The following bug report has been submitted:
Platform: Windows-10-10.0.22000
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\andyp\Documents\Scripps\Farzan lab\B cell editing in vivo
> evolution\eCD4\Modeling\gp120CD4 pdb\6MEOCD4mutanalysisV3.2.cxs" format
> session
Log from Wed Feb 23 22:37:25 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\panan\Desktop\ChimeraX\6MEOCD4mutanalysisV3.1.cxs format
> session
Log from Mon Jan 31 10:21:07 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\panan\Desktop\ChimeraX\6MEOCD4mutanalysisV3.cxs format session
Log from Mon Jan 31 09:29:36 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\panan\Desktop\ChimeraX\6MEOCD4mutanalysisV2.cxs format session
Log from Wed Dec 22 13:06:50 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\panan\OneDrive\Documents\Andi Pan\Scripps\Farzan lab\B cell
> editing in vivo evolution\eCD4\Modeling\gp120CD4
> pdb\6MEOCD4gp120mutsitev1.cxs" format session
Log from Tue Dec 21 15:11:06 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\panan\Desktop\ChimeraX\2NY2_v1.cxs format session
Log from Fri Dec 17 13:52:00 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\panan\Desktop\ChimeraX\2NY2_v1.cxs format session
Log from Fri Dec 17 11:47:43 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\panan\Desktop\ChimeraX\2NY2_v1.cxs format session
Log from Fri Dec 17 11:35:35 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\panan\Desktop\ChimeraX\gp120CD4 v3.cxs" format session
Log from Tue Aug 3 16:46:19 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\panan\Desktop\ChimeraX\gp120CD4 v3.cxs" format session
Log from Mon Aug 2 23:48:12 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\panan\Desktop\ChimeraX\gp120CD4 v2.cxs" format session
Log from Mon Aug 2 23:24:59 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\panan\Desktop\ChimeraX\gp120CD4 v1.cxs" format session
Log from Mon Aug 2 18:19:42 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\panan\Desktop\ChimeraX\gp120CD4.cxs format session
Log from Sat Jul 31 22:59:11 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> help help:quickstart
> 2B4C
Unknown command: 2B4C
> fetch 2B4C
Unknown command: fetch 2B4C
> open 2B4C
Summary of feedback from opening 2B4C fetched from pdb
---
notes | Fetching compressed mmCIF 2b4c from
http://files.rcsb.org/download/2b4c.cif
Fetching CCD NAG from http://ligand-expo.rcsb.org/reports/N/NAG/NAG.cif
Fetching CCD FUC from http://ligand-expo.rcsb.org/reports/F/FUC/FUC.cif
Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif
Fetching CCD XYL from http://ligand-expo.rcsb.org/reports/X/XYL/XYL.cif
2b4c title:
Crystal structure of HIV-1 JR-FL gp120 core protein containing the third
variable region (V3) complexed with CD4 and the X5 antibody [more info...]
Chain information for 2b4c #1
---
Chain | Description
C | T-cell surface glycoprotein CD4
G | envelope glycoprotein
H | anti-HIV-1 gp120 immunoglobulin X5 heavy chain
L | anti-HIV-1 gp120 immunoglobulin X5 light chain
Non-standard residues in 2b4c #1
---
FUC — alpha-L-fucopyranose
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
SO4 — sulfate ion
XYL — Xylitol
2b4c mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
> hide /H
> hide /L
> H
Unknown command: H
> sequence chain #1/G
Alignment identifier is 1/G
> select /L
1641 atoms, 1675 bonds, 216 residues, 1 model selected
> delete
Missing or invalid "atoms" argument: empty atom specifier
> delete /L
> delete /H
> save C:/Users/panan/Desktop/ChimeraX/gp120CD4.cxs
> select /C
1363 atoms, 1384 bonds, 175 residues, 1 model selected
> select /G
2702 atoms, 2763 bonds, 343 residues, 1 model selected
> style sel ball
Changed 2702 atom styles
> style sel ball
Changed 2702 atom styles
> style sel sphere
Changed 2702 atom styles
> style sel sphere
Changed 2702 atom styles
> style sel sphere
Changed 2702 atom styles
> style sel stick
Changed 2702 atom styles
> style sel ball
Changed 2702 atom styles
> style sel stick
Changed 2702 atom styles
> hide sel cartoons
> show sel cartoons
> show sel atoms
> style sel stick
Changed 2702 atom styles
> style sel ball
Changed 2702 atom styles
> lighting simple
> lighting soft
> lighting full
> select
4089 atoms, 4173 bonds, 520 residues, 1 model selected
> ~select #1
Nothing selected
> select /C
1363 atoms, 1384 bonds, 175 residues, 1 model selected
No Surface models open
> style sel sphere
Changed 1363 atom styles
> style sel ball
Changed 1363 atom styles
> show sel cartoons
> show sel atoms
> hide sel cartoons
> show sel cartoons
> style sel ball
Changed 1363 atom styles
> style sel stick
Changed 1363 atom styles
> select clear
> save C:/Users/panan/Desktop/ChimeraX/gp120CD4.cxs
——— End of log from Sat Jul 31 22:59:11 2021 ———
opened ChimeraX session
> select /C:70
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 3 residues, 1 model selected
> select up
1363 atoms, 1384 bonds, 175 residues, 1 model selected
> select up
4089 atoms, 4173 bonds, 520 residues, 1 model selected
> select up
4089 atoms, 4173 bonds, 520 residues, 1 model selected
> select up
4089 atoms, 4173 bonds, 520 residues, 1 model selected
> style sel stick
Changed 4089 atom styles
> hide sel atoms
> select clear
> select /C:96
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
74 atoms, 74 bonds, 10 residues, 1 model selected
> select up
1363 atoms, 1384 bonds, 175 residues, 1 model selected
> color sel bychain
> select clear
Alignment identifier is 1/G
Alignment identifier is 1/C
> select
> /C:3-7,12-14,27-29,35-39,44-46,55-56,69-71,81-86,89-90,93-102,114-119,127-131,137-139,143-146,155-163,166-174
617 atoms, 610 bonds, 78 residues, 1 model selected
> select /C:58-65,75-79,150-154
151 atoms, 150 bonds, 18 residues, 1 model selected
> select /C:43
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /C:43-50
61 atoms, 62 bonds, 8 residues, 1 model selected
> select /C:29
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /C:29-64
286 atoms, 289 bonds, 36 residues, 1 model selected
> style sel ball
Changed 286 atom styles
> style sel ball
Changed 286 atom styles
> hide sel atoms
> show sel atoms
> style sel ball
Changed 286 atom styles
> style sel stick
Changed 286 atom styles
> style sel ball
Changed 286 atom styles
> style sel stick
Changed 286 atom styles
> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> undo
> label sel text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> undo
> undo
> undo
> redo
> label sel attribute label_one_letter_code
> style sel stick
Changed 286 atom styles
> save "C:/Users/panan/Desktop/ChimeraX/gp120CD4 v1.cxs"
> hbonds sel reveal true
51 hydrogen bonds found
> label sel text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> show (sel-residues & sidechain) target ab
> ui tool show "Color Actions"
> select clear
> color bychain
> undo
> select /G: 364-373, 421-430
156 atoms, 157 bonds, 20 residues, 1 model selected
> select /G: 364-373, 421-430, 255-257
176 atoms, 176 bonds, 23 residues, 1 model selected
> save "C:/Users/panan/Desktop/ChimeraX/gp120CD4 v1.cxs"
> label sel text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> style sel stick
Changed 176 atom styles
> show sel atoms
> save "C:/Users/panan/Desktop/ChimeraX/gp120CD4 v1.cxs"
——— End of log from Mon Aug 2 18:19:42 2021 ———
opened ChimeraX session
> select /G: 255, 257, 364-373, 382, 421-430, 475
189 atoms, 187 bonds, 24 residues, 1 model selected
> ui windowfill toggle
> ui windowfill toggle
> select /G: 255, 257, 364-373, 382, 421-430
181 atoms, 180 bonds, 23 residues, 1 model selected
> hbonds sel reveal true
35 hydrogen bonds found
> ui tool show "Color Actions"
> color sel yellow target c
> save "C:/Users/panan/Desktop/ChimeraX/gp120CD4 v2.cxs"
——— End of log from Mon Aug 2 23:24:59 2021 ———
opened ChimeraX session
> view sel
> select /c
1363 atoms, 1384 bonds, 175 residues, 1 model selected
> mlp sel
Map values for surface "2b4c_C SES surface": minimum -27.22, mean -5.892,
maximum 26.44
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 2b4c_C SES surface #1.3: minimum, -12.22, mean 0.50,
maximum 15.07
To also show corresponding color key, enter the above coulombic command and
add key true
> undo
> undo
> save "C:/Users/panan/Desktop/ChimeraX/gp120CD4 v3.cxs"
——— End of log from Mon Aug 2 23:48:12 2021 ———
opened ChimeraX session
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select clear
> show atoms
> show atoms
> hide atoms
> select /G: 255, 257, 364-373, 382, 421-430 /C: 25-64
511 atoms, 517 bonds, 19 pseudobonds, 63 residues, 2 models selected
> show sel atoms
> select clear
> save "C:/Users/panan/Desktop/ChimeraX/gp120CD4 v3.cxs"
——— End of log from Tue Aug 3 16:46:19 2021 ———
opened ChimeraX session
> select
> /C:3-7,12-14,27-29,35-39,44-46,55-56,69-71,81-86,89-90,93-102,114-119,127-131,137-139,143-146,155-163,166-174
617 atoms, 610 bonds, 78 residues, 1 model selected
> select /G:98-114,335-350,368-372,475-481
388 atoms, 391 bonds, 3 pseudobonds, 45 residues, 2 models selected
> select /C:29-64
286 atoms, 289 bonds, 36 residues, 1 model selected
> select clear
> select /C:23
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> style sel stick
Changed 6 atom styles
> style sel sphere
Changed 6 atom styles
> style sel ball
Changed 6 atom styles
> color (#!1 & sel) orange
> label (#!1 & sel) attribute label_one_letter_code
> label (#!1 & sel) text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> select clear
> select /C:24
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!1 & sel) orange
> label (#!1 & sel) text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> style sel stick
Changed 8 atom styles
> show sel atoms
> style sel ball
Changed 8 atom styles
> style sel ball
Changed 8 atom styles
> select /G:477
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /G:478
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /G:476
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /G:477
19 atoms, 17 bonds, 2 residues, 1 model selected
> select add /G:478
27 atoms, 24 bonds, 3 residues, 1 model selected
> color sel orange
> label sel attribute name
> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> style sel stick
Changed 27 atom styles
> show sel atoms
> style sel ball
Changed 27 atom styles
> save C:/Users/panan/Desktop/ChimeraX/2b4c_gp120CD4mutation_analysis_v1.cxs
> close session
> open "C:/Users/panan/OneDrive/Documents/Andi Pan/Scripps/Farzan lab/B cell
> editing in vivo evolution/eCD4/Modeling/gp120CD4
> pdb/2ny2chainBgp120CD417b.pdb"
2ny2chainBgp120CD417b.pdb title:
Hiv-1 GP120 envelope glycoprotein (T123C, T257S, S334A, S375W, G431C)
complexed with CD4 and antibody 17B [more info...]
Chain information for 2ny2chainBgp120CD417b.pdb #1
---
Chain | Description
A | envelope glycoprotein GP120
B | T-cell surface antigen T4/LEU-3
C | antibody 17B, light chain
D | antibody 17B, heavy chain
Non-standard residues in 2ny2chainBgp120CD417b.pdb #1
---
EDO — 1,2-ethanediol (ethylene glycol)
FRU — β-D-fructofuranose
GLC — α-D-glucopyranose
HEZ — hexane-1,6-diol
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose
> select /C/D
3681 atoms, 3397 bonds, 1 pseudobond, 799 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select clear
> select clear
Drag select of 22 atoms, 24 bonds
> delete atoms sel
> delete bonds sel
> select clear
> select /E:2@O4
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select clear
Drag select of 3 atoms, 2 residues, 6 bonds
> select clear
> select /B:1
Nothing selected
> select /B:10
Nothing selected
> select /B#10
1510 atoms, 1434 bonds, 279 residues, 1 model selected
> select #B:10
Expected an objects specifier or a keyword
> select :10
Nothing selected
> select /B: 10
Nothing selected
> select /B: 23
Nothing selected
> select /B
1510 atoms, 1434 bonds, 279 residues, 1 model selected
> select clear
> select /B
1510 atoms, 1434 bonds, 279 residues, 1 model selected
> select clear
> select /B:1001
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Build Structure"
> save C:/Users/panan/Desktop/ChimeraX/2NY2_v1.cxs
——— End of log from Fri Dec 17 11:35:35 2021 ———
opened ChimeraX session
> select /B:
> 1,2,3,4,5,6,7,8,10,11,12,13,15,17,18,19,21,22,23,24,30,32,76,78,80,144,145,156,157,158
2 atoms, 2 residues, 1 model selected
> select /B: 1, 2, 3, 4, 5, 6, 7
Nothing selected
> select /B:
> 1001,1002,1003,1004100,1005,1006,1007,1008,1010,1011,1012,1013,1015,1017,1018,1019,1021,1022,1023,1024,1030,1032,1076,1078,1080,1144,1145,1156,1157,1158
225 atoms, 214 bonds, 29 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 225 atom styles
> style sel ball
Changed 225 atom styles
> style sel stick
Changed 225 atom styles
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> color (#!1 & sel) medium blue
> color (#!1 & sel) light sea green
> ui tool show "Color Actions"
> color sel forest green
> color sel orange
> color sel orange red
> color sel orange
> color sel orange red
> color sel red
> color sel orange red
> label (#!1 & sel) attribute label_specifier
> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> show sel cartoons
> show sel surfaces
> hide sel surfaces
> save C:/Users/panan/Desktop/ChimeraX/2NY2_v1.cxs
——— End of log from Fri Dec 17 11:47:43 2021 ———
opened ChimeraX session
> select clear
> select /B
1510 atoms, 1434 bonds, 279 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cornflower blue
> color sel forest green
> color sel lime
> color sel forest green
> set bgColor white
> select clear
> select /A
2728 atoms, 2589 bonds, 1 pseudobond, 521 residues, 2 models selected
> color sel purple
> select clear
> undo
> undo
> undo
> select clear
> select /B:
> 1001,1002,1003,1004100,1005,1006,1007,1008,1010,1011,1012,1013,1015,1017,1018,1019,1021,1022,1023,1024,1030,1032,1076,1078,1080,1144,1145,1156,1157,1158
225 atoms, 214 bonds, 29 residues, 1 model selected
> color sel orange
> select clear
> set bgColor black
> select /A: 270
7 atoms, 6 bonds, 1 residue, 1 model selected
> save C:/Users/panan/Desktop/ChimeraX/2NY4.fa
No alignments open!
> Sel /A:189-198,207,209,246-255,282,298,300
Unknown command: Sel /A:189-198,207,209,246-255,282,298,300
> select clear
> ui tool show Contacts
Illegal contacts 'color' attribute value (Color([1.0, 1.0, 0.49803922, 1.0])),
leaving attribute unchanged
Illegal contacts 'color' attribute value (Color([1.0, 1.0, 0.49803922, 1.0])),
leaving attribute unchanged
> select /A:477
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
103 atoms, 105 bonds, 11 residues, 1 model selected
> select up
2728 atoms, 2589 bonds, 521 residues, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> undo
> undo
> undo
> select clear
> Sel /A:189-198
Unknown command: Sel /A:189-198
> Sel /A:189
Unknown command: Sel /A:189
> Sel /C:189
Unknown command: Sel /C:189
> select /A
2728 atoms, 2589 bonds, 1 pseudobond, 521 residues, 2 models selected
> select /A:189
Nothing selected
> select /A: 189
Nothing selected
> select /A
2728 atoms, 2589 bonds, 1 pseudobond, 521 residues, 2 models selected
> select /A
2728 atoms, 2589 bonds, 1 pseudobond, 521 residues, 2 models selected
> select /A:254
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:189
Nothing selected
> select /A:198
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:190
Nothing selected
> select /A:194
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:192
Nothing selected
> select /A:193
Nothing selected
> select /A:300
Nothing selected
> select /A:298
4 atoms, 3 bonds, 1 residue, 1 model selected
> Sel /A:194-198,207,209,246-255,282,299
Unknown command: Sel /A:194-198,207,209,246-255,282,299
> Sel /A:194-198
Unknown command: Sel /A:194-198
> Sel /A:194:198
Unknown command: Sel /A:194:198
> Sel /A:194,195,196,197,198,207,209,282,299
Unknown command: Sel /A:194,195,196,197,198,207,209,282,299
> Sel /A:194,195,196,197,198
Unknown command: Sel /A:194,195,196,197,198
> select /A:194,195,196,197,198
31 atoms, 30 bonds, 5 residues, 1 model selected
> select /A:194,195,196,197,198,207,209,246-255,282,299
136 atoms, 132 bonds, 19 residues, 1 model selected
> select /A:194-198,207,209,246-255,282,299
136 atoms, 132 bonds, 19 residues, 1 model selected
> select /A:194-198,207,209,246-255,282,298,300
135 atoms, 131 bonds, 19 residues, 1 model selected
> select /A:189-198,207,209,246-255,282,298,300
135 atoms, 131 bonds, 19 residues, 1 model selected
> save C:/Users/panan/Desktop/ChimeraX/2NY2_v1.cxs
——— End of log from Fri Dec 17 13:52:00 2021 ———
opened ChimeraX session
> open "C:/Users/panan/OneDrive/Documents/Andi Pan/Scripps/Farzan lab/B cell
> editing in vivo evolution/eCD4/Modeling/gp120CD4 pdb/6meoCD4gp160CCR5.pdb"
6meoCD4gp160CCR5.pdb title:
Structural basis of coreceptor recognition by hiv-1 envelope spike [more
info...]
Chain information for 6meoCD4gp160CCR5.pdb #2
---
Chain | Description
A | T-cell surface antigen T4/LEU-3
B | C-C chemokine receptor type 5
G | envelope glycoprotein GP160
Non-standard residues in 6meoCD4gp160CCR5.pdb #2
---
A2G — 2-acetamido-2-deoxy-α-D-galactopyranose
BMA — β-D-mannopyranose
MAN — α-D-mannopyranose
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2ny2chainBgp120CD417b.pdb, chain A (#1) with 6meoCD4gp160CCR5.pdb,
chain G (#2), sequence alignment score = 1175.5
RMSD between 278 pruned atom pairs is 0.905 angstroms; (across all 301 pairs:
3.460)
> select clear
> close session
> open "C:\Users\panan\OneDrive\Documents\Andi Pan\Scripps\Farzan lab\B cell
> editing in vivo evolution\eCD4\Modeling\gp120CD4 pdb\6meoCD4gp160CCR5.pdb"
> format pdb
6meoCD4gp160CCR5.pdb title:
Structural basis of coreceptor recognition by hiv-1 envelope spike [more
info...]
Chain information for 6meoCD4gp160CCR5.pdb #1
---
Chain | Description
A | T-cell surface antigen T4/LEU-3
B | C-C chemokine receptor type 5
G | envelope glycoprotein GP160
Non-standard residues in 6meoCD4gp160CCR5.pdb #1
---
A2G — 2-acetamido-2-deoxy-α-D-galactopyranose
BMA — β-D-mannopyranose
MAN — α-D-mannopyranose
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose
> select /A
1370 atoms, 1391 bonds, 176 residues, 1 model selected
> ui tool show "Color Actions"
> color sel forest green
> select clear
> select /G:189-198,207,209,246-255,282,298,300
180 atoms, 175 bonds, 25 residues, 1 model selected
> open "C:/Users/panan/OneDrive/Documents/Andi Pan/Scripps/Farzan lab/B cell
> editing in vivo evolution/eCD4/Modeling/gp120CD4
> pdb/2ny2chainBgp120CD417b.pdb"
2ny2chainBgp120CD417b.pdb title:
Hiv-1 GP120 envelope glycoprotein (T123C, T257S, S334A, S375W, G431C)
complexed with CD4 and antibody 17B [more info...]
Chain information for 2ny2chainBgp120CD417b.pdb #2
---
Chain | Description
A | envelope glycoprotein GP120
B | T-cell surface antigen T4/LEU-3
C | antibody 17B, light chain
D | antibody 17B, heavy chain
Non-standard residues in 2ny2chainBgp120CD417b.pdb #2
---
EDO — 1,2-ethanediol (ethylene glycol)
FRU — β-D-fructofuranose
GLC — α-D-glucopyranose
HEZ — hexane-1,6-diol
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose
> close session
> open "C:\Users\panan\OneDrive\Documents\Andi Pan\Scripps\Farzan lab\B cell
> editing in vivo evolution\eCD4\Modeling\gp120CD4 pdb\6meoCD4gp160CCR5.pdb"
> format pdb
6meoCD4gp160CCR5.pdb title:
Structural basis of coreceptor recognition by hiv-1 envelope spike [more
info...]
Chain information for 6meoCD4gp160CCR5.pdb #1
---
Chain | Description
A | T-cell surface antigen T4/LEU-3
B | C-C chemokine receptor type 5
G | envelope glycoprotein GP160
Non-standard residues in 6meoCD4gp160CCR5.pdb #1
---
A2G — 2-acetamido-2-deoxy-α-D-galactopyranose
BMA — β-D-mannopyranose
MAN — α-D-mannopyranose
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose
> select /A
1370 atoms, 1391 bonds, 176 residues, 1 model selected
> color sel dim gray
> color sel forest green
> select /A:
> 1,2,3,4,5,6,7,8,9,10,11,12,13，15,17,18,19,21,22,23,24,30,32,76,78,80,144,145,156,157,158
Expected an objects specifier or a keyword
> select /A:
> 1,2,3,4,5,6,7,8,9,10,11,12,13，15,17,18,19,21,22,23,24,30,32,76,78,80,144,145,156,157,158
Expected an objects specifier or a keyword
> select
> /A:1,2,3,4,5,6,7,8,9,10,11,12,13，15,17,18,19,21,22,23,24,30,32,76,78,80,144,145,156,157,158
Expected an objects specifier or a keyword
> select /A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:1，2
Expected an objects specifier or a keyword
> select /A:1,2
18 atoms, 17 bonds, 2 residues, 1 model selected
> select
> /A:1,2,3,4,5,6,7,8,9,10,11,12,13,15,17,18,19,21,22,23,24,30,32,76,78,80,144,145,156,157,158
236 atoms, 227 bonds, 31 residues, 1 model selected
> color sel orange
> select clear
> select
> /A:1,2,3,4,5,6,7,8,9,10,11,12,13,15,17,18,19,21,22,23,24,30,32,76,78,80,144,145,156,157,158
236 atoms, 227 bonds, 31 residues, 1 model selected
> show sel atoms
> undo
> undo
> undo
> undo
> undo
> show sel atoms
> style sel stick
Changed 236 atom styles
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> show sel atoms
> show sel atoms
> hide sel atoms
> select
> /A:1,2,3,4,5,6,7,8,9,10,11,12,13,15,17,18,19,21,22,23,24,30,32,76,78,80,144,145,156,157,158
236 atoms, 227 bonds, 31 residues, 1 model selected
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> select clear
> select
> /A:1,2,3,4,5,6,7,8,9,10,11,12,13,15,17,18,19,21,22,23,24,30,32,76,78,80,144,145,156,157,158
236 atoms, 227 bonds, 31 residues, 1 model selected
> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
No Surface models open
> save "C:/Users/panan/OneDrive/Documents/Andi Pan/Scripps/Farzan lab/B cell
> editing in vivo evolution/eCD4/Modeling/gp120CD4
> pdb/6MEOCD4gp120mutsitev1.cxs"
> color sel orange
> select clear
> select /A158
Nothing selected
> select /A
1370 atoms, 1391 bonds, 176 residues, 1 model selected
> color sel forest green
> select /A:
> 1,2,3,4,5,6,7,8,9,10,11,12,13，15,17,18,19,21,22,23,24,30,32,76,78,80,144,145,156,157,158
Expected an objects specifier or a keyword
> select /A:
> 1,2,3,4,5,6,7,8,9,10,11,12,13,15,17,18,19,21,22,23,24,30,32,76,78,80,144,145,156,157,158
236 atoms, 227 bonds, 31 residues, 1 model selected
> select /A:
> 1,2,3,4,5,6,7,8,9,10,11,12,13,15,17,18,19,21,22,23,24,30,32,76,78,80,144,145,156,157,158
236 atoms, 227 bonds, 31 residues, 1 model selected
> color sel orange
> select /G:225,227,249-253,332-341,350,386-395
233 atoms, 234 bonds, 28 residues, 1 model selected
> select /G:454
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select /G:454
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /G:455
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /G:456
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> select add /G:454
20 atoms, 17 bonds, 3 residues, 1 model selected
> select subtract /G:454
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add /G:454
20 atoms, 17 bonds, 3 residues, 1 model selected
> select add /G:457
29 atoms, 25 bonds, 4 residues, 1 model selected
> show sel atoms
> select /G:457
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
Drag select of 13 residues, 1 pseudobonds
> show sel atoms
> select clear
Drag select of 11 atoms, 6 residues, 1 pseudobonds, 6 bonds
> style sel stick
Changed 30 atom styles
> show sel atoms
> select clear
> select /G:127
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 5 residues
> show sel atoms
> select clear
> select /G:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /G:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel reveal true
0 hydrogen bonds found
> label sel text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select /A:
> 1,2,3,4,5,6,7,8,9,10,11,12,13,15,17,18,19,21,22,23,24,30,32,76,78,80,144,145,156,157,158
236 atoms, 227 bonds, 31 residues, 1 model selected
> label sel text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> save "C:/Users/panan/OneDrive/Documents/Andi Pan/Scripps/Farzan lab/B cell
> editing in vivo evolution/eCD4/Modeling/gp120CD4
> pdb/6MEOCD4gp120mutsitev1.cxs"
——— End of log from Tue Dec 21 15:11:06 2021 ———
opened ChimeraX session
> mlp sel
Map values for surface "6meoCD4gp160CCR5.pdb_A SES surface": minimum -26.95,
mean -5.653, maximum 22.58
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> show sel surfaces
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
/A VAL 176 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6meoCD4gp160CCR5.pdb_A SES surface #1.4: minimum, -12.46,
mean 0.41, maximum 16.20
To also show corresponding color key, enter the above coulombic command and
add key true
> select /A
1370 atoms, 1391 bonds, 176 residues, 1 model selected
> coulombic sel
Coulombic values for 6meoCD4gp160CCR5.pdb_A SES surface #1.4: minimum, -12.46,
mean 0.41, maximum 16.20
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> select /A:
> 1,2,3,4,5,6,7,8,9,10,11,12,13,15,17,18,19,21,22,23,24,30,32,76,78,80,144,145,156,157,158
236 atoms, 227 bonds, 31 residues, 1 model selected
> select /A:
> 1,2,3,4,5,6,7,8,9,10,11,12,13,15,17,18,19,21,22,23,24,30,32,76,78,80,144,145,156,157,158
236 atoms, 227 bonds, 31 residues, 1 model selected
> label (#!1 & sel) attribute label_one_letter_code
> view sel
> select clear
Drag select of 10 residues
> show sel atoms
> select clear
> select clear
Drag select of 81 atoms, 40 residues, 65 bonds
> mlp sel
Map values for surface "6meoCD4gp160CCR5.pdb_A SES surface": minimum -26.95,
mean -5.653, maximum 22.58
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> coulombic sel
Coulombic values for 6meoCD4gp160CCR5.pdb_A SES surface #1.4: minimum, -12.46,
mean 0.41, maximum 16.20
To also show corresponding color key, enter the above coulombic command and
add key true
> color bfactor sel
299 atoms, 40 residues, 1 surfaces, atom bfactor range 82.8 to 147
> mlp sel
Map values for surface "6meoCD4gp160CCR5.pdb_A SES surface": minimum -26.95,
mean -5.653, maximum 22.58
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Coulombic values for 6meoCD4gp160CCR5.pdb_A SES surface #1.4: minimum, -12.46,
mean 0.41, maximum 16.20
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> undo
> undo
> undo
> undo
> select clear
> select /A:99
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:10@CA
1 atom, 1 residue, 1 model selected
Drag select of 133 atoms, 74 residues, 114 bonds
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/G ILE 131
/G ASP 187
/G ASN 188
/G THR 189
/G SER 190
/G TYR 191
/G ARG 192
/G GLY 491
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6meoCD4gp160CCR5.pdb_A SES surface #1.4: minimum, -12.46,
mean 0.41, maximum 16.20
Coulombic values for 6meoCD4gp160CCR5.pdb_G SES surface #1.5: minimum, -20.62,
mean -1.66, maximum 14.94
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> mlp sel
Map values for surface "6meoCD4gp160CCR5.pdb_A SES surface": minimum -26.95,
mean -5.653, maximum 22.58
Map values for surface "6meoCD4gp160CCR5.pdb_G SES surface": minimum -28.55,
mean -4.658, maximum 24.7
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> show sel surfaces
> hide sel surfaces
> coulombic sel
Coulombic values for 6meoCD4gp160CCR5.pdb_A SES surface #1.4: minimum, -12.46,
mean 0.41, maximum 16.20
Coulombic values for 6meoCD4gp160CCR5.pdb_G SES surface #1.5: minimum, -20.62,
mean -1.66, maximum 14.94
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> mlp sel
Map values for surface "6meoCD4gp160CCR5.pdb_A SES surface": minimum -26.95,
mean -5.653, maximum 22.58
Map values for surface "6meoCD4gp160CCR5.pdb_G SES surface": minimum -28.55,
mean -4.658, maximum 24.7
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> select clear
Drag select of 148 atoms, 74 residues, 123 bonds
> mlp sel
Map values for surface "6meoCD4gp160CCR5.pdb_A SES surface": minimum -26.95,
mean -5.653, maximum 22.58
Map values for surface "6meoCD4gp160CCR5.pdb_B SES surface": minimum -26.54,
mean 2.822, maximum 154.9
Map values for surface "6meoCD4gp160CCR5.pdb_G SES surface": minimum -28.55,
mean -4.658, maximum 24.7
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> select clear
> select /A:94
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /A:93
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel atoms
> hide sel atoms
Drag select of 98 atoms, 51 residues, 76 bonds
> mlp sel
Map values for surface "6meoCD4gp160CCR5.pdb_A SES surface": minimum -26.95,
mean -5.653, maximum 22.58
Map values for surface "6meoCD4gp160CCR5.pdb_G SES surface": minimum -28.55,
mean -4.658, maximum 24.7
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> select clear
> select /A:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:74
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:31
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 68 atoms, 36 residues, 50 bonds
> mlp sel
Map values for surface "6meoCD4gp160CCR5.pdb_A SES surface": minimum -26.95,
mean -5.653, maximum 22.58
Map values for surface "6meoCD4gp160CCR5.pdb_G SES surface": minimum -28.55,
mean -4.658, maximum 24.7
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "6meoCD4gp160CCR5.pdb_A SES surface": minimum -26.95,
mean -5.653, maximum 22.58
Map values for surface "6meoCD4gp160CCR5.pdb_G SES surface": minimum -28.55,
mean -4.658, maximum 24.7
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Coulombic values for 6meoCD4gp160CCR5.pdb_A SES surface #1.4: minimum, -12.46,
mean 0.41, maximum 16.20
Coulombic values for 6meoCD4gp160CCR5.pdb_G SES surface #1.5: minimum, -20.62,
mean -1.66, maximum 14.94
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> select /A:32@CA
1 atom, 1 residue, 1 model selected
> hbonds sel reveal true
0 hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel reveal true
0 hydrogen bonds found
> ui tool show Distances
> select /A:32@OD1
1 atom, 1 residue, 1 model selected
> select add /A:32@CG
1 atom, 1 bond, 1 residue, 1 model selected
> ui tool show Distances
> select clear
Drag select of 13 atoms, 26 residues, 9 bonds
> mlp sel
Map values for surface "6meoCD4gp160CCR5.pdb_A SES surface": minimum -26.95,
mean -5.653, maximum 22.58
Map values for surface "6meoCD4gp160CCR5.pdb_B SES surface": minimum -26.54,
mean 0.5726, maximum 24.72
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
/B GLN 313 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue TYS (net charge -1) with am1-bcc method
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.2.5/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\panan\AppData\Local\Temp\tmpdyqml4c6\ante.in.mol2 -fi mol2 -o
C:\Users\panan\AppData\Local\Temp\tmpdyqml4c6\ante.out.mol2 -fo mol2 -c bcc
-nc -1 -j 5 -s 2 -dr n
(TYS) ``
(TYS) `Welcome to antechamber 20.0: molecular input file processor.`
(TYS) ``
(TYS) `Info: Finished reading file
(C:\Users\panan\AppData\Local\Temp\tmpdyqml4c6\ante.in.mol2); atoms read (36),
bonds read (36).`
(TYS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(TYS) `Running: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(TYS) `/usr/bin/antechamber: Fatal Error!`
(TYS) `Cannot properly run "C:/Program Files/ChimeraX
1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac".`
(TYS) `No such file or directory`
Failure running ANTECHAMBER for residue TYS Check reply log for details
> select clear
> undo
> hide sel surfaces
Drag select of 13 atoms, 26 residues, 9 bonds
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
/B GLN 313 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue TYS (net charge -1) with am1-bcc method
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.2.5/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\panan\AppData\Local\Temp\tmpw7nu4ghb\ante.in.mol2 -fi mol2 -o
C:\Users\panan\AppData\Local\Temp\tmpw7nu4ghb\ante.out.mol2 -fo mol2 -c bcc
-nc -1 -j 5 -s 2 -dr n
(TYS) ``
(TYS) `Welcome to antechamber 20.0: molecular input file processor.`
(TYS) ``
(TYS) `Info: Finished reading file
(C:\Users\panan\AppData\Local\Temp\tmpw7nu4ghb\ante.in.mol2); atoms read (36),
bonds read (36).`
(TYS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(TYS) `Running: C:/Program Files/ChimeraX 1.2.5/bin/amber20/bin/bondtype -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(TYS) `/usr/bin/antechamber: Fatal Error!`
(TYS) `Cannot properly run "C:/Program Files/ChimeraX
1.2.5/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac".`
(TYS) `No such file or directory`
Failure running ANTECHAMBER for residue TYS Check reply log for details
> select /A:19
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /A:18
11 atoms, 9 bonds, 2 residues, 2 models selected
> select add /A:17
18 atoms, 15 bonds, 3 residues, 2 models selected
> select add /A:16
24 atoms, 20 bonds, 4 residues, 2 models selected
> select add /A:15
31 atoms, 26 bonds, 5 residues, 2 models selected
> coulombic sel
Coulombic values for 6meoCD4gp160CCR5.pdb_A SES surface #1.4: minimum, -12.46,
mean 0.41, maximum 16.20
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> undo
> hide sel surfaces
> select add /A:14
39 atoms, 33 bonds, 6 residues, 2 models selected
> select add /A:20
48 atoms, 41 bonds, 7 residues, 2 models selected
> select add /A:65
52 atoms, 44 bonds, 8 residues, 2 models selected
> coulombic sel
Coulombic values for 6meoCD4gp160CCR5.pdb_A SES surface #1.4: minimum, -12.46,
mean 0.41, maximum 16.20
To also show corresponding color key, enter the above coulombic command and
add key true
> select add /A:90
61 atoms, 52 bonds, 9 residues, 2 models selected
> coulombic sel
Coulombic values for 6meoCD4gp160CCR5.pdb_A SES surface #1.4: minimum, -12.46,
mean 0.41, maximum 16.20
To also show corresponding color key, enter the above coulombic command and
add key true
> select add /A:89
70 atoms, 60 bonds, 10 residues, 2 models selected
> coulombic sel
Coulombic values for 6meoCD4gp160CCR5.pdb_A SES surface #1.4: minimum, -12.46,
mean 0.41, maximum 16.20
To also show corresponding color key, enter the above coulombic command and
add key true
> select add /A:87
79 atoms, 68 bonds, 11 residues, 2 models selected
> select add /A:88
87 atoms, 75 bonds, 12 residues, 2 models selected
> coulombic sel
Coulombic values for 6meoCD4gp160CCR5.pdb_A SES surface #1.4: minimum, -12.46,
mean 0.41, maximum 16.20
To also show corresponding color key, enter the above coulombic command and
add key true
> select add /A:91
96 atoms, 83 bonds, 13 residues, 2 models selected
> coulombic sel
Coulombic values for 6meoCD4gp160CCR5.pdb_A SES surface #1.4: minimum, -12.46,
mean 0.41, maximum 16.20
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> mlp sel
Map values for surface "6meoCD4gp160CCR5.pdb_A SES surface": minimum -26.95,
mean -5.653, maximum 22.58
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Coulombic values for 6meoCD4gp160CCR5.pdb_A SES surface #1.4: minimum, -12.46,
mean 0.41, maximum 16.20
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> select clear
> select /A:87
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /A:88
17 atoms, 15 bonds, 2 residues, 2 models selected
> show sel atoms
> hide sel atoms
Drag select of 30 atoms, 49 residues, 27 bonds
> mlp sel
Map values for surface "6meoCD4gp160CCR5.pdb_A SES surface": minimum -26.95,
mean -5.653, maximum 22.58
Map values for surface "6meoCD4gp160CCR5.pdb_G SES surface": minimum -28.55,
mean -4.658, maximum 24.7
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Coulombic values for 6meoCD4gp160CCR5.pdb_A SES surface #1.4: minimum, -12.46,
mean 0.41, maximum 16.20
Coulombic values for 6meoCD4gp160CCR5.pdb_G SES surface #1.5: minimum, -20.62,
mean -1.66, maximum 14.94
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> select clear
Drag select of 33 atoms, 35 residues, 29 bonds
> coulombic sel
Coulombic values for 6meoCD4gp160CCR5.pdb_A SES surface #1.4: minimum, -12.46,
mean 0.41, maximum 16.20
Coulombic values for 6meoCD4gp160CCR5.pdb_G SES surface #1.5: minimum, -20.62,
mean -1.66, maximum 14.94
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> undo
> hide sel surfaces
> select clear
Drag select of 1 atoms, 9 residues
> coulombic sel
Coulombic values for 6meoCD4gp160CCR5.pdb_A SES surface #1.4: minimum, -12.46,
mean 0.41, maximum 16.20
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> select clear
Drag select of 10 atoms, 5 residues, 8 bonds
> coulombic sel
Coulombic values for 6meoCD4gp160CCR5.pdb_G SES surface #1.5: minimum, -20.62,
mean -1.66, maximum 14.94
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> select clear
Drag select of 6 atoms, 10 residues, 4 bonds
> coulombic sel
Coulombic values for 6meoCD4gp160CCR5.pdb_A SES surface #1.4: minimum, -12.46,
mean 0.41, maximum 16.20
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> select clear
> select add /A:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /A:31
14 atoms, 12 bonds, 2 residues, 2 models selected
> hbonds sel reveal true
3 hydrogen bonds found
> select clear
> select /A:78
8 atoms, 7 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
1 hydrogen bonds found
> select /A:75
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> save C:/Users/panan/Desktop/ChimeraX/6MEOCD4mutanalysisV2.cxs
——— End of log from Wed Dec 22 13:06:50 2021 ———
opened ChimeraX session
> set bgColor white
> set bgColor gray
> set bgColor black
> select /A
1370 atoms, 1391 bonds, 1 pseudobond, 176 residues, 2 models selected
> hide sel atoms
> color (#!1 & sel) forest green
> select /A
1370 atoms, 1391 bonds, 1 pseudobond, 176 residues, 2 models selected
> select /A:135
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:18,30,32,35,66,138
46 atoms, 40 bonds, 6 residues, 1 model selected
> color (#!1 & sel) cyan
> color (#!1 & sel) blue
> show sel atoms
> select /B
2576 atoms, 2649 bonds, 314 residues, 1 model selected
> select /G
3212 atoms, 3296 bonds, 2 pseudobonds, 406 residues, 2 models selected
> save C:/Users/panan/Desktop/ChimeraX/6MEOCD4mutanalysisV3.cxs
> show sel surfaces
> mlp sel
Map values for surface "6meoCD4gp160CCR5.pdb_G SES surface": minimum -28.55,
mean -4.658, maximum 24.7
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> select /A
1370 atoms, 1391 bonds, 1 pseudobond, 176 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> select /G
3212 atoms, 3296 bonds, 2 pseudobonds, 406 residues, 2 models selected
> show sel surfaces
> select /A:18,30,32,35,66,138
46 atoms, 40 bonds, 6 residues, 1 model selected
> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> label (#!1 & sel) text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select /G
3212 atoms, 3296 bonds, 2 pseudobonds, 406 residues, 2 models selected
> hide sel surfaces
> select clear
> select /G:322
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /G:456
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /G:455
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /G:456
16 atoms, 14 bonds, 2 residues, 2 models selected
> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select /G:193
8 atoms, 7 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select /G:129
8 atoms, 7 bonds, 1 residue, 1 model selected
> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select /A:43
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select /G
3212 atoms, 3296 bonds, 2 pseudobonds, 406 residues, 2 models selected
> show sel surfaces
> select clear
Drag select of 6meoCD4gp160CCR5.pdb_G SES surface, 25117 of 432588 triangles,
cap far, 44 of 1110 triangles, 98 atoms, 45 residues, 100 bonds
> hide sel atoms
Drag select of 6meoCD4gp160CCR5.pdb_G SES surface, 1011 of 432588 triangles,
15 atoms, 16 bonds
> hide sel atoms
> select /G
3212 atoms, 3296 bonds, 2 pseudobonds, 406 residues, 2 models selected
> coulombic sel
Coulombic values for 6meoCD4gp160CCR5.pdb_G SES surface #1.5: minimum, -20.62,
mean -1.66, maximum 14.94
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> select /A:18,30,32,35,66,138
46 atoms, 40 bonds, 6 residues, 1 model selected
> color (#!1 & sel) orange
> select clear
> select /A:18,30,32,35,66,138
46 atoms, 40 bonds, 6 residues, 1 model selected
> color (#!1 & sel) cyan
> select clear
> select /A:18,30,32,35,66,138
46 atoms, 40 bonds, 6 residues, 1 model selected
> color (#!1 & sel) magenta
> select clear
> select /A:18,30,32,35,66,138
46 atoms, 40 bonds, 6 residues, 1 model selected
> color (#!1 & sel) yellow
> select clear
> save C:/Users/panan/Desktop/ChimeraX/6MEOCD4mutanalysisV3.cxs
——— End of log from Mon Jan 31 09:29:36 2022 ———
opened ChimeraX session
> select /G
3212 atoms, 3296 bonds, 2 pseudobonds, 406 residues, 2 models selected
> hide sel surfaces
> select clear
> select /G
3212 atoms, 3296 bonds, 2 pseudobonds, 406 residues, 2 models selected
> surface style #!1.5 solid
> show sel surfaces
> surface style #!1.5 mesh
> surface style #1.5 dot
> surface style #!1.5 solid
> rainbow sel
> undo
> color sel byhetero
> undo
> color (#!1 & sel) orange red
> color (#!1 & sel) orange
> select clear
> save C:/Users/panan/Desktop/ChimeraX/6MEOCD4mutanalysisV3.1.cxs
——— End of log from Mon Jan 31 10:21:07 2022 ———
opened ChimeraX session
> lighting full
> set bgColor white
> set bgColor gray
> set bgColor white
> select /B
2576 atoms, 2649 bonds, 314 residues, 1 model selected
> color (#!1 & sel) red
> select clear
> ui tool show Distances
> select /B:311
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> select /A:111
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /B:313
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:151
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:152
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:114
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:151
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
Exactly two atoms must be selected!
> select /A:110
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:311
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:110 /b:311
20 atoms, 19 bonds, 2 residues, 1 model selected
> ui tool show Distances
> select clear
> select /A:18,30,32,35,66
38 atoms, 33 bonds, 5 residues, 1 model selected
> color (#!1 & sel) cyan
> select clear
> save C:/Users/panan/Desktop/ChimeraX/6MEOCD4mutanalysisV3.2.cxs
——— End of log from Wed Feb 23 22:37:25 2022 ———
opened ChimeraX session
> open "C:/Users/andyp/Documents/Scripps/Farzan lab/B cell editing in vivo
> evolution/eCD4/Modeling/gp120CD4 pdb/6MEOCD4mutanalysisV4.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 725, in restore
obj = sm.restore_snapshot(self, data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1346, in restore_snapshot
s.set_state_from_snapshot(session, data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1353, in set_state_from_snapshot
Structure.set_state_from_snapshot(self, session, data['structure state'])
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\structure.py", line 214, in set_state_from_snapshot
StructureData.set_state_from_snapshot(self, session, data['structure state'])
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1799, in set_state_from_snapshot
f(self._c_pointer, data['version'], tuple(data['ints']),
tuple(data['floats']), tuple(data['misc']))
TypeError: Don't know how to restore new session data; update your version of
ChimeraX
opened ChimeraX session
> open "C:/Users/andyp/Documents/Scripps/Farzan lab/B cell editing in vivo
> evolution/eCD4/Modeling/gp120CD4 pdb/6MEOCD4mutanalysisV4.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 725, in restore
obj = sm.restore_snapshot(self, data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1346, in restore_snapshot
s.set_state_from_snapshot(session, data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1353, in set_state_from_snapshot
Structure.set_state_from_snapshot(self, session, data['structure state'])
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\structure.py", line 214, in set_state_from_snapshot
StructureData.set_state_from_snapshot(self, session, data['structure state'])
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1799, in set_state_from_snapshot
f(self._c_pointer, data['version'], tuple(data['ints']),
tuple(data['floats']), tuple(data['misc']))
TypeError: Don't know how to restore new session data; update your version of
ChimeraX
opened ChimeraX session
OpenGL version: 3.3.0 NVIDIA 512.72
OpenGL renderer: NVIDIA GeForce RTX 3050 Ti Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: XPS 15 9520
OS: Microsoft Windows 11 Home (Build 22000)
Memory: 34,014,814,208
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700H
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
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
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
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
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
File attachment: 6MEOCD4mutanalysisV4.cxs
6MEOCD4mutanalysisV4.cxs
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
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