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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