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Opened 2 years ago
Closed 2 years ago
#8924 closed defect (duplicate)
'textureSampler' : syntax error
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | 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: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
warnings | QOpenGLShader::compile(Fragment): ERROR: 4:1: 'textureSampler' :
syntax error syntax error
*** Problematic Fragment shader source code ***
#version 110
#ifdef GL_KHR_blend_equation_advanced
#extension GL_ARB_fragment_coord_conventions : enable
#extension GL_KHR_blend_equation_advanced : enable
#endif
#define lowp
#define mediump
#define highp
#line 1
varying highp vec2 uv;uniform sampler2DRect textureSampler;uniform bool
swizzle;uniform highp float opacity;void main() { highp vec4 tmpFragColor =
texture2DRect(textureSampler,uv); tmpFragColor.a *= opacity; gl_FragColor =
swizzle ? tmpFragColor.bgra : tmpFragColor;}
***
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:/Workshop/Molecules/pvagans/vina/pvagans/withmini_kollam/M2.pdb
M2.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) lit3_A163CY271C [more
info...]
Chain information for M2.pdb #1
---
Chain | Description
B | No description available
> rainbow
> ui tool show "Add Hydrogens"
> addh
Summary of feedback from adding hydrogens to M2.pdb #1
---
notes | No usable SEQRES records for M2.pdb (#1) chain B; guessing termini
instead
Chain-initial residues that are actual N termini: /B ASP 27
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /B PRO 418
Chain-final residues that are not actual C termini:
388 hydrogen bonds
3021 hydrogens added
> close session
> open C:/Workshop/Molecules/pvagans/vina/pvagans/withmini_kollam/M2_387.pdb
Chain information for M2_387.pdb #1
---
Chain | Description
B | No description available
> rainbow
> select add #1
3090 atoms, 3162 bonds, 393 residues, 1 model selected
> select subtract #1
Nothing selected
> ui tool show "Add Hydrogens"
> addh
Summary of feedback from adding hydrogens to M2_387.pdb #1
---
notes | No usable SEQRES records for M2_387.pdb (#1) chain B; guessing termini
instead
Chain-initial residues that are actual N termini: /B ASP 27
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /B PRO 418
Chain-final residues that are not actual C termini:
405 hydrogen bonds
3028 hydrogens added
> hide cartoons
[Repeated 1 time(s)]
> show cartoons
> hide atoms
[Repeated 1 time(s)]
> show atoms
> select add #1
6118 atoms, 6190 bonds, 393 residues, 1 model selected
> hide sel atoms
> close session
> open "D:/phd project/Pantoea vagans C9-1/engineering/PVmonomerphyk.pdb"
PVmonomerphyk.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) pantoea vagans phyk [more
info...]
Chain information for PVmonomerphyk.pdb #1
---
Chain | Description
B | No description available
> rainbow
> ui tool show "Add Hydrogens"
> addh
Summary of feedback from adding hydrogens to PVmonomerphyk.pdb #1
---
notes | No usable SEQRES records for PVmonomerphyk.pdb (#1) chain B; guessing
termini instead
Chain-initial residues that are actual N termini: /B ASP 27
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /B PRO 418
Chain-final residues that are not actual C termini:
390 hydrogen bonds
3025 hydrogens added
Alignment identifier is 1/B
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:271
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:271
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:271
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:271
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:163,271
31 atoms, 30 bonds, 2 residues, 1 model selected
> view sel
> show (sel-residues & sidechain) target ab
> view sel
[Repeated 1 time(s)]
> ui mousemode right distance
> distance /B:271@CB /B:163@CB
Distance between /B TYR 271 CB and ALA 163 CB: 3.748Å
> ui mousemode right label
> label #1/B:163
> label #1/B:271
> ui mousemode right "move label"
[Repeated 2 time(s)]
> color sel byelement
> label sel atoms attribute element
> hide #2.1 models
> show #2.1 models
> select add #2.1
31 atoms, 30 bonds, 2 residues, 2 models selected
> select subtract #2.1
31 atoms, 30 bonds, 2 residues, 1 model selected
> undo
[Repeated 2 time(s)]
> redo
> ~label sel atoms
> ui mousemode right "move label"
> lighting soft
> style sel ball
Changed 31 atom styles
> style sel stick
Changed 31 atom styles
> show sel atoms
> view sel
> save C:\Users\Asmi\Desktop\image1.png supersample 3
> select clear
> save C:\Users\Asmi\Desktop\image2.png supersample 3
> set bgColor white
> set bgColor #ffffff00
> lighting simple
> view
> undo
> lighting full
> ui mousemode right "move label"
[Repeated 1 time(s)]
> color #2.1 #ff5500ff models
> color #2.1 #ff557fff models
> color #2.1 #ff5500ff models
> color #2.1 red models
> color #2.1 #be0000ff models
> lighting simple
> lighting soft
> lighting full
> color byhetero
> lighting soft
> lighting simple
> save C:\Users\Asmi\Desktop\image1.png supersample 3
> save "D:/phd project/TAC/15_3_23_TAC/M2.tif" width 798 height 507
> supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\Asmi\Desktop\movie4.mp4
Movie saved to \C:Users\\...\Desktop\movie4.mp4
> hide #!2 models
> select /B:163,271
31 atoms, 30 bonds, 1 pseudobond, 2 residues, 2 models selected
> mlp sel
Map values for surface "PVmonomerphyk.pdb_B SES surface": minimum -28.91, mean
-4.599, maximum 22.54
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "PVmonomerphyk.pdb_B SES surface": minimum -28.91, mean
-4.599, maximum 22.54
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "PVmonomerphyk.pdb_B SES surface": minimum -28.91, mean
-4.599, maximum 22.54
To also show corresponding color key, enter the above mlp command and add key
true
> select subtract #1.2
1 model selected
> select add #1.2
6084 atoms, 392 residues, 1 model selected
> select subtract #1.2
1 model selected
> select add #1.1
1 model selected
> select subtract #1.1
Nothing selected
> select /B:163,271
31 atoms, 30 bonds, 1 pseudobond, 2 residues, 2 models selected
> mlp sel
Map values for surface "PVmonomerphyk.pdb_B SES surface": minimum -28.91, mean
-4.599, maximum 22.54
To also show corresponding color key, enter the above mlp command and add key
true
> rainbow sel
[Repeated 3 time(s)]
> select add #1
6084 atoms, 6157 bonds, 1 pseudobond, 392 residues, 4 models selected
> select subtract #1.2
2 models selected
> select subtract #1.1
Nothing selected
> select add #1
6084 atoms, 6157 bonds, 1 pseudobond, 392 residues, 3 models selected
> rainbow sel
> select subtract #1.2
2 models selected
> select add #1.2
6084 atoms, 392 residues, 2 models selected
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> select add #1
6084 atoms, 6157 bonds, 1 pseudobond, 392 residues, 4 models selected
> select subtract #1
1 model selected
> select /B:163,271
31 atoms, 30 bonds, 1 pseudobond, 2 residues, 2 models selected
> color (#!1 & sel) byelement
> ui tool show H-Bonds
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> view sel
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & backbone) target ab
> show (#!1 & sel-residues & sidechain) target ab
> ui tool show H-Bonds
> hbonds sel showDist true twoColors true select 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 PVmonomerphyk.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ALA 163 N /B GLN 159 O /B ALA 163 H 2.947 1.964
/B LYS 167 N /B ALA 163 O /B LYS 167 H 3.232 2.265
2 hydrogen bonds found
1 strict hydrogen bonds found
> hbonds sel showDist true select 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 PVmonomerphyk.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ALA 163 N /B GLN 159 O /B ALA 163 H 2.947 1.964
/B LYS 167 N /B ALA 163 O /B LYS 167 H 3.232 2.265
2 hydrogen bonds found
> hide #!1.3 models
> select clear
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel showDist true select 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 PVmonomerphyk.pdb
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ALA 163 N /B GLN 159 O /B ALA 163 H 2.947 1.964
/B LYS 167 N /B ALA 163 O /B LYS 167 H 3.232 2.265
2 hydrogen bonds found
> show #!1.3 models
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & backbone) target ab
> show (#!1 & sel-residues & sidechain) target ab
> select /B:271
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:271
21 atoms, 21 bonds, 1 residue, 1 model selected
> hbonds sel showDist true select 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 PVmonomerphyk.pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ASP 156 N /B TYR 271 OH /B ASP 156 H 2.937 2.012
/B TYR 271 OH /B GLN 159 OE1 /B TYR 271 HH 2.828 2.049
/B ARG 275 N /B TYR 271 O /B ARG 275 H 2.964 1.975
/B ARG 275 NE /B TYR 271 OH /B ARG 275 HE 2.988 2.025
4 hydrogen bonds found
> hbonds sel select 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 PVmonomerphyk.pdb
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ASP 156 N /B TYR 271 OH /B ASP 156 H 2.937 2.012
/B TYR 271 OH /B GLN 159 OE1 /B TYR 271 HH 2.828 2.049
/B ARG 275 N /B TYR 271 O /B ARG 275 H 2.964 1.975
/B ARG 275 NE /B TYR 271 OH /B ARG 275 HE 2.988 2.025
/B ARG 275 NH1 /B GLN 159 OE1 /B ARG 275 HH11 2.737 1.742
5 hydrogen bonds found
> select /B:271
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:271
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:271
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:271
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:163,271
31 atoms, 30 bonds, 1 pseudobond, 2 residues, 2 models selected
> hbonds sel select 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 PVmonomerphyk.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/B ASP 156 N /B TYR 271 OH /B ASP 156 H 2.937 2.012
/B ALA 163 N /B GLN 159 O /B ALA 163 H 2.947 1.964
/B LYS 167 N /B ALA 163 O /B LYS 167 H 3.232 2.265
/B TYR 271 OH /B GLN 159 OE1 /B TYR 271 HH 2.828 2.049
/B ARG 275 N /B TYR 271 O /B ARG 275 H 2.964 1.975
/B ARG 275 NE /B TYR 271 OH /B ARG 275 HE 2.988 2.025
6 hydrogen bonds found
> view sel
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & backbone) target ab
> show (#!1 & sel-residues & sidechain) target ab
> lighting soft
> color (#!1 & sel) byelement
> select /B:275
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /B:275
24 atoms, 23 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byelement
> select /B:159
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /B:159
17 atoms, 16 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byelement
> select /B:156
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:156
12 atoms, 11 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byelement
> select /B:167
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:137-167
473 atoms, 475 bonds, 2 pseudobonds, 31 residues, 2 models selected
> select /B:167
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:167
22 atoms, 21 bonds, 1 residue, 1 model selected
> color (#!1 & sel) byelement
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:271
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:163,271
31 atoms, 30 bonds, 1 pseudobond, 2 residues, 2 models selected
> style sel ball
Changed 31 atom styles
> style sel stick
Changed 31 atom styles
> lighting simple
> color #1.3 #5500ffff models
> color #1.3 #0055ffff models
> color #1.3 cyan models
> color #1.3 #009090ff models
> color #1.3 #55aaffff models
> color #1.3 #305f8fff models
> color #1.3 #aa00ffff models
> color #1.3 #3b0059ff models
> color #1.3 #510079ff models
> color #1.3 #ff007fff models
> color #1.3 #550000ff models
> color #1.3 blue models
> color #1.3 #5500ffff models
> color #1.3 #55ffffff models
> color #1.3 #55ff7fff models
> color #1.3 #ffff7fff models
> color #1.3 #ff55ffff models
> color #1.3 #55557fff models
> color #1.3 #0055ffff models
> color #1.3 #003cb4ff models
> ui mousemode right "move label"
> ui mousemode right label
> label delete residues
> label #1/B:275
> label #1/B:156
> label #1/B:159
> label #1/B:271
> label #1/B:163
> label delete residues
> label #1/B:163
> label #1/B:167
> label #1/B:271
> label #1/B:275
> label #1/B:156
> label #1/B:159
> ui mousemode right "move label"
[Repeated 1 time(s)]
> set bgColor black
> set bgColor transparent
> set bgColor white
> set bgColor #ffffff00
> set bgColor black
> set bgColor transparent
> set bgColor white
> set bgColor #ffffff00
> save "D:/phd project/TAC/15_3_23_TAC/M2_hbond.tif" width 1220 height 507
> supersample 3
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\Asmi\Desktop\movie4.mp4
Movie saved to \C:Users\\...\Desktop\movie4.mp4
> hide #1.3 models
> ui tool show Contacts
> select /B:271
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:271
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:163,271
31 atoms, 30 bonds, 1 pseudobond, 2 residues, 2 models selected
> contacts sel saveFile "D:/phd project/TAC/15_3_23_TAC/M2_contacts"
> resSeparation 5 ignoreHiddenModels true select true reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
28 contacts
atom1 atom2 overlap distance
/B TYR 271 HH /B ASP 156 H 0.108 1.892
/B TYR 271 OH /B ASP 156 H 0.088 2.012
/B TYR 271 HH /B GLN 159 OE1 -0.029 2.049
/B TYR 271 CE1 /B GLN 159 OE1 -0.119 3.239
/B TYR 271 HH /B ASP 156 N -0.168 2.793
/B TYR 271 CZ /B GLN 159 CB -0.179 3.489
/B TYR 271 OH /B THR 155 HA -0.207 2.707
/B TYR 271 OH /B ASP 156 N -0.212 2.937
/B TYR 271 CZ /B GLN 159 OE1 -0.214 3.244
/B ALA 163 CB /B TYR 271 HB3 -0.244 2.944
/B TYR 271 HH /B ASP 156 HB2 -0.250 2.250
/B ALA 163 CB /B VAL 269 CG1 -0.288 3.688
/B TYR 271 HH /B GLN 159 HB2 -0.293 2.293
/B TYR 271 OH /B THR 155 CA -0.307 3.507
/B TYR 271 OH /B GLN 159 OE1 -0.308 2.828
/B TYR 271 HE2 /B THR 155 HB -0.321 2.321
/B TYR 271 CZ /B GLN 159 HB2 -0.321 2.931
/B TYR 271 CE2 /B GLU 160 N -0.325 3.650
/B TYR 271 HE2 /B GLU 160 HB2 -0.331 2.331
/B TYR 271 HE1 /B GLN 159 OE1 -0.336 2.756
/B TYR 271 CE1 /B GLN 159 HB3 -0.344 3.044
/B ALA 163 CB /B TYR 271 CB -0.348 3.748
/B TYR 271 CE1 /B GLN 159 CD -0.351 3.661
/B TYR 271 CE1 /B GLN 159 CB -0.352 3.752
/B ALA 163 CB /B VAL 269 HG13 -0.354 3.054
/B ALA 163 HB3 /B VAL 269 HG13 -0.359 2.359
/B TYR 271 CE2 /B GLN 159 CB -0.372 3.772
/B TYR 271 CD2 /B GLU 160 HA -0.380 3.080
28 contacts
> set bgColor black
> set bgColor transparent
> select clear
> hide #1.4 models
> select /B:271
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:271
21 atoms, 21 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel resSeparation 5 ignoreHiddenModels true reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
25 contacts
atom1 atom2 overlap distance
/B TYR 271 HH /B ASP 156 H 0.108 1.892
/B TYR 271 OH /B ASP 156 H 0.088 2.012
/B TYR 271 HH /B GLN 159 OE1 -0.029 2.049
/B TYR 271 CE1 /B GLN 159 OE1 -0.119 3.239
/B TYR 271 HH /B ASP 156 N -0.168 2.793
/B TYR 271 CZ /B GLN 159 CB -0.179 3.489
/B TYR 271 OH /B THR 155 HA -0.207 2.707
/B TYR 271 OH /B ASP 156 N -0.212 2.937
/B TYR 271 CZ /B GLN 159 OE1 -0.214 3.244
/B TYR 271 HB3 /B ALA 163 CB -0.244 2.944
/B TYR 271 HH /B ASP 156 HB2 -0.250 2.250
/B TYR 271 HH /B GLN 159 HB2 -0.293 2.293
/B TYR 271 OH /B THR 155 CA -0.307 3.507
/B TYR 271 OH /B GLN 159 OE1 -0.308 2.828
/B TYR 271 HE2 /B THR 155 HB -0.321 2.321
/B TYR 271 CZ /B GLN 159 HB2 -0.321 2.931
/B TYR 271 CE2 /B GLU 160 N -0.325 3.650
/B TYR 271 HE2 /B GLU 160 HB2 -0.331 2.331
/B TYR 271 HE1 /B GLN 159 OE1 -0.336 2.756
/B TYR 271 CE1 /B GLN 159 HB3 -0.344 3.044
/B TYR 271 CB /B ALA 163 CB -0.348 3.748
/B TYR 271 CE1 /B GLN 159 CD -0.351 3.661
/B TYR 271 CE1 /B GLN 159 CB -0.352 3.752
/B TYR 271 CE2 /B GLN 159 CB -0.372 3.772
/B TYR 271 CD2 /B GLU 160 HA -0.380 3.080
25 contacts
> show #1.4 models
> contacts sel resSeparation 5 ignoreHiddenModels true select true reveal true
> log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
25 contacts
atom1 atom2 overlap distance
/B TYR 271 HH /B ASP 156 H 0.108 1.892
/B TYR 271 OH /B ASP 156 H 0.088 2.012
/B TYR 271 HH /B GLN 159 OE1 -0.029 2.049
/B TYR 271 CE1 /B GLN 159 OE1 -0.119 3.239
/B TYR 271 HH /B ASP 156 N -0.168 2.793
/B TYR 271 CZ /B GLN 159 CB -0.179 3.489
/B TYR 271 OH /B THR 155 HA -0.207 2.707
/B TYR 271 OH /B ASP 156 N -0.212 2.937
/B TYR 271 CZ /B GLN 159 OE1 -0.214 3.244
/B TYR 271 HB3 /B ALA 163 CB -0.244 2.944
/B TYR 271 HH /B ASP 156 HB2 -0.250 2.250
/B TYR 271 HH /B GLN 159 HB2 -0.293 2.293
/B TYR 271 OH /B THR 155 CA -0.307 3.507
/B TYR 271 OH /B GLN 159 OE1 -0.308 2.828
/B TYR 271 HE2 /B THR 155 HB -0.321 2.321
/B TYR 271 CZ /B GLN 159 HB2 -0.321 2.931
/B TYR 271 CE2 /B GLU 160 N -0.325 3.650
/B TYR 271 HE2 /B GLU 160 HB2 -0.331 2.331
/B TYR 271 HE1 /B GLN 159 OE1 -0.336 2.756
/B TYR 271 CE1 /B GLN 159 HB3 -0.344 3.044
/B TYR 271 CB /B ALA 163 CB -0.348 3.748
/B TYR 271 CE1 /B GLN 159 CD -0.351 3.661
/B TYR 271 CE1 /B GLN 159 CB -0.352 3.752
/B TYR 271 CE2 /B GLN 159 CB -0.372 3.772
/B TYR 271 CD2 /B GLU 160 HA -0.380 3.080
25 contacts
> contacts sel saveFile "D:/phd project/TAC/15_3_23_TAC/M2_Y271_contacts"
> resSeparation 5 ignoreHiddenModels true select true reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
31 contacts
atom1 atom2 overlap distance
/B GLN 159 OE1 /B ARG 275 HH11 0.278 1.742
/B TYR 271 HH /B ASP 156 H 0.108 1.892
/B TYR 271 OH /B ASP 156 H 0.088 2.012
/B TYR 271 HH /B GLN 159 OE1 -0.029 2.049
/B GLN 159 CD /B ARG 275 HH11 -0.065 2.675
/B GLN 159 OE1 /B ARG 275 NH1 -0.092 2.737
/B TYR 271 CE1 /B GLN 159 OE1 -0.119 3.239
/B ASP 156 N /B TYR 271 HH -0.168 2.793
/B GLN 159 CB /B TYR 271 CZ -0.179 3.489
/B TYR 271 OH /B THR 155 HA -0.207 2.707
/B TYR 271 OH /B ASP 156 N -0.212 2.937
/B TYR 271 CZ /B GLN 159 OE1 -0.214 3.244
/B ALA 163 CB /B TYR 271 HB3 -0.244 2.944
/B TYR 271 HH /B ASP 156 HB2 -0.250 2.250
/B ALA 163 CB /B VAL 269 CG1 -0.288 3.688
/B TYR 271 HH /B GLN 159 HB2 -0.293 2.293
/B THR 155 CA /B TYR 271 OH -0.307 3.507
/B TYR 271 OH /B GLN 159 OE1 -0.308 2.828
/B THR 155 HB /B TYR 271 HE2 -0.321 2.321
/B TYR 271 CZ /B GLN 159 HB2 -0.321 2.931
/B GLN 159 CD /B ARG 275 NH1 -0.324 3.559
/B TYR 271 CE2 /B GLU 160 N -0.325 3.650
/B TYR 271 HE2 /B GLU 160 HB2 -0.331 2.331
/B GLN 159 OE1 /B TYR 271 HE1 -0.336 2.756
/B TYR 271 CE1 /B GLN 159 HB3 -0.344 3.044
/B ALA 163 CB /B TYR 271 CB -0.348 3.748
/B TYR 271 CE1 /B GLN 159 CD -0.351 3.661
/B GLN 159 CB /B TYR 271 CE1 -0.352 3.752
/B ALA 163 CB /B VAL 269 HG13 -0.354 3.054
/B GLN 159 CB /B TYR 271 CE2 -0.372 3.772
/B TYR 271 CD2 /B GLU 160 HA -0.380 3.080
31 contacts
> hide #1.4 models
> show #1.4 models
> hide #1.4 models
> show #1.4 models
> hide #1.4 models
> show #1.4 models
> select add #1.4
29 atoms, 31 pseudobonds, 8 residues, 3 models selected
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> view sel
> hide #1.4 models
> select add #1
6084 atoms, 6157 bonds, 38 pseudobonds, 392 residues, 6 models selected
> show #1.4 models
> hide #1.4 models
> show #1.4 models
> hide #1.4 models
> show #1.4 models
> close session
> open "D:/phd project/Pantoea vagans C9-1/engineering/PVmonomerphyk.pdb"
PVmonomerphyk.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) pantoea vagans phyk [more
info...]
Chain information for PVmonomerphyk.pdb #1
---
Chain | Description
B | No description available
> rainbow
> ui tool show "Add Hydrogens"
> addh
Summary of feedback from adding hydrogens to PVmonomerphyk.pdb #1
---
notes | No usable SEQRES records for PVmonomerphyk.pdb (#1) chain B; guessing
termini instead
Chain-initial residues that are actual N termini: /B ASP 27
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /B PRO 418
Chain-final residues that are not actual C termini:
390 hydrogen bonds
3025 hydrogens added
Alignment identifier is 1/B
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> show (sel-residues & sidechain) target ab
> view sel
> color sel byhetero
> color sel byelement
> label sel atoms
> ui mousemode right label
> label delete residues
> ui mousemode right "map eraser"
> ui mousemode right label
> label delete residues
[Repeated 2 time(s)]
> ui mousemode right label
> label delete residues
> label #1/B:163
> ~label sel atoms
> ui tool show Contacts
> contacts sel resSeparation 5 ignoreHiddenModels true select true reveal true
> log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
5 contacts
atom1 atom2 overlap distance
/B ALA 163 CB /B TYR 271 HB3 -0.244 2.944
/B ALA 163 CB /B VAL 269 CG1 -0.288 3.688
/B ALA 163 CB /B TYR 271 CB -0.348 3.748
/B ALA 163 CB /B VAL 269 HG13 -0.354 3.054
/B ALA 163 HB3 /B VAL 269 HG13 -0.359 2.359
5 contacts
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> show (sel-residues & sidechain) target ab
> contacts sel resSeparation 5 ignoreHiddenModels true select true showDist
> true reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
8 contacts
atom1 atom2 overlap distance
/B VAL 269 HG13 /B LYS 164 HD2 -0.049 2.049
/B ALA 163 CB /B TYR 271 HB3 -0.244 2.944
/B VAL 269 CG1 /B LYS 164 HD2 -0.279 2.979
/B ALA 163 CB /B VAL 269 CG1 -0.288 3.688
/B VAL 269 HG13 /B LYS 164 CD -0.330 3.030
/B ALA 163 CB /B TYR 271 CB -0.348 3.748
/B ALA 163 CB /B VAL 269 HG13 -0.354 3.054
/B VAL 269 HG13 /B ALA 163 HB3 -0.359 2.359
8 contacts
> contacts sel resSeparation 5 ignoreHiddenModels true select true showDist
> true reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
11 contacts
atom1 atom2 overlap distance
/B VAL 269 HG13 /B LYS 164 HD2 -0.049 2.049
/B LYS 164 HD2 /B VAL 269 HG21 -0.082 2.082
/B LYS 164 CD /B VAL 269 HG21 -0.112 2.812
/B ALA 163 CB /B TYR 271 HB3 -0.244 2.944
/B VAL 269 CG1 /B LYS 164 HD2 -0.279 2.979
/B ALA 163 CB /B VAL 269 CG1 -0.288 3.688
/B LYS 164 HD2 /B VAL 269 CG2 -0.309 3.009
/B VAL 269 HG13 /B LYS 164 CD -0.330 3.030
/B ALA 163 CB /B TYR 271 CB -0.348 3.748
/B ALA 163 CB /B VAL 269 HG13 -0.354 3.054
/B VAL 269 HG13 /B ALA 163 HB3 -0.359 2.359
11 contacts
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:163
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel resSeparation 5 ignoreHiddenModels true showDist true reveal
> true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
5 contacts
atom1 atom2 overlap distance
/B ALA 163 CB /B TYR 271 HB3 -0.244 2.944
/B ALA 163 CB /B VAL 269 CG1 -0.288 3.688
/B ALA 163 CB /B TYR 271 CB -0.348 3.748
/B ALA 163 CB /B VAL 269 HG13 -0.354 3.054
/B ALA 163 HB3 /B VAL 269 HG13 -0.359 2.359
5 contacts
> contacts sel resSeparation 5 ignoreHiddenModels true showDist true reveal
> true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
5 contacts
atom1 atom2 overlap distance
/B ALA 163 CB /B TYR 271 HB3 -0.244 2.944
/B ALA 163 CB /B VAL 269 CG1 -0.288 3.688
/B ALA 163 CB /B TYR 271 CB -0.348 3.748
/B ALA 163 CB /B VAL 269 HG13 -0.354 3.054
/B ALA 163 HB3 /B VAL 269 HG13 -0.359 2.359
5 contacts
> ui mousemode right label
> label #1/B:271
> label #1/B:269
> view sel
> set bgColor white
> set bgColor #ffffff00
> ui mousemode right distance
> ui mousemode right "color key"
> key fontSize 25
> key fontSize 26
> key fontSize 27
> key fontSize 26
> key fontSize 25
> key fontSize 24
> key fontSize 23
> key fontSize 22
> key fontSize 21
> key fontSize 20
> key delete
> ui mousemode right distance
> ui mousemode right label
> label delete residues
> ui mousemode right label
> label delete residues
[Repeated 1 time(s)]
> label #1/B:271
> label #1/B:269
> ui tool show Contacts
> ui tool show Distances
> ui tool show Contacts
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\struct_measure\tool.py", line 626, in clear_status
if s.apc_status_label.text() == s.apc_status_tip:
RuntimeError: wrapped C/C++ object of type QLabel has been deleted
RuntimeError: wrapped C/C++ object of type QLabel has been deleted
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\struct_measure\tool.py", line 626, in clear_status
if s.apc_status_label.text() == s.apc_status_tip:
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 20.19.15.4835
OpenGL renderer: Intel(R) HD Graphics 4400
OpenGL vendor: Intel
Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: Inspiron 11 - 3148
OS: Microsoft Windows 10 Home Single Language (Build 19045)
Memory: 4,219,842,560
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i3-4030U CPU @ 1.90GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
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: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 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: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
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-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
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
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pywin32: 303
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
WMI: 1.5.1
zipp: 3.11.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → 'textureSampler' : syntax error |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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