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Opened 2 years ago
Closed 2 years ago
#9024 closed defect (can't reproduce)
UnicodeDecodeError opening PDB file
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| 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: Windows-10-10.0.19045
ChimeraX Version: 1.6rc202304072249 (2023-04-07 22:49:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6rc202304072249 (2023-04-07)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\Users\alber\OneDrive\Desktop\LWM reserch\Furin Project\Docking
> analysis\cluspro.933182.000.10\cluspro.933182\modified.pdb" format pdb
No such file/path: C:\Users\alber\OneDrive\Desktop\LWM reserch\Furin
Project\Docking analysis\cluspro.933182.000.10\cluspro.933182\modified.pdb
> open "C:\Users\alber\OneDrive\Desktop\LWM reserch\Furin Project\Docking
> analysis\cluspro.933182.000.10\cluspro.933182\modified.pdb" format pdb
No such file/path: C:\Users\alber\OneDrive\Desktop\LWM reserch\Furin
Project\Docking analysis\cluspro.933182.000.10\cluspro.933182\modified.pdb
> open "C:/Users/alber/OneDrive/Desktop/LWM reserch/Furin Project/Docking
> analysis/Standard Dock/cluspro.933182/modified.pdb"
Summary of feedback from opening C:/Users/alber/OneDrive/Desktop/LWM
reserch/Furin Project/Docking analysis/Standard
Dock/cluspro.933182/modified.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Ignored bad PDB record found on line 4434
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
74 messages similar to the above omitted
Chain information for modified.pdb #1
---
Chain | Description
A | No description available
> ui tool show "Selection Inspector"
> ui mousemode right zoom
> ui tool show ViewDockX
No suitable models found for ViewDockX
> view
> ui windowfill toggle
[Repeated 1 time(s)]
> ui tool show "Command Line Interface"
> select add #1
4510 atoms, 4596 bonds, 474 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
4510 atoms, 4596 bonds, 474 residues, 1 model selected
> hide #1 models
> select subtract #1
Nothing selected
> show #1 models
> interfaces ~solvent
1 buried areas: A X 523
> select add #1
4510 atoms, 4596 bonds, 474 residues, 1 model selected
> select subtract #1
Nothing selected
> interfaces ~solvent
1 buried areas: A X 523
Alignment identifier is 1/A
> ~hbonds
> hbonds reveal true
531 hydrogen bonds found
> ~hbonds
[Repeated 1 time(s)]
> hbonds reveal true
531 hydrogen bonds found
> hbonds reveal true
531 hydrogen bonds found
> hbonds reveal true
531 hydrogen bonds found
> ~hbonds
> undo
[Repeated 2 time(s)]
> show #1 models
> view
> style sphere
Changed 4510 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> select add #1
4510 atoms, 4596 bonds, 474 residues, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 4510 atom styles
> style sel ball
Changed 4510 atom styles
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> show sel atoms
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> hide target m
[Repeated 1 time(s)]
> show #1 models
> view clip false
[Repeated 1 time(s)]
> log metadata #1
The model has no metadata
> log chains #1
Chain information for modified.pdb #1
---
Chain | Description
A | No description available
> show target m
> select subtract #1
Nothing selected
> color bychain
> rainbow
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for modified.pdb_A SES surface #1.1: minimum, -20.78, mean
-2.79, maximum 11.77
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp
Map values for surface "modified.pdb_A SES surface": minimum -30.29, mean
-6.442, maximum 22.84
To also show corresponding color key, enter the above mlp command and add key
true
> view clip false
> color bychain
> color byhetero
> color bynucleotide
> color bypolymer
> rainbow
> coulombic
Coulombic values for modified.pdb_A SES surface #1.1: minimum, -20.78, mean
-2.79, maximum 11.77
To also show corresponding color key, enter the above coulombic command and
add key true
> color bfactor
4510 atoms, 474 residues, 1 surfaces, atom bfactor range 0 to 0
> mlp
Map values for surface "modified.pdb_A SES surface": minimum -30.29, mean
-6.442, maximum 22.84
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic
Coulombic values for modified.pdb_A SES surface #1.1: minimum, -20.78, mean
-2.79, maximum 11.77
To also show corresponding color key, enter the above coulombic command and
add key true
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides fill
> style nucleic stick
Changed 0 atom styles
> nucleotides slab
> style nucleic stick
Changed 0 atom styles
> set bgColor white
> set bgColor #ffffff00
> set bgColor gray
> set bgColor #80808000
> set bgColor black
> set bgColor transparent
> set bgColor white
> set bgColor #ffffff00
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting simple
> lighting full
> view
[Repeated 3 time(s)]
> view orient
[Repeated 1 time(s)]
> lighting shadows false
> show surfaces
> select add #1.1
4431 atoms, 473 residues, 1 model selected
> show sel surfaces
> select subtract #1.1
1 model selected
> view clip false
> rainbow
> style stick
Changed 4510 atom styles
> select add #1
4510 atoms, 4596 bonds, 474 residues, 1 model selected
> select subtract #1
1 model selected
> select add #1
4510 atoms, 4596 bonds, 474 residues, 1 model selected
> style sel stick
Changed 4510 atom styles
> style sel ball
Changed 4510 atom styles
> rainbow sel
> show sel cartoons
[Repeated 1 time(s)]
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> show sel atoms
> show sel cartoons
> hide sel atoms
> show sel atoms
> color sel byhetero
> color sel bychain
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel ball
Changed 4510 atom styles
> style sel stick
Changed 4510 atom styles
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> ui mousemode right distance
[Repeated 1 time(s)]
> ui mousemode right "link markers"
[Repeated 1 time(s)]
> ui mousemode right "move markers"
> ui mousemode right "resize markers"
> ui mousemode right "delete markers"
> ui mousemode right "mark point"
> ui mousemode right "mark center"
> ui mousemode right "mark surface"
> ui mousemode right "mark plane"
> ui mousemode right "mark maximum"
> volume style surface
No volumes specified
> color sel bypolymer
> view #1 clip false
> ui mousemode right zoom
> ui mousemode right select
Drag select of 393 atoms, 61 residues, 359 bonds
Drag select of 212 atoms, 35 residues, 203 bonds
Drag select of 590 atoms, 101 residues, 544 bonds
> color sel byhetero
> color sel bychain
> show sel surfaces
> coulombic sel
Coulombic values for modified.pdb_A SES surface #1.1: minimum, -20.78, mean
-2.79, maximum 11.77
To also show corresponding color key, enter the above coulombic command and
add key true
Drag select of modified.pdb_A SES surface, 60 of 331580 triangles, 2 atoms, 2
residues, 3 bonds
Drag select of 1 residues
> ui mousemode right zoom
> show #!1 target m
> view #1 clip false
[Repeated 1 time(s)]
> show sel surfaces
> select subtract #1.1
1 model selected
> select add #1.1
4431 atoms, 473 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> color sel bychain
> select coil
2611 atoms, 2639 bonds, 278 residues, 1 model selected
> color (#!1 & sel) light gray
> select helix
868 atoms, 866 bonds, 97 residues, 1 model selected
> color (#!1 & sel) cyan
> select strand
952 atoms, 950 bonds, 98 residues, 1 model selected
> color (#!1 & sel) cornflower blue
> close #1.1
> close
> open "C:/Users/alber/OneDrive/Desktop/LWM reserch/Furin Project/Docking
> analysis/Standard Dock/cluspro.933182/model.000.01.pdb"
Summary of feedback from opening C:/Users/alber/OneDrive/Desktop/LWM
reserch/Furin Project/Docking analysis/Standard
Dock/cluspro.933182/model.000.01.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
74 messages similar to the above omitted
Chain information for model.000.01.pdb #1
---
Chain | Description
A | No description available
> close
> open "C:/Users/alber/OneDrive/Desktop/LWM reserch/Furin Project/Docking
> analysis/Standard Dock/cluspro.933182/model.000.00.pdb"
Summary of feedback from opening C:/Users/alber/OneDrive/Desktop/LWM
reserch/Furin Project/Docking analysis/Standard
Dock/cluspro.933182/model.000.00.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
74 messages similar to the above omitted
Chain information for model.000.00.pdb #1
---
Chain | Description
A | No description available
> show surfaces
> close
> open "C:\Users\alber\OneDrive\Desktop\LWM reserch\Furin Project\Docking
> analysis\Standard Dock\cluspro.933182\model.000.00.pdb" format pdb
No such file/path: C:\Users\alber\OneDrive\Desktop\LWM reserch\Furin
Project\Docking analysis\Standard Dock\cluspro.933182\model.000.00.pdb
> open "C:/Users/alber/OneDrive/Desktop/LWM reserch/Furin Project/Docking
> analysis/Standard Dock/cluspro.933182/New folder/furin.pdb"
Summary of feedback from opening C:/Users/alber/OneDrive/Desktop/LWM
reserch/Furin Project/Docking analysis/Standard Dock/cluspro.933182/New
folder/furin.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Chain information for furin.pdb #1
---
Chain | Description
A | No description available
> open "C:/Users/alber/OneDrive/Desktop/LWM reserch/Furin Project/Docking
> analysis/Standard Dock/cluspro.933182/New folder/lignad.pdb"
> select add #1
4431 atoms, 4514 bonds, 473 residues, 1 model selected
> show sel surfaces
> mlp sel
Map values for surface "furin.pdb_A SES surface": minimum -30.29, mean -6.442,
maximum 22.84
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for furin.pdb_A SES surface #1.1: minimum, -20.78, mean
-2.79, maximum 11.77
To also show corresponding color key, enter the above coulombic command and
add key true
> select subtract #1
1 model selected
> select add #2
79 atoms, 82 bonds, 1 residue, 1 model selected
> ui mousemode right label
> label #1/A:411
> label #1/A:403
> label #1/A:399
> label #2/X:1
> label #1/A:581
> label #1/A:402
> label #1/A:437
> label #1/A:400
> label #1/A:401
> label #1/A:399
> label #1/A:581
> label #1/A:404
> label #1/A:428
> label #1/A:402
> label #1/A:419
[Repeated 1 time(s)]
> label #1/A:581
> label #1/A:399
> label #1/A:578
> label #1/A:442
> label #1/A:437
> label #1/A:399
> ui mousemode right "move label"
> ui mousemode right distance
> ui mousemode right label
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue A00 (net charge -32) with am1-bcc method
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\alber\AppData\Local\Temp\tmp700ds1ih\ante.in.mol2 -fi mol2 -o
C:\Users\alber\AppData\Local\Temp\tmp700ds1ih\ante.out.mol2 -fo mol2 -c bcc
-nc -32 -j 5 -s 2 -dr n
(A00) ``
(A00) `Welcome to antechamber 20.0: molecular input file processor.`
(A00) ``
(A00) `Info: Finished reading file
(C:\Users\alber\AppData\Local\Temp\tmp700ds1ih\ante.in.mol2); atoms read (79),
bonds read (82).`
(A00) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(A00) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(A00) `bash.exe: warning: could not find /tmp, please create!`
(A00) ``
(A00) ``
(A00) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(A00) `bash.exe: warning: could not find /tmp, please create!`
(A00) `Info: Total number of electrons: 606; net charge: -32`
(A00) ``
(A00) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`
(A00) `bash.exe: warning: could not find /tmp, please create!`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =208
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: S : M.J.S.DEWAR et al. INORG. CHEM., 29, 3881, (1990)
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 292
| QMMM: diag iterations used for timing = 3
| QMMM:
| QMMM: Internal diag routine = 0.135857 seconds
| QMMM: Dspev diag routine = 0.118384 seconds
| QMMM: Dspevd diag routine = 0.093803 seconds
| QMMM: Dspevx diag routine = 0.350503 seconds
| QMMM: Dsyev diag routine = 0.124380 seconds
| QMMM: Dsyevd diag routine = 0.095317 seconds
| QMMM: Dsyevr diag routine = 0.098196 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.051807 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 C 15.4370 -43.1960 6.7750
QMMM: 2 2 O 10.8200 -42.2850 7.4940
QMMM: 3 3 C 14.2550 -43.6950 7.6370
QMMM: 4 4 O 13.1300 -42.8110 7.4010
QMMM: 5 5 O 12.1800 -42.2530 9.4700
QMMM: 6 6 C 14.5920 -43.8440 9.1430
QMMM: 7 7 O 15.2080 -45.1020 9.4300
QMMM: 8 8 O 11.6030 -44.3620 8.4350
QMMM: 9 9 C 15.4370 -42.6850 9.7060
QMMM: 10 10 O 14.6330 -41.5330 9.9930
QMMM: 11 11 C 16.6620 -42.3670 8.8240
QMMM: 12 12 O 16.3020 -42.2110 7.4150
QMMM: 13 13 C 17.8040 -43.3420 9.0830
QMMM: 14 14 O 18.8900 -42.9220 9.4480
QMMM: 15 15 O 17.6480 -44.5460 8.9580
QMMM: 16 16 S 11.8250 -42.9560 8.2640
QMMM: 17 17 N 20.6240 -44.4900 4.2800
QMMM: 18 18 C 18.6400 -45.6500 3.1630
QMMM: 19 19 O 21.9750 -45.0360 6.2360
QMMM: 20 20 S 21.9640 -45.2070 4.8140
QMMM: 21 21 C 19.3260 -45.1850 4.4680
QMMM: 22 22 O 21.7810 -46.5770 4.4490
QMMM: 23 23 S 15.8270 -41.6910 1.9590
QMMM: 24 24 C 18.3680 -44.5330 5.5100
QMMM: 25 25 O 19.0240 -43.6040 6.3590
QMMM: 26 26 O 22.9820 -44.4750 4.1380
QMMM: 27 27 C 17.0300 -43.9300 5.0460
QMMM: 28 28 O 16.0870 -44.2910 6.0880
QMMM: 29 29 O 15.8170 -41.2780 3.3260
QMMM: 30 30 C 16.5690 -44.5410 3.7090
QMMM: 31 31 O 17.6720 -44.6560 2.7630
QMMM: 32 32 O 17.0980 -41.6250 1.3000
QMMM: 33 33 C 15.2980 -43.8900 3.1270
QMMM: 34 34 O 15.5620 -43.2300 1.8730
QMMM: 35 35 O 14.7960 -41.1600 1.1220
QMMM: 36 36 C 17.8690 -50.6480 2.4620
QMMM: 37 37 O 20.7410 -50.1120 5.8340
QMMM: 38 38 C 19.1370 -49.7720 2.5590
QMMM: 39 39 O 19.4950 -49.5190 3.9320
QMMM: 40 40 O 20.9560 -51.4080 3.8280
QMMM: 41 41 C 19.0060 -48.4380 1.7940
QMMM: 42 42 O 19.1390 -48.5990 0.3740
QMMM: 43 43 O 18.9360 -51.5140 5.1140
QMMM: 44 44 C 17.7300 -47.6620 2.1500
QMMM: 45 45 O 17.9580 -46.9130 3.3760
QMMM: 46 46 C 16.4710 -48.5690 2.1840
QMMM: 47 47 O 16.7180 -49.8480 2.8570
QMMM: 48 48 C 15.8650 -48.7340 0.7960
QMMM: 49 49 O 16.5760 -48.9800 -0.1680
QMMM: 50 50 O 14.6650 -48.6210 0.6630
QMMM: 51 51 S 20.0640 -50.7320 4.7300
QMMM: 52 52 N 17.4240 -53.1980 -3.0320
QMMM: 53 53 C 18.0930 -54.6120 -1.0370
QMMM: 54 54 O 19.4270 -54.3660 -1.4650
QMMM: 55 55 O 17.5120 -53.5050 -5.3790
QMMM: 56 56 S 17.5230 -54.3000 -4.1830
QMMM: 57 57 C 17.1180 -53.5680 -1.6290
QMMM: 58 58 O 18.8370 -54.8200 -3.9510
QMMM: 59 59 S 19.5820 -55.5880 3.8060
QMMM: 60 60 C 17.1400 -52.2520 -0.8170
QMMM: 61 61 O 16.1480 -51.3240 -1.2840
QMMM: 62 62 O 16.3990 -55.1530 -3.9800
QMMM: 63 63 C 17.2040 -52.3560 0.7280
QMMM: 64 64 O 17.8110 -51.0940 1.0900
QMMM: 65 65 O 20.1120 -55.1330 5.0590
QMMM: 66 66 C 18.1650 -53.5000 1.1510
QMMM: 67 67 O 17.9270 -54.7090 0.3910
QMMM: 68 68 O 18.3550 -56.3190 3.8160
QMMM: 69 69 C 18.0720 -53.8500 2.6460
QMMM: 70 70 O 19.3970 -54.2190 3.0720
QMMM: 71 71 O 20.6850 -56.0890 3.0350
QMMM: 72 72 H 16.1980 -44.9690 9.2100
QMMM: 73 73 H 13.6670 -41.7990 9.8080
QMMM: 74 74 H 20.8470 -44.5100 3.2820
QMMM: 75 75 H 19.2330 -42.8680 5.6970
QMMM: 76 76 H 18.2220 -48.8970 0.0650
QMMM: 77 77 H 16.7340 -52.5080 -3.2980
QMMM: 78 78 H 19.3120 -54.4480 -2.4640
QMMM: 79 79 H 16.3190 -50.4390 -0.8090
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
Failure running ANTECHAMBER for residue A00 Check reply log for details
> select add #1
4510 atoms, 4596 bonds, 474 residues, 3 models selected
> select subtract #2
4431 atoms, 4514 bonds, 473 residues, 3 models selected
> color sel byhetero
> color sel bychain
> label #1/A:417
> select subtract #1
1 model selected
> select add #2
79 atoms, 82 bonds, 1 residue, 1 model selected
> rainbow sel
[Repeated 1 time(s)]
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue A00 (net charge -32) with am1-bcc method
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\alber\AppData\Local\Temp\tmpd6hk6djy\ante.in.mol2 -fi mol2 -o
C:\Users\alber\AppData\Local\Temp\tmpd6hk6djy\ante.out.mol2 -fo mol2 -c bcc
-nc -32 -j 5 -s 2 -dr n
(A00) ``
(A00) `Welcome to antechamber 20.0: molecular input file processor.`
(A00) ``
(A00) `Info: Finished reading file
(C:\Users\alber\AppData\Local\Temp\tmpd6hk6djy\ante.in.mol2); atoms read (79),
bonds read (82).`
(A00) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(A00) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(A00) `bash.exe: warning: could not find /tmp, please create!`
(A00) ``
(A00) ``
(A00) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(A00) `bash.exe: warning: could not find /tmp, please create!`
(A00) `Info: Total number of electrons: 606; net charge: -32`
(A00) ``
(A00) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`
(A00) `bash.exe: warning: could not find /tmp, please create!`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =208
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: S : M.J.S.DEWAR et al. INORG. CHEM., 29, 3881, (1990)
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 292
| QMMM: diag iterations used for timing = 3
| QMMM:
| QMMM: Internal diag routine = 0.198979 seconds
| QMMM: Dspev diag routine = 0.159998 seconds
| QMMM: Dspevd diag routine = 0.111438 seconds
| QMMM: Dspevx diag routine = 0.397268 seconds
| QMMM: Dsyev diag routine = 0.165363 seconds
| QMMM: Dsyevd diag routine = 0.115191 seconds
| QMMM: Dsyevr diag routine = 0.099021 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.052011 seconds
| QMMM:
| QMMM: Using dsyevr routine (diag_routine=7).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 C 15.4370 -43.1960 6.7750
QMMM: 2 2 O 10.8200 -42.2850 7.4940
QMMM: 3 3 C 14.2550 -43.6950 7.6370
QMMM: 4 4 O 13.1300 -42.8110 7.4010
QMMM: 5 5 O 12.1800 -42.2530 9.4700
QMMM: 6 6 C 14.5920 -43.8440 9.1430
QMMM: 7 7 O 15.2080 -45.1020 9.4300
QMMM: 8 8 O 11.6030 -44.3620 8.4350
QMMM: 9 9 C 15.4370 -42.6850 9.7060
QMMM: 10 10 O 14.6330 -41.5330 9.9930
QMMM: 11 11 C 16.6620 -42.3670 8.8240
QMMM: 12 12 O 16.3020 -42.2110 7.4150
QMMM: 13 13 C 17.8040 -43.3420 9.0830
QMMM: 14 14 O 18.8900 -42.9220 9.4480
QMMM: 15 15 O 17.6480 -44.5460 8.9580
QMMM: 16 16 S 11.8250 -42.9560 8.2640
QMMM: 17 17 N 20.6240 -44.4900 4.2800
QMMM: 18 18 C 18.6400 -45.6500 3.1630
QMMM: 19 19 O 21.9750 -45.0360 6.2360
QMMM: 20 20 S 21.9640 -45.2070 4.8140
QMMM: 21 21 C 19.3260 -45.1850 4.4680
QMMM: 22 22 O 21.7810 -46.5770 4.4490
QMMM: 23 23 S 15.8270 -41.6910 1.9590
QMMM: 24 24 C 18.3680 -44.5330 5.5100
QMMM: 25 25 O 19.0240 -43.6040 6.3590
QMMM: 26 26 O 22.9820 -44.4750 4.1380
QMMM: 27 27 C 17.0300 -43.9300 5.0460
QMMM: 28 28 O 16.0870 -44.2910 6.0880
QMMM: 29 29 O 15.8170 -41.2780 3.3260
QMMM: 30 30 C 16.5690 -44.5410 3.7090
QMMM: 31 31 O 17.6720 -44.6560 2.7630
QMMM: 32 32 O 17.0980 -41.6250 1.3000
QMMM: 33 33 C 15.2980 -43.8900 3.1270
QMMM: 34 34 O 15.5620 -43.2300 1.8730
QMMM: 35 35 O 14.7960 -41.1600 1.1220
QMMM: 36 36 C 17.8690 -50.6480 2.4620
QMMM: 37 37 O 20.7410 -50.1120 5.8340
QMMM: 38 38 C 19.1370 -49.7720 2.5590
QMMM: 39 39 O 19.4950 -49.5190 3.9320
QMMM: 40 40 O 20.9560 -51.4080 3.8280
QMMM: 41 41 C 19.0060 -48.4380 1.7940
QMMM: 42 42 O 19.1390 -48.5990 0.3740
QMMM: 43 43 O 18.9360 -51.5140 5.1140
QMMM: 44 44 C 17.7300 -47.6620 2.1500
QMMM: 45 45 O 17.9580 -46.9130 3.3760
QMMM: 46 46 C 16.4710 -48.5690 2.1840
QMMM: 47 47 O 16.7180 -49.8480 2.8570
QMMM: 48 48 C 15.8650 -48.7340 0.7960
QMMM: 49 49 O 16.5760 -48.9800 -0.1680
QMMM: 50 50 O 14.6650 -48.6210 0.6630
QMMM: 51 51 S 20.0640 -50.7320 4.7300
QMMM: 52 52 N 17.4240 -53.1980 -3.0320
QMMM: 53 53 C 18.0930 -54.6120 -1.0370
QMMM: 54 54 O 19.4270 -54.3660 -1.4650
QMMM: 55 55 O 17.5120 -53.5050 -5.3790
QMMM: 56 56 S 17.5230 -54.3000 -4.1830
QMMM: 57 57 C 17.1180 -53.5680 -1.6290
QMMM: 58 58 O 18.8370 -54.8200 -3.9510
QMMM: 59 59 S 19.5820 -55.5880 3.8060
QMMM: 60 60 C 17.1400 -52.2520 -0.8170
QMMM: 61 61 O 16.1480 -51.3240 -1.2840
QMMM: 62 62 O 16.3990 -55.1530 -3.9800
QMMM: 63 63 C 17.2040 -52.3560 0.7280
QMMM: 64 64 O 17.8110 -51.0940 1.0900
QMMM: 65 65 O 20.1120 -55.1330 5.0590
QMMM: 66 66 C 18.1650 -53.5000 1.1510
QMMM: 67 67 O 17.9270 -54.7090 0.3910
QMMM: 68 68 O 18.3550 -56.3190 3.8160
QMMM: 69 69 C 18.0720 -53.8500 2.6460
QMMM: 70 70 O 19.3970 -54.2190 3.0720
QMMM: 71 71 O 20.6850 -56.0890 3.0350
QMMM: 72 72 H 16.1980 -44.9690 9.2100
QMMM: 73 73 H 13.6670 -41.7990 9.8080
QMMM: 74 74 H 20.8470 -44.5100 3.2820
QMMM: 75 75 H 19.2330 -42.8680 5.6970
QMMM: 76 76 H 18.2220 -48.8970 0.0650
QMMM: 77 77 H 16.7340 -52.5080 -3.2980
QMMM: 78 78 H 19.3120 -54.4480 -2.4640
QMMM: 79 79 H 16.3190 -50.4390 -0.8090
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
Failure running ANTECHAMBER for residue A00 Check reply log for details
> color bfactor sel
79 atoms, 1 residues, atom bfactor range 0 to 0
> color bfactor sel
79 atoms, 1 residues, atom bfactor range 0 to 0
> mlp sel
mlp: no amino acids specified
> style sel stick
Changed 79 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> mlp sel
mlp: no amino acids specified
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> show sel atoms
> hide sel atoms
> show sel atoms
> show sel cartoons
> hide sel cartoons
[Repeated 1 time(s)]
> select add #1
4510 atoms, 4596 bonds, 474 residues, 3 models selected
> select subtract #2
4431 atoms, 4514 bonds, 473 residues, 3 models selected
> coulombic sel
Coulombic values for furin.pdb_A SES surface #1.1: minimum, -20.78, mean
-2.79, maximum 11.77
To also show corresponding color key, enter the above coulombic command and
add key true
> select subtract #1
1 model selected
> select add #2
79 atoms, 82 bonds, 1 residue, 1 model selected
> color sel hot pink
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue A00 (net charge -32) with am1-bcc method
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\alber\AppData\Local\Temp\tmpresdlc4c\ante.in.mol2 -fi mol2 -o
C:\Users\alber\AppData\Local\Temp\tmpresdlc4c\ante.out.mol2 -fo mol2 -c bcc
-nc -32 -j 5 -s 2 -dr n
(A00) ``
(A00) `Welcome to antechamber 20.0: molecular input file processor.`
(A00) ``
(A00) `Info: Finished reading file
(C:\Users\alber\AppData\Local\Temp\tmpresdlc4c\ante.in.mol2); atoms read (79),
bonds read (82).`
(A00) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(A00) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(A00) `bash.exe: warning: could not find /tmp, please create!`
(A00) ``
(A00) ``
(A00) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(A00) `bash.exe: warning: could not find /tmp, please create!`
(A00) `Info: Total number of electrons: 606; net charge: -32`
(A00) ``
(A00) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`
(A00) `bash.exe: warning: could not find /tmp, please create!`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =208
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: S : M.J.S.DEWAR et al. INORG. CHEM., 29, 3881, (1990)
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 292
| QMMM: diag iterations used for timing = 3
| QMMM:
| QMMM: Internal diag routine = 0.194364 seconds
| QMMM: Dspev diag routine = 0.119315 seconds
| QMMM: Dspevd diag routine = 0.090327 seconds
| QMMM: Dspevx diag routine = 0.350129 seconds
| QMMM: Dsyev diag routine = 0.123924 seconds
| QMMM: Dsyevd diag routine = 0.096918 seconds
| QMMM: Dsyevr diag routine = 0.097628 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.051320 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 C 15.4370 -43.1960 6.7750
QMMM: 2 2 O 10.8200 -42.2850 7.4940
QMMM: 3 3 C 14.2550 -43.6950 7.6370
QMMM: 4 4 O 13.1300 -42.8110 7.4010
QMMM: 5 5 O 12.1800 -42.2530 9.4700
QMMM: 6 6 C 14.5920 -43.8440 9.1430
QMMM: 7 7 O 15.2080 -45.1020 9.4300
QMMM: 8 8 O 11.6030 -44.3620 8.4350
QMMM: 9 9 C 15.4370 -42.6850 9.7060
QMMM: 10 10 O 14.6330 -41.5330 9.9930
QMMM: 11 11 C 16.6620 -42.3670 8.8240
QMMM: 12 12 O 16.3020 -42.2110 7.4150
QMMM: 13 13 C 17.8040 -43.3420 9.0830
QMMM: 14 14 O 18.8900 -42.9220 9.4480
QMMM: 15 15 O 17.6480 -44.5460 8.9580
QMMM: 16 16 S 11.8250 -42.9560 8.2640
QMMM: 17 17 N 20.6240 -44.4900 4.2800
QMMM: 18 18 C 18.6400 -45.6500 3.1630
QMMM: 19 19 O 21.9750 -45.0360 6.2360
QMMM: 20 20 S 21.9640 -45.2070 4.8140
QMMM: 21 21 C 19.3260 -45.1850 4.4680
QMMM: 22 22 O 21.7810 -46.5770 4.4490
QMMM: 23 23 S 15.8270 -41.6910 1.9590
QMMM: 24 24 C 18.3680 -44.5330 5.5100
QMMM: 25 25 O 19.0240 -43.6040 6.3590
QMMM: 26 26 O 22.9820 -44.4750 4.1380
QMMM: 27 27 C 17.0300 -43.9300 5.0460
QMMM: 28 28 O 16.0870 -44.2910 6.0880
QMMM: 29 29 O 15.8170 -41.2780 3.3260
QMMM: 30 30 C 16.5690 -44.5410 3.7090
QMMM: 31 31 O 17.6720 -44.6560 2.7630
QMMM: 32 32 O 17.0980 -41.6250 1.3000
QMMM: 33 33 C 15.2980 -43.8900 3.1270
QMMM: 34 34 O 15.5620 -43.2300 1.8730
QMMM: 35 35 O 14.7960 -41.1600 1.1220
QMMM: 36 36 C 17.8690 -50.6480 2.4620
QMMM: 37 37 O 20.7410 -50.1120 5.8340
QMMM: 38 38 C 19.1370 -49.7720 2.5590
QMMM: 39 39 O 19.4950 -49.5190 3.9320
QMMM: 40 40 O 20.9560 -51.4080 3.8280
QMMM: 41 41 C 19.0060 -48.4380 1.7940
QMMM: 42 42 O 19.1390 -48.5990 0.3740
QMMM: 43 43 O 18.9360 -51.5140 5.1140
QMMM: 44 44 C 17.7300 -47.6620 2.1500
QMMM: 45 45 O 17.9580 -46.9130 3.3760
QMMM: 46 46 C 16.4710 -48.5690 2.1840
QMMM: 47 47 O 16.7180 -49.8480 2.8570
QMMM: 48 48 C 15.8650 -48.7340 0.7960
QMMM: 49 49 O 16.5760 -48.9800 -0.1680
QMMM: 50 50 O 14.6650 -48.6210 0.6630
QMMM: 51 51 S 20.0640 -50.7320 4.7300
QMMM: 52 52 N 17.4240 -53.1980 -3.0320
QMMM: 53 53 C 18.0930 -54.6120 -1.0370
QMMM: 54 54 O 19.4270 -54.3660 -1.4650
QMMM: 55 55 O 17.5120 -53.5050 -5.3790
QMMM: 56 56 S 17.5230 -54.3000 -4.1830
QMMM: 57 57 C 17.1180 -53.5680 -1.6290
QMMM: 58 58 O 18.8370 -54.8200 -3.9510
QMMM: 59 59 S 19.5820 -55.5880 3.8060
QMMM: 60 60 C 17.1400 -52.2520 -0.8170
QMMM: 61 61 O 16.1480 -51.3240 -1.2840
QMMM: 62 62 O 16.3990 -55.1530 -3.9800
QMMM: 63 63 C 17.2040 -52.3560 0.7280
QMMM: 64 64 O 17.8110 -51.0940 1.0900
QMMM: 65 65 O 20.1120 -55.1330 5.0590
QMMM: 66 66 C 18.1650 -53.5000 1.1510
QMMM: 67 67 O 17.9270 -54.7090 0.3910
QMMM: 68 68 O 18.3550 -56.3190 3.8160
QMMM: 69 69 C 18.0720 -53.8500 2.6460
QMMM: 70 70 O 19.3970 -54.2190 3.0720
QMMM: 71 71 O 20.6850 -56.0890 3.0350
QMMM: 72 72 H 16.1980 -44.9690 9.2100
QMMM: 73 73 H 13.6670 -41.7990 9.8080
QMMM: 74 74 H 20.8470 -44.5100 3.2820
QMMM: 75 75 H 19.2330 -42.8680 5.6970
QMMM: 76 76 H 18.2220 -48.8970 0.0650
QMMM: 77 77 H 16.7340 -52.5080 -3.2980
QMMM: 78 78 H 19.3120 -54.4480 -2.4640
QMMM: 79 79 H 16.3190 -50.4390 -0.8090
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
Failure running ANTECHAMBER for residue A00 Check reply log for details
> select subtract #2
Nothing selected
> select add #1
4431 atoms, 4514 bonds, 473 residues, 2 models selected
> mlp sel
Map values for surface "furin.pdb_A SES surface": minimum -30.29, mean -6.442,
maximum 22.84
To also show corresponding color key, enter the above mlp command and add key
true
> label #1/A:412
> color (#!1 & sel) byelement
> mlp sel
Map values for surface "furin.pdb_A SES surface": minimum -30.29, mean -6.442,
maximum 22.84
To also show corresponding color key, enter the above mlp command and add key
true
> select add #2
4510 atoms, 4596 bonds, 474 residues, 4 models selected
> select subtract #1
79 atoms, 82 bonds, 1 residue, 2 models selected
> color sel byelement
> select subtract #2
Nothing selected
> label delete residues
> label #1/A:510
> color bypolymer
> label #2/X:1
> close
> open "C:/Users/alber/OneDrive/Desktop/LWM reserch/Furin Project/Docking
> analysis/Standard Dock/cluspro.933182/New folder/model.000.00.pdb"
Summary of feedback from opening C:/Users/alber/OneDrive/Desktop/LWM
reserch/Furin Project/Docking analysis/Standard Dock/cluspro.933182/New
folder/model.000.00.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
74 messages similar to the above omitted
Chain information for model.000.00.pdb #1
---
Chain | Description
A | No description available
> show surfaces
> select add #1
4510 atoms, 4596 bonds, 474 residues, 1 model selected
> label #1/A:577
> select add #1.2
4510 atoms, 4596 bonds, 474 residues, 3 models selected
> select subtract #1
1 model selected
> select add #1.2
1 model selected
> select subtract #1.2
Nothing selected
> label #1/A:581
> ui mousemode right translate
> undo
[Repeated 2 time(s)]
> hide #1.2 models
> select subtract #1.2
4510 atoms, 4596 bonds, 474 residues, 2 models selected
> color sel bychain
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> ui mousemode right zoom
> hide sel surfaces
> rainbow sel
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for model.000.00.pdb_A SES surface #1.1: minimum, -20.78,
mean -2.79, maximum 11.77
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp sel
Map values for surface "model.000.00.pdb_A SES surface": minimum -30.29, mean
-6.442, maximum 22.84
To also show corresponding color key, enter the above mlp command and add key
true
> show sel surfaces
> hide sel surfaces
> select subtract #1.1
79 atoms, 82 bonds, 1 residue, 2 models selected
> close #1.1
> close
> open "C:/Users/alber/OneDrive/Desktop/LWM reserch/Furin Project/Docking
> analysis/Standard Dock/cluspro.933182/New folder/lignad.pdb"
> open "C:/Users/alber/OneDrive/Desktop/LWM reserch/Furin Project/Docking
> analysis/Standard Dock/cluspro.933182/New folder/furin.pdb"
Summary of feedback from opening C:/Users/alber/OneDrive/Desktop/LWM
reserch/Furin Project/Docking analysis/Standard Dock/cluspro.933182/New
folder/furin.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK original generated coordinate pdb file
Chain information for furin.pdb #2
---
Chain | Description
A | No description available
> view #1 clip false
> lighting simple
> select add #1
79 atoms, 82 bonds, 1 residue, 1 model selected
> select add #2
4510 atoms, 4596 bonds, 474 residues, 2 models selected
> lighting simple
> lighting soft
> lighting full
> select subtract #1
4431 atoms, 4514 bonds, 473 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #1
79 atoms, 82 bonds, 1 residue, 1 model selected
> select subtract #1
Nothing selected
> select add #2
4431 atoms, 4514 bonds, 473 residues, 1 model selected
> show sel surfaces
> select subtract #2
1 model selected
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> select add #1
79 atoms, 82 bonds, 1 residue, 1 model selected
> select add #2
4510 atoms, 4596 bonds, 474 residues, 2 models selected
> lighting shadows false
> lighting flat
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting full
[Repeated 2 time(s)]
> select subtract #1
4431 atoms, 4514 bonds, 473 residues, 2 models selected
> select subtract #2
1 model selected
> ui mousemode right zoom
> save C:\Users\alber\Desktop\image2.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\alber\Desktop\movie1.mp4
Movie saved to \C:Users\\...\Desktop\movie1.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\alber\Desktop\movie2.mp4
Movie saved to \C:Users\\...\Desktop\movie2.mp4
> cd "C:/Users/alber/OneDrive/Desktop/LWM reserch/Furin Project/Docking
> analysis/Standard Dock/cluspro.933182/New folder"
Current working directory is: C:\Users\alber\OneDrive\Desktop\LWM
reserch\Furin Project\Docking analysis\Standard Dock\cluspro.933182\New folder
> save C:\Users\alber\Desktop\image3.png supersample 3
> save C:\Users\alber\Desktop\image4.png supersample 3
> cd "C:/Users/alber/OneDrive/Desktop/LWM reserch/Furin Project/Docking
> analysis/Standard Dock/cluspro.933182/New folder"
Current working directory is: C:\Users\alber\OneDrive\Desktop\LWM
reserch\Furin Project\Docking analysis\Standard Dock\cluspro.933182\New folder
> view
> save C:\Users\alber\Desktop\image5.png supersample 3
> save C:\Users\alber\Desktop\image6.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\alber\Desktop\movie3.mp4
Movie saved to \C:Users\\...\Desktop\movie3.mp4
> select add #1
79 atoms, 82 bonds, 1 residue, 1 model selected
> view #1 clip false
> hide sel surfaces
> select subtract #1
Nothing selected
> select add #2
4431 atoms, 4514 bonds, 473 residues, 1 model selected
> hide sel surfaces
> select subtract #2
1 model selected
> ui tool show ViewDockX
No suitable models found for ViewDockX
> select add #1
79 atoms, 82 bonds, 1 residue, 1 model selected
> select add #2
4510 atoms, 4596 bonds, 474 residues, 2 models selected
> ui tool show ViewDockX
No suitable models found for ViewDockX
> close #1
> close
> open "C:/Users/alber/OneDrive/Desktop/LWM reserch/Furin Project/Docking
> analysis/Standard Dock/cluspro.933182/New folder/furin.pdb"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\pdb\\__init__.py", line 34, in open
return pdb.open_pdb(session, data, file_name, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\pdb\pdb.py",
line 78, in open_pdb
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,
File "C:\Program Files\ChimeraX\bin\lib\codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xc8 in position 99:
invalid continuation byte
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xc8 in position 99:
invalid continuation byte
File "C:\Program Files\ChimeraX\bin\lib\codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
See log for complete Python traceback.
> open "C:/Users/alber/OneDrive/Desktop/LWM reserch/Furin Project/Docking
> analysis/Standard Dock/cluspro.933182/New folder/furin.pdb"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\pdb\\__init__.py", line 34, in open
return pdb.open_pdb(session, data, file_name, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\pdb\pdb.py",
line 78, in open_pdb
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,
File "C:\Program Files\ChimeraX\bin\lib\codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xc8 in position 99:
invalid continuation byte
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xc8 in position 99:
invalid continuation byte
File "C:\Program Files\ChimeraX\bin\lib\codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 31.0.101.2111
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: HP
Model: HP Laptop 15-da0xxx
OS: Microsoft Windows 10 Home Single Language (Build 19045)
Memory: 4,201,746,432
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i3-8130U CPU @ 2.20GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9
ChimeraX-AddH: 2.2.4
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6rc202304072249
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
comtypes: 1.1.14
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.2.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.0
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.2.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pywin32: 305
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
WMI: 1.5.1
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → UnicodeDecodeError opening PDB file |
comment:2 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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Would need the furin.pdb in order to debug.