.771
/A MET 62 N /A GLY 58 O /A MET 62 H 2.839 1.875
/A THR 63 N /A GLN 59 O /A THR 63 H 2.763 1.807
/A THR 63 OG1 /A GLN 59 O /A THR 63 HG1 2.727 1.913
/A THR 63 OG1 /A TYR 60 O /A THR 63 HG1 3.285 2.625
/A LYS 64 N /A TYR 60 O /A LYS 64 H 2.747 1.865
/A LYS 64 NZ /A HOH 113 O /A LYS 64 HZ1 3.091 2.159
/A ARG 65 N /A MET 62 O /A ARG 65 H 3.247 2.318
/A LEU 66 N /A ILE 61 O /A LEU 66 H 2.913 1.906
/A ASP 68 N /A ILE 74 O /A ASP 68 H 3.061 2.146
/A GLU 69 N /A GLU 69 OE2 /A GLU 69 H 2.627 1.875
/A GLN 71 N /A ASP 68 O /A GLN 71 H 3.302 2.455
/A GLN 72 N /A ASP 68 O /A GLN 72 H 2.670 1.730
/A HIS 73 N /A GLN 71 O /A HIS 73 H 2.893 2.013
/A VAL 75 N /A PHE 91 O /A VAL 75 H 2.871 1.862
/A TYR 76 N /A LEU 66 O /A TYR 76 H 2.394 1.499
/A CYS 77 N /A PRO 89 O /A CYS 77 H 2.916 2.184
/A CYS 77 SG /A VAL 88 O /A CYS 77 HG 3.308 2.124
/A LEU 82 N /A ASP 80 OD2 /A LEU 82 H 2.773 1.774
/A ASP 84 N /A ASP 80 O /A ASP 84 H 3.263 2.265
/A LEU 85 N /A LEU 81 O /A LEU 85 H 2.862 1.948
/A PHE 86 N /A LEU 82 O /A PHE 86 H 2.702 1.760
/A GLY 87 N /A GLY 83 O /A GLY 87 H 2.556 1.791
/A VAL 88 N /A GLY 83 O /A VAL 88 H 3.376 2.475
/A PHE 91 N /A VAL 75 O /A PHE 91 H 3.130 2.223
/A SER 92 N /A GLU 95 OE1 /A SER 92 H 2.645 1.737
/A VAL 93 N /A HIS 73 O /A VAL 93 H 2.970 2.003
/A LYS 94 N /A SER 92 OG /A LYS 94 H 2.899 1.985
/A LYS 94 NZ /A HOH 115 O /A LYS 94 HZ1 2.701 1.692
/A GLU 95 N /A SER 92 O /A GLU 95 H 3.082 2.097
/A HIS 96 N /A SO4 112 O2 /A HIS 96 H 3.071 2.081
/A ARG 97 N /A SO4 112 O3 /A ARG 97 H 3.430 2.453
/A ARG 97 NE /A SO4 112 O1 /A ARG 97 HE 2.622 2.042
/A ARG 97 NH1 /A HOH 13 O /A ARG 97 HH11 2.590 1.854
/A ILE 99 N /A GLU 95 O /A ILE 99 H 3.147 2.155
/A TYR 100 N /A HIS 96 O /A TYR 100 H 2.915 1.977
/A THR 101 N /A ARG 97 O /A THR 101 H 2.708 1.703
/A THR 101 OG1 /A ARG 97 O /A THR 101 HG1 3.246 2.458
/A MET 102 N /A LYS 98 O /A MET 102 H 2.952 2.096
/A ILE 103 N /A ILE 99 O /A ILE 103 H 2.813 1.807
/A TYR 104 N /A TYR 100 O /A TYR 104 H 2.947 1.982
/A ARG 105 N /A THR 101 O /A ARG 105 H 3.174 2.358
/A ARG 105 N /A MET 102 O /A ARG 105 H 3.260 2.478
/A ARG 105 NH1 /A PHE 86 O /A ARG 105 HH12 3.391 2.389
/A ASN 106 N /A ILE 103 O /A ASN 106 H 2.808 1.893
/A ASN 106 ND2 /A LEU 85 O /A ASN 106 HD22 3.170 2.246
/A ASN 106 ND2 /A MET 102 O /A ASN 106 HD21 2.648 1.886
/A LEU 107 N /A TYR 104 O /A LEU 107 H 3.398 2.531
/A VAL 108 N /A ARG 29 O /A VAL 108 H 2.845 2.055
/A VAL 110 N /A LEU 27 O /A VAL 110 H 3.276 2.470
/A HOH 114 O /A VAL 109 O /A HOH 114 H1 2.990 2.033
/A HOH 1002 O /A VAL 41 O /A HOH 1002 H1 3.095 2.137
90 hydrogen bonds found
> hbonds sel restrict cross showDist true reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 3lbk.pdb
14 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A HOH 4 O /A PHE 55 O /A HOH 4 H2 2.708 2.010
/A HOH 8 O /A GLY 42 O /A HOH 8 H1 2.688 1.730
/A HOH 9 O /A SER 90 O /A HOH 9 H1 3.023 2.066
/A HOH 11 O /A THR 63 O /A HOH 11 H1 3.612 2.655
/A HOH 14 O /A ASP 46 OD1 /A HOH 14 H1 2.494 1.536
/A HOH 15 O /A VAL 110 O /A HOH 15 H1 3.484 2.527
/A LYS 64 NZ /A HOH 113 O /A LYS 64 HZ1 3.091 2.159
/A LYS 94 NZ /A HOH 115 O /A LYS 94 HZ1 2.701 1.692
/A HIS 96 N /A SO4 112 O2 /A HIS 96 H 3.071 2.081
/A ARG 97 N /A SO4 112 O3 /A ARG 97 H 3.430 2.453
/A ARG 97 NE /A SO4 112 O1 /A ARG 97 HE 2.622 2.042
/A ARG 97 NH1 /A HOH 13 O /A ARG 97 HH11 2.590 1.854
/A HOH 114 O /A VAL 109 O /A HOH 114 H1 2.990 2.033
/A HOH 1002 O /A VAL 41 O /A HOH 1002 H1 3.095 2.137
14 hydrogen bonds found
> hbonds sel restrict cross reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 3lbk.pdb
14 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A HOH 4 O /A PHE 55 O /A HOH 4 H2 2.708 2.010
/A HOH 8 O /A GLY 42 O /A HOH 8 H1 2.688 1.730
/A HOH 9 O /A SER 90 O /A HOH 9 H1 3.023 2.066
/A HOH 11 O /A THR 63 O /A HOH 11 H1 3.612 2.655
/A HOH 14 O /A ASP 46 OD1 /A HOH 14 H1 2.494 1.536
/A HOH 15 O /A VAL 110 O /A HOH 15 H1 3.484 2.527
/A LYS 64 NZ /A HOH 113 O /A LYS 64 HZ1 3.091 2.159
/A LYS 94 NZ /A HOH 115 O /A LYS 94 HZ1 2.701 1.692
/A HIS 96 N /A SO4 112 O2 /A HIS 96 H 3.071 2.081
/A ARG 97 N /A SO4 112 O3 /A ARG 97 H 3.430 2.453
/A ARG 97 NE /A SO4 112 O1 /A ARG 97 HE 2.622 2.042
/A ARG 97 NH1 /A HOH 13 O /A ARG 97 HH11 2.590 1.854
/A HOH 114 O /A VAL 109 O /A HOH 114 H1 2.990 2.033
/A HOH 1002 O /A VAL 41 O /A HOH 1002 H1 3.095 2.137
14 hydrogen bonds found
> hide (#!1 & sel) target a
> select ::name="K23"
47 atoms, 51 bonds, 1 model selected
> ui tool show H-Bonds
> hbonds reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 3lbk.pdb
94 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A HOH 4 O /A K23 1 O11 /A HOH 4 H1 2.573 1.843
/A HOH 4 O /A PHE 55 O /A HOH 4 H2 2.708 2.010
/A HOH 8 O /A GLY 42 O /A HOH 8 H1 2.688 1.730
/A HOH 9 O /A SER 90 O /A HOH 9 H1 3.023 2.066
/A HOH 10 O /A HOH 12 O /A HOH 10 H1 2.688 1.731
/A HOH 11 O /A THR 63 O /A HOH 11 H1 3.612 2.655
/A HOH 14 O /A ASP 46 OD1 /A HOH 14 H1 2.494 1.536
/A HOH 15 O /A VAL 110 O /A HOH 15 H1 3.484 2.527
/A VAL 28 N /A TYR 48 O /A VAL 28 H 2.589 1.627
/A ARG 29 N /A VAL 108 O /A ARG 29 H 2.871 1.912
/A LYS 31 N /A ASN 106 O /A LYS 31 H 2.686 1.702
/A LYS 31 NZ /A ARG 105 O /A LYS 31 HZ1 2.613 1.820
/A LEU 35 N /A LYS 31 O /A LEU 35 H 2.955 1.949
/A LYS 36 N /A PRO 32 O /A LYS 36 H 2.856 1.906
/A LYS 36 NZ /A GLU 33 OE2 /A LYS 36 HZ1 3.517 2.721
/A LEU 37 N /A GLU 33 O /A LEU 37 H 3.059 2.072
/A LEU 38 N /A LEU 34 O /A LEU 38 H 2.619 1.641
/A LYS 39 N /A LEU 35 O /A LYS 39 H 2.808 1.855
/A SER 40 N /A LYS 36 O /A SER 40 H 2.897 2.016
/A SER 40 OG /A LEU 37 O /A SER 40 HG 2.513 1.786
/A VAL 41 N /A LEU 38 O /A VAL 41 H 3.321 2.573
/A GLY 42 N /A LYS 39 O /A GLY 42 H 2.756 1.852
/A ALA 43 N /A LEU 38 O /A ALA 43 H 3.144 2.251
/A GLN 44 NE2 /A GLY 42 O /A GLN 44 HE21 3.465 2.464
/A LYS 45 NZ /A THR 47 O /A LYS 45 HZ1 2.549 1.640
/A LYS 45 NZ /A GLU 52 OE1 /A LYS 45 HZ2 3.330 2.507
/A LYS 45 NZ /A GLU 52 OE2 /A LYS 45 HZ2 3.177 2.199
/A TYR 48 N /A VAL 28 O /A TYR 48 H 2.728 1.786
/A TYR 48 OH /A LYS 45 O /A TYR 48 HH 2.644 1.825
/A THR 49 N /A GLU 52 OE1 /A THR 49 H 3.068 2.070
/A THR 49 OG1 /A GLU 52 OE1 /A THR 49 HG1 2.330 1.569
/A VAL 53 N /A THR 49 O /A VAL 53 H 3.017 2.129
/A LEU 54 N /A MET 50 O /A LEU 54 H 2.471 1.478
/A PHE 55 N /A LYS 51 O /A PHE 55 H 2.819 1.844
/A TYR 56 N /A GLU 52 O /A TYR 56 H 3.164 2.155
/A LEU 57 N /A VAL 53 O /A LEU 57 H 2.936 1.987
/A GLY 58 N /A LEU 54 O /A GLY 58 H 3.036 2.029
/A GLN 59 N /A PHE 55 O /A GLN 59 H 3.107 2.149
/A TYR 60 N /A TYR 56 O /A TYR 60 H 2.819 1.892
/A TYR 60 OH /A ASP 80 OD2 /A TYR 60 HH 2.452 1.505
/A ILE 61 N /A LEU 57 O /A ILE 61 H 2.762 1.771
/A MET 62 N /A GLY 58 O /A MET 62 H 2.839 1.875
/A THR 63 N /A GLN 59 O /A THR 63 H 2.763 1.807
/A THR 63 OG1 /A GLN 59 O /A THR 63 HG1 2.727 1.913
/A THR 63 OG1 /A TYR 60 O /A THR 63 HG1 3.285 2.625
/A LYS 64 N /A TYR 60 O /A LYS 64 H 2.747 1.865
/A LYS 64 NZ /A HOH 113 O /A LYS 64 HZ1 3.091 2.159
/A ARG 65 N /A MET 62 O /A ARG 65 H 3.247 2.318
/A LEU 66 N /A ILE 61 O /A LEU 66 H 2.913 1.906
/A ASP 68 N /A ILE 74 O /A ASP 68 H 3.061 2.146
/A GLU 69 N /A GLU 69 OE2 /A GLU 69 H 2.627 1.875
/A GLN 71 N /A ASP 68 O /A GLN 71 H 3.302 2.455
/A GLN 72 N /A ASP 68 O /A GLN 72 H 2.670 1.730
/A HIS 73 N /A GLN 71 O /A HIS 73 H 2.893 2.013
/A VAL 75 N /A PHE 91 O /A VAL 75 H 2.871 1.862
/A TYR 76 N /A LEU 66 O /A TYR 76 H 2.394 1.499
/A CYS 77 N /A PRO 89 O /A CYS 77 H 2.916 2.184
/A CYS 77 SG /A VAL 88 O /A CYS 77 HG 3.308 2.124
/A LEU 82 N /A ASP 80 OD2 /A LEU 82 H 2.773 1.774
/A ASP 84 N /A ASP 80 O /A ASP 84 H 3.263 2.265
/A LEU 85 N /A LEU 81 O /A LEU 85 H 2.862 1.948
/A PHE 86 N /A LEU 82 O /A PHE 86 H 2.702 1.760
/A GLY 87 N /A GLY 83 O /A GLY 87 H 2.556 1.791
/A VAL 88 N /A GLY 83 O /A VAL 88 H 3.376 2.475
/A PHE 91 N /A VAL 75 O /A PHE 91 H 3.130 2.223
/A SER 92 N /A GLU 95 OE1 /A SER 92 H 2.645 1.737
/A VAL 93 N /A HIS 73 O /A VAL 93 H 2.970 2.003
/A LYS 94 N /A SER 92 OG /A LYS 94 H 2.899 1.985
/A LYS 94 NZ /A HOH 115 O /A LYS 94 HZ1 2.701 1.692
/A GLU 95 N /A SER 92 O /A GLU 95 H 3.082 2.097
/A HIS 96 N /A SO4 112 O2 /A HIS 96 H 3.071 2.081
/A ARG 97 N /A SO4 112 O3 /A ARG 97 H 3.430 2.453
/A ARG 97 NE /A SO4 112 O1 /A ARG 97 HE 2.622 2.042
/A ARG 97 NH1 /A HOH 13 O /A ARG 97 HH11 2.590 1.854
/A ILE 99 N /A GLU 95 O /A ILE 99 H 3.147 2.155
/A TYR 100 N /A HIS 96 O /A TYR 100 H 2.915 1.977
/A THR 101 N /A ARG 97 O /A THR 101 H 2.708 1.703
/A THR 101 OG1 /A ARG 97 O /A THR 101 HG1 3.246 2.458
/A MET 102 N /A LYS 98 O /A MET 102 H 2.952 2.096
/A ILE 103 N /A ILE 99 O /A ILE 103 H 2.813 1.807
/A TYR 104 N /A TYR 100 O /A TYR 104 H 2.947 1.982
/A ARG 105 N /A THR 101 O /A ARG 105 H 3.174 2.358
/A ARG 105 N /A MET 102 O /A ARG 105 H 3.260 2.478
/A ARG 105 NH1 /A PHE 86 O /A ARG 105 HH12 3.391 2.389
/A ASN 106 N /A ILE 103 O /A ASN 106 H 2.808 1.893
/A ASN 106 ND2 /A LEU 85 O /A ASN 106 HD22 3.170 2.246
/A ASN 106 ND2 /A MET 102 O /A ASN 106 HD21 2.648 1.886
/A LEU 107 N /A TYR 104 O /A LEU 107 H 3.398 2.531
/A VAL 108 N /A ARG 29 O /A VAL 108 H 2.845 2.055
/A VAL 110 N /A LEU 27 O /A VAL 110 H 3.276 2.470
/A HOH 114 O /A VAL 109 O /A HOH 114 H1 2.990 2.033
/A HOH 1001 O /A HOH 1003 O /A HOH 1001 H1 2.139 1.181
/A HOH 1002 O /A VAL 41 O /A HOH 1002 H1 3.095 2.137
/A HOH 1007 O /A K23 1 O12 /A HOH 1007 H1 3.346 2.388
94 hydrogen bonds found
> hbonds sel reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 3lbk.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A HOH 4 O /A K23 1 O11 /A HOH 4 H1 2.573 1.843
/A HOH 1007 O /A K23 1 O12 /A HOH 1007 H1 3.346 2.388
2 hydrogen bonds found
> select protein
1443 atoms, 1457 bonds, 1 model selected
> hide (#!1 & sel) target a
> select clear
> transparency 50
> select ::name="K23"
47 atoms, 51 bonds, 1 model selected
> color sel byelement
> select clear
> select ::name="K23"
47 atoms, 51 bonds, 1 model selected
> surface sel
> surface style (#!1 & sel) mesh
> surface style (#!1 & sel) dot
> surface hidePatches (#!1 & sel)
> surface (#!1 & sel)
> surface hidePatches (#!1 & sel)
> select clear
> save ./3lbk_drug.jpg width 1265 height 804 supersample 3
> preset "overall look" interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> preset "molecular surfaces" "atomic coloring (transparent)"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "molecular surfaces" "chain id coloring (opaque)"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> preset "molecular surfaces" "ghostly white"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "overall look" interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
> save /home/jitesh/3lbk_drug2.jpg width 1265 height 804 supersample 3
> preset "molecular surfaces" "ghostly white"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> ui mousemode right "mark surface"
> marker #3 position 7.338,16.19,4.077 color yellow radius 1
> marker #3 position 9.781,15.9,0.527 color yellow radius 1
> marker #3 position 9.288,16.28,-2.079 color yellow radius 1
> marker #3 position 7.26,17.04,3.557 color yellow radius 1
> marker #3 position 6.973,17.96,3.283 color yellow radius 1
> marker #3 position 6.933,18.87,2.88 color yellow radius 1
> marker #3 position 6.892,19.78,2.476 color yellow radius 1
> marker #3 position 6.852,20.7,2.072 color yellow radius 1
> marker #3 position 6.811,21.61,1.669 color yellow radius 1
> marker #3 position 6.771,22.53,1.265 color yellow radius 1
> select clear
> ui mousemode right "delete markers"
> ui mousemode right "delete markers"
> ui mousemode right "delete markers"
> marker delete #3:10
> marker delete #3:9
> marker delete #3:8
> marker delete #3:7
> marker delete #3:6
> marker delete #3:5
> marker delete #3:4
> marker delete #3:1
> marker delete #3:2
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 202, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 363, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1607, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/medical_toolbar/__init__.py", line 22, in run_provider
actions.run_provider(session, name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/medical_toolbar/actions.py", line 17, in run_provider
open_dicom(session)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/medical_toolbar/actions.py", line 22, in open_dicom
session.ui.main_window.folder_open_cb(session)
AttributeError: 'MainWindow' object has no attribute 'folder_open_cb'
AttributeError: 'MainWindow' object has no attribute 'folder_open_cb'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/medical_toolbar/actions.py", line 22, in open_dicom
session.ui.main_window.folder_open_cb(session)
See log for complete Python traceback.
> open /home/jitesh/Downloads/dicom_viewer_Mrbrain format dicom
> close session
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 202, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 363, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1607, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/medical_toolbar/__init__.py", line 22, in run_provider
actions.run_provider(session, name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/medical_toolbar/actions.py", line 17, in run_provider
open_dicom(session)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/medical_toolbar/actions.py", line 22, in open_dicom
session.ui.main_window.folder_open_cb(session)
AttributeError: 'MainWindow' object has no attribute 'folder_open_cb'
AttributeError: 'MainWindow' object has no attribute 'folder_open_cb'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/medical_toolbar/actions.py", line 22, in open_dicom
session.ui.main_window.folder_open_cb(session)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 390.138
OpenGL renderer: GeForce MX130/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Acer
Model: Aspire A515-51G
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
CPU: 4 Intel(R) Core(TM) i5-7200U CPU @ 2.50GHz
Cache Size: 3072 KB
Memory:
total used free shared buff/cache available
Mem: 7.7Gi 2.9Gi 2.2Gi 266Mi 2.6Gi 4.2Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 620 [8086:5916] (rev 02)
Subsystem: Acer Incorporated [ALI] HD Graphics 620 [1025:1193]
Kernel driver in use: i915
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Open DICOM via icon: 'MainWindow' object has no attribute 'folder_open_cb' |
comment:2 by , 5 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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