Changes between Initial Version and Version 2 of Ticket #2902


Ignore:
Timestamp:
Mar 2, 2020, 11:01:47 AM (6 years ago)
Author:
Tom Goddard
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #2902

    • Property Component Unassigned → Input/Output
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Saved image is 1/4
    • Property Version → 0.9

  • Ticket #2902 – Description

    initial v2  
    1111How to cite UCSF ChimeraX 
    1212
    13 > open
    14 /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure4/Enc_DyP_background_transparency3.cxs
    1513
    16 opened ChimeraX session 
    17 
    18 > view orient cofr false
    19 
    20 > lighting simple
    21 
    22 > toolshed show "Side View"
    23 
    24 > lighting soft
    25 
    26 > lighting full
    27 
    28 > lighting soft
    29 
    30 > lighting full
    31 
    32 > lighting soft
    33 
    34 > lighting full
    35 
    36 > open /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final-
    37 coot-2_C2_manualC2.pdb
    38 
    39 Summary of feedback from opening
    40 /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final-
    41 coot-2_C2_manualC2.pdb 
    42 --- 
    43 warnings | Ignored bad PDB record found on line 150 
    44 ALLOWED : 4.56 % 
    45  
    46 Ignored bad PDB record found on line 151 
    47 CIS-PROLINE : 0.0 
    48  
    49 Ignored bad PDB record found on line 152 
    50 CIS-GENERAL : 0.0 
    51  
    52 Ignored bad PDB record found on line 153 
    53 FAVORED : 95.44 % 
    54  
    55 Ignored bad PDB record found on line 154 
    56 OUTLIERS : 0.00 % 
    57  
    58 16 messages similar to the above omitted 
    59  
    60 Chain information for DyP_final-coot-2_C2_manualC2.pdb #2 
    61 --- 
    62 Chain | Description 
    63 A B C D E F G H I J K L | No description available 
    64  
    65 
    66 > hide #!2 models
    67 
    68 > lighting simple
    69 
    70 > show #!2 models
    71 
    72 > hide #!3 models
    73 
    74 > show #!3 models
    75 
    76 > hide #!2 models
    77 
    78 > show #!2 models
    79 
    80 > hide #!3 models
    81 
    82 > select #2
    83 
    84 29124 atoms, 29880 bonds, 48 pseudobonds, 1 model selected 
    85 
    86 > style selAtoms stick
    87 
    88 Changed 29124 atom styles 
    89 
    90 > show selAtoms ribbons
    91 
    92 > hide selAtoms
    93 
    94 > select clear
    95 
    96 > lighting soft
    97 
    98 > close session
    99 
    100 > open
    101 /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure4/Enc_DyP_background_transparency3.cxs
    102 
    103 opened ChimeraX session 
    104 
    105 > close session
    106 
    107 > open /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Enc_final_I1.pdb
    108 
    109 Summary of feedback from opening
    110 /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Enc_final_I1.pdb 
    111 --- 
    112 warnings | Ignored bad PDB record found on line 242 
    113 ALLOWED : 3.80 % 
    114  
    115 Ignored bad PDB record found on line 243 
    116 CIS-PROLINE : 0.0 
    117  
    118 Ignored bad PDB record found on line 244 
    119 CIS-GENERAL : 0.0 
    120  
    121 Ignored bad PDB record found on line 245 
    122 FAVORED : 95.44 % 
    123  
    124 Ignored bad PDB record found on line 246 
    125 OUTLIERS : 0.76 % 
    126  
    127 16 messages similar to the above omitted 
    128  
    129 Chain information for Enc_final_I1.pdb 
    130 --- 
    131 Chain | Description 
    132 1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
    133 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A 1.22/A 1.23/A
    134 1.24/A 1.25/A 1.26/A 1.27/A 1.28/A 1.29/A 1.30/A 1.31/A 1.32/A 1.33/A 1.34/A
    135 1.35/A 1.36/A 1.37/A 1.38/A 1.39/A 1.40/A 1.41/A 1.42/A 1.43/A 1.44/A 1.45/A
    136 1.46/A 1.47/A 1.48/A 1.49/A 1.50/A 1.51/A 1.52/A 1.53/A 1.54/A 1.55/A 1.56/A
    137 1.57/A 1.58/A 1.59/A 1.60/A | No description available 
    138  
    139 
    140 > lighting simple
    141 
    142 > close session
    143 
    144 > open
    145 /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure2/shell_outside_cartoon.cxs
    146 
    147 opened ChimeraX session 
    148 
    149 > lighting simple
    150 
    151 > select #1.41
    152 
    153 2025 atoms, 2067 bonds, 1 model selected 
    154 
    155 > select clear
    156 
    157 > lighting simple
    158 
    159 > lighting simple
    160 
    161 > view orient cofr false
    162 
    163 > open /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final-
    164 coot-2_C2_manualC2.pdb
    165 
    166 Summary of feedback from opening
    167 /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final-
    168 coot-2_C2_manualC2.pdb 
    169 --- 
    170 warnings | Ignored bad PDB record found on line 150 
    171 ALLOWED : 4.56 % 
    172  
    173 Ignored bad PDB record found on line 151 
    174 CIS-PROLINE : 0.0 
    175  
    176 Ignored bad PDB record found on line 152 
    177 CIS-GENERAL : 0.0 
    178  
    179 Ignored bad PDB record found on line 153 
    180 FAVORED : 95.44 % 
    181  
    182 Ignored bad PDB record found on line 154 
    183 OUTLIERS : 0.00 % 
    184  
    185 16 messages similar to the above omitted 
    186  
    187 Chain information for DyP_final-coot-2_C2_manualC2.pdb #2 
    188 --- 
    189 Chain | Description 
    190 A B C D E F G H I J K L | No description available 
    191  
    192 
    193 > style selAtoms stick
    194 
    195 Changed 150624 atom styles 
    196 
    197 > select #2
    198 
    199 29124 atoms, 29880 bonds, 48 pseudobonds, 1 model selected 
    200 
    201 > show selAtoms ribbons
    202 
    203 > hide selAtoms
    204 
    205 > close #2
    206 
    207 > open /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final-
    208 coot-3_C2expand.pdb
    209 
    210 Summary of feedback from opening
    211 /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final-
    212 coot-3_C2expand.pdb 
    213 --- 
    214 warnings | Ignored bad PDB record found on line 150 
    215 ALLOWED : 4.56 % 
    216  
    217 Ignored bad PDB record found on line 151 
    218 CIS-PROLINE : 0.0 
    219  
    220 Ignored bad PDB record found on line 152 
    221 CIS-GENERAL : 0.0 
    222  
    223 Ignored bad PDB record found on line 153 
    224 FAVORED : 95.44 % 
    225  
    226 Ignored bad PDB record found on line 154 
    227 OUTLIERS : 0.00 % 
    228  
    229 16 messages similar to the above omitted 
    230  
    231 Chain information for DyP_final-coot-3_C2expand.pdb 
    232 --- 
    233 Chain | Description 
    234 2.1/A 2.2/A 2.1/B 2.2/B 2.1/C 2.2/C 2.1/D 2.2/D 2.1/E 2.2/E 2.1/F 2.2/F | No
    235 description available 
    236  
    237 
    238 > style selAtoms stick
    239 
    240 Changed 150624 atom styles 
    241 
    242 > show selAtoms
    243 
    244 > close session
    245 
    246 > open
    247 /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure2/shell_outside_cartoon.cxs
    248 
    249 opened ChimeraX session 
    250 
    251 > view orient cofr false
    252 
    253 > open /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final-
    254 coot-3_C2expand.pdb
    255 
    256 Summary of feedback from opening
    257 /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final-
    258 coot-3_C2expand.pdb 
    259 --- 
    260 warnings | Ignored bad PDB record found on line 150 
    261 ALLOWED : 4.56 % 
    262  
    263 Ignored bad PDB record found on line 151 
    264 CIS-PROLINE : 0.0 
    265  
    266 Ignored bad PDB record found on line 152 
    267 CIS-GENERAL : 0.0 
    268  
    269 Ignored bad PDB record found on line 153 
    270 FAVORED : 95.44 % 
    271  
    272 Ignored bad PDB record found on line 154 
    273 OUTLIERS : 0.00 % 
    274  
    275 16 messages similar to the above omitted 
    276  
    277 Chain information for DyP_final-coot-3_C2expand.pdb 
    278 --- 
    279 Chain | Description 
    280 2.1/A 2.2/A 2.1/B 2.2/B 2.1/C 2.2/C 2.1/D 2.2/D 2.1/E 2.2/E 2.1/F 2.2/F | No
    281 description available 
    282  
    283 
    284 > lighting simple
    285 
    286 > select #1.41
    287 
    288 2025 atoms, 2067 bonds, 1 model selected 
    289 
    290 > select clear
    291 
    292 > select clear
    293 
    294 > select #2
    295 
    296 29124 atoms, 29880 bonds, 48 pseudobonds, 3 models selected 
    297 
    298 > show selAtoms ribbons
    299 
    300 > style selAtoms stick
    301 
    302 Changed 29124 atom styles 
    303 
    304 > hide selAtoms
    305 
    306 > hide selAtoms
    307 
    308 > show selAtoms ribbons
    309 
    310 > hide selAtoms surfaces
    311 
    312 > select clear
    313 
    314 > toolshed show "Side View"
    315 
    316 > lighting full
    317 
    318 > lighting soft
    319 
    320 > lighting simple
    321 
    322 > lighting soft
    323 
    324 > lighting full
    325 
    326 > lighting simple
    327 
    328 > select #1
    329 
    330 121500 atoms, 124020 bonds, 1 model selected 
    331 
    332 > hide selAtoms ribbons
    333 
    334 > show selAtoms surfaces
    335 
    336 > select clear
    337 
    338 > select #1
    339 
    340 121500 atoms, 124020 bonds, 45 models selected 
    341 
    342 > hide selAtoms surfaces
    343 
    344 > show selAtoms ribbons
    345 
    346 > select clear
    347 
    348 > select #2
    349 
    350 29124 atoms, 29880 bonds, 48 pseudobonds, 3 models selected 
    351 
    352 > preset cartoons/nucleotides cylinders/stubs
    353 
    354 Changed 0 atom styles 
    355 Preset expands to these ChimeraX commands: surf hide; style
    356 (protein|nucleic|solvent) & @@draw_mode=0 stick; cartoon; cartoon style modeh
    357 def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20;
    358 cartoon style ~(nucleic|strand) x round; cartoon style (nucleic|strand) x
    359 rect; cartoon style protein modeh tube rad 2 sides 24 thick 0.6; cartoon style
    360 nucleic x round width 1.6 thick 1.6; nucleotides stubs 
    361 
    362 > select clear
    363 
    364 > lighting simple
    365 
    366 > lighting simple
    367 
    368 > open /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final-
    369 coot-2_C2_manualC2.pdb
    370 
    371 Summary of feedback from opening
    372 /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final-
    373 coot-2_C2_manualC2.pdb 
    374 --- 
    375 warnings | Ignored bad PDB record found on line 150 
    376 ALLOWED : 4.56 % 
    377  
    378 Ignored bad PDB record found on line 151 
    379 CIS-PROLINE : 0.0 
    380  
    381 Ignored bad PDB record found on line 152 
    382 CIS-GENERAL : 0.0 
    383  
    384 Ignored bad PDB record found on line 153 
    385 FAVORED : 95.44 % 
    386  
    387 Ignored bad PDB record found on line 154 
    388 OUTLIERS : 0.00 % 
    389  
    390 16 messages similar to the above omitted 
    391  
    392 Chain information for DyP_final-coot-2_C2_manualC2.pdb #3 
    393 --- 
    394 Chain | Description 
    395 A B C D E F G H I J K L | No description available 
    396  
    397 
    398 > view orient cofr false
    399 
    400 > close #3
    401 
    402 > lighting soft
    403 
    404 > lighting full
    405 
    406 > lighting simple
    407 
    408 > lighting soft
    409 
    410 > lighting full
    411 
    412 > lighting simple
    413 
    414 > set silhouettes true
    415 
    416 > set silhouettes false
    417 
    418 > lighting shadows true
    419 
    420 > lighting simple
    421 
    422 > lighting shadows true
    423 
    424 > lighting full
    425 
    426 > lighting simple
    427 
    428 > lighting simple
    429 
    430 > lighting simple
    431 
    432 > lighting shadows true
    433 
    434 > lighting shadows false
    435 
    436 > lighting shadows true
    437 
    438 > view orient cofr false
    439 
    440 > lighting simple
    441 
    442 > lighting simple
    443 
    444 > lighting simple
    445 
    446 > open /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final-
    447 coot-0_manualC2.pdb
    448 
    449 Summary of feedback from opening
    450 /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final-
    451 coot-0_manualC2.pdb 
    452 --- 
    453 warnings | Ignored bad PDB record found on line 156 
    454 ALLOWED : 4.23 % 
    455  
    456 Ignored bad PDB record found on line 157 
    457 CIS-PROLINE : 0.0 
    458  
    459 Ignored bad PDB record found on line 158 
    460 CIS-GENERAL : 0.0 
    461  
    462 Ignored bad PDB record found on line 159 
    463 FAVORED : 95.77 % 
    464  
    465 Ignored bad PDB record found on line 160 
    466 OUTLIERS : 0.00 % 
    467  
    468 16 messages similar to the above omitted 
    469  
    470 Chain information for DyP_final-coot-0_manualC2.pdb #3 
    471 --- 
    472 Chain | Description 
    473 A B C D E F G H I J K L | No description available 
    474  
    475 
    476 > close #3
    477 
    478 > open
    479 /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/RSrefine_4gu7_coot-0_chainA_expand12_real_space_refined-
    480 coot-1.pdb
    481 
    482 Summary of feedback from opening
    483 /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/RSrefine_4gu7_coot-0_chainA_expand12_real_space_refined-
    484 coot-1.pdb 
    485 --- 
    486 warnings | Ignored bad PDB record found on line 32 
    487 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 
    488  
    489 Ignored bad PDB record found on line 33 
    490 DEVIATIONS FROM IDEAL VALUES. 
    491  
    492 Ignored bad PDB record found on line 34 
    493 BOND : 0.007 0.050 29904 
    494  
    495 Ignored bad PDB record found on line 35 
    496 ANGLE : 0.851 10.479 40908 
    497  
    498 Ignored bad PDB record found on line 36 
    499 CHIRALITY : 0.051 0.241 4392 
    500  
    501 16 messages similar to the above omitted 
    502  
    503 Chain information for RSrefine_4gu7_coot-0_chainA_expand12_real_space_refined-
    504 coot-1.pdb #3 
    505 --- 
    506 Chain | Description 
    507 A B C D E F G H I J K L | No description available 
    508  
    509 
    510 > select #3
    511 
    512 29102 atoms, 29859 bonds, 48 pseudobonds, 1 model selected 
    513 
    514 > style selAtoms stick
    515 
    516 Changed 29102 atom styles 
    517 
    518 > show selAtoms ribbons
    519 
    520 > hide selAtoms
    521 
    522 > select clear
    523 
    524 > close session
    525 
    526 > open /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure3/Enc-DyP_map.cxs
    527 
    528 opened ChimeraX session 
    529 
    530 > close session
    531 
    532 > open
    533 /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure4/DyP_2hexamer_interaction_1.cxs
    534 
    535 opened ChimeraX session 
    536 
    537 > open /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Enc_final_I1.pdb
    538 
    539 Summary of feedback from opening
    540 /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Enc_final_I1.pdb 
    541 --- 
    542 warnings | Ignored bad PDB record found on line 242 
    543 ALLOWED : 3.80 % 
    544  
    545 Ignored bad PDB record found on line 243 
    546 CIS-PROLINE : 0.0 
    547  
    548 Ignored bad PDB record found on line 244 
    549 CIS-GENERAL : 0.0 
    550  
    551 Ignored bad PDB record found on line 245 
    552 FAVORED : 95.44 % 
    553  
    554 Ignored bad PDB record found on line 246 
    555 OUTLIERS : 0.76 % 
    556  
    557 16 messages similar to the above omitted 
    558  
    559 Chain information for Enc_final_I1.pdb 
    560 --- 
    561 Chain | Description 
    562 2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A 2.11/A 2.12/A
    563 2.13/A 2.14/A 2.15/A 2.16/A 2.17/A 2.18/A 2.19/A 2.20/A 2.21/A 2.22/A 2.23/A
    564 2.24/A 2.25/A 2.26/A 2.27/A 2.28/A 2.29/A 2.30/A 2.31/A 2.32/A 2.33/A 2.34/A
    565 2.35/A 2.36/A 2.37/A 2.38/A 2.39/A 2.40/A 2.41/A 2.42/A 2.43/A 2.44/A 2.45/A
    566 2.46/A 2.47/A 2.48/A 2.49/A 2.50/A 2.51/A 2.52/A 2.53/A 2.54/A 2.55/A 2.56/A
    567 2.57/A 2.58/A 2.59/A 2.60/A | No description available 
    568  
    569 
    570 > lighting simple
    571 
    572 > view orient cofr false
    573 
    574 > view orient cofr false
    575 
    576 > view orient cofr false
    577 
    578 > hide #!1.1 models
    579 
    580 > open /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final-
    581 coot-3_C2expand.pdb
    582 
    583 Summary of feedback from opening
    584 /Users/Peter_Higgs_Mu/Downloads/Cargo/phenix_4gu7/DyP_final-
    585 coot-3_C2expand.pdb 
    586 --- 
    587 warnings | Ignored bad PDB record found on line 150 
    588 ALLOWED : 4.56 % 
    589  
    590 Ignored bad PDB record found on line 151 
    591 CIS-PROLINE : 0.0 
    592  
    593 Ignored bad PDB record found on line 152 
    594 CIS-GENERAL : 0.0 
    595  
    596 Ignored bad PDB record found on line 153 
    597 FAVORED : 95.44 % 
    598  
    599 Ignored bad PDB record found on line 154 
    600 OUTLIERS : 0.00 % 
    601  
    602 16 messages similar to the above omitted 
    603  
    604 Chain information for DyP_final-coot-3_C2expand.pdb 
    605 --- 
    606 Chain | Description 
    607 3.1/A 3.2/A 3.1/B 3.2/B 3.1/C 3.2/C 3.1/D 3.2/D 3.1/E 3.2/E 3.1/F 3.2/F | No
    608 description available 
    609  
    610 
    611 > hide #!3.2 models
    612 
    613 > show #!1.1 models
    614 
    615 > hide #!1.1 models
    616 
    617 > select #1.1
    618 
    619 14562 atoms, 14942 bonds, 28 pseudobonds, 3 models selected 
    620 
    621 > show selAtoms ribbons
    622 
    623 > hide selAtoms ribbons
    624 
    625 > show selAtoms
    626 
    627 > hide selAtoms surfaces
    628 
    629 > style selAtoms sphere
    630 
    631 Changed 14562 atom styles 
    632 
    633 > hide #!3 models
    634 
    635 > show #!3 models
    636 
    637 > hide #!3 models
    638 
    639 > select #1.1
    640 
    641 14562 atoms, 14942 bonds, 28 pseudobonds, 3 models selected 
    642 
    643 > select #1.1
    644 
    645 14562 atoms, 14942 bonds, 28 pseudobonds, 3 models selected 
    646 
    647 > show #!1.1 models
    648 
    649 > show #!3 models
    650 
    651 > hide #!3 models
    652 
    653 > select clear
    654 
    655 > hide #!2 models
    656 
    657 > hide #!3.1 models
    658 
    659 > show #!3.1 models
    660 
    661 > hide #!3.1 models
    662 
    663 > show #!3.1 models
    664 
    665 > hide #!3.1 models
    666 
    667 > show #!3.1 models
    668 
    669 > hide #!3.1 models
    670 
    671 > hide #!3 models
    672 
    673 > show #!3 models
    674 
    675 > hide #!3 models
    676 
    677 > show #!3 models
    678 
    679 > show #!3.1 models
    680 
    681 > hide #!3.1 models
    682 
    683 > show #!3.1 models
    684 
    685 > hide #!3.1 models
    686 
    687 > show #!3.1 models
    688 
    689 > hide #!3.1 models
    690 
    691 > show #!3.1 models
    692 
    693 > hide #!3.1 models
    694 
    695 > show #!3.1 models
    696 
    697 > hide #!3.1 models
    698 
    699 > show #!3.1 models
    700 
    701 > hide #!3.1 models
    702 
    703 > show #!3.1 models
    704 
    705 > hide #!3.1 models
    706 
    707 > show #!3.1 models
    708 
    709 > hide #!3.1 models
    710 
    711 > show #!3.2 models
    712 
    713 > show #!3.1 models
    714 
    715 > hide #!3.2 models
    716 
    717 > show #!3.2 models
    718 
    719 > hide #!1.1 models
    720 
    721 > show #!1.1 models
    722 
    723 > hide #!1.2 models
    724 
    725 > color #3.2/D #371e72
    726 
    727 > show #!1.2 models
    728 
    729 > hide #!1.2 models
    730 
    731 > color #3.2/C #1b5689
    732 
    733 > show #!1.2 models
    734 
    735 > hide #!1.2 models
    736 
    737 > color #3.2/F #c6495c
    738 
    739 > show #!1.2 models
    740 
    741 > hide #!1.2 models
    742 
    743 > color #3.2/B #fffd90
    744 
    745 > show #!1.2 models
    746 
    747 > hide #!1.2 models
    748 
    749 > color #3.2/A #49e177
    750 
    751 > show #!1.2 models
    752 
    753 > hide #!1.2 models
    754 
    755 > color #3.2/E #6d8a16
    756 
    757 > hide #!1 models
    758 
    759 > show #!1 models
    760 
    761 > close #1
    762 
    763 > show #!2 models
    764 
    765 > hide #!2 models
    766 
    767 > show #!2 models
    768 
    769 > show #!2 models
    770 
    771 > view orient cofr false
    772 
    773 > view cofr false
    774 
    775 > view cofr false
    776 
    777 > view orient cofr false
    778 
    779 > view orient cofr false
    780 
    781 > view cofr false
    782 
    783 > select #2
    784 
    785 121500 atoms, 124020 bonds, 1 model selected 
    786 
    787 > preset cartoons/nucleotides cylinders/stubs
    788 
    789 Changed 28608 atom styles 
    790 Preset expands to these ChimeraX commands: surf hide; style
    791 (protein|nucleic|solvent) & @@draw_mode=0 stick; cartoon; cartoon style modeh
    792 def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20;
    793 cartoon style ~(nucleic|strand) x round; cartoon style (nucleic|strand) x
    794 rect; cartoon style protein modeh tube rad 2 sides 24 thick 0.6; cartoon style
    795 nucleic x round width 1.6 thick 1.6; nucleotides stubs 
    796 
    797 > select clear
    798 
    799 > select #3
    800 
    801 29124 atoms, 29880 bonds, 48 pseudobonds, 3 models selected 
    802 
    803 > hide selAtoms
    804 
    805 > hide selAtoms
    806 
    807 > hide selAtoms surfaces
    808 
    809 > select #2
    810 
    811 121500 atoms, 124020 bonds, 1 model selected 
    812 
    813 > hide selAtoms surfaces
    814 
    815 > hide selAtoms
    816 
    817 > select #3
    818 
    819 29124 atoms, 29880 bonds, 48 pseudobonds, 3 models selected 
    820 
    821 > toolshed show "Side View"
    822 
    823 > view orient cofr false
    824 
    825 > view cofr false
    826 
    827 > view orient cofr false
    828 
    829 > select clear
    830 
    831 > lighting shadows true
    832 
    833 > lighting full
    834 
    835 > lighting soft
    836 
    837 > lighting full
    838 
    839 > lighting soft
    840 
    841 > lighting simple
    842 
    843 > lighting simple
    844 
    845 > lighting simple
    846 
    847 > lighting simple
    848 
    849 > set silhouettes true
    850 
    851 > set silhouettes false
    852 
    853 > set silhouettes true
    854 
    855 > set silhouettes false
    856 
    857 > lighting simple
    858 
    859 > lighting flat
    860 
    861 > lighting flat
    862 
    863 > lighting simple
    864 
    865 > lighting simple
    866 
    867 > lighting simple
    868 
    869 > set silhouettes false
    870 
    871 > lighting simple
    872 
    873 > lighting simple
    874 
    875 > lighting shadows true
    876 
    877 > lighting shadows false
    878 
    879 > lighting shadows true
    880 
    881 > lighting shadows false
    882 
    883 > lighting shadows true
    884 
    885 > lighting shadows false
    886 
    887 Unknown command: scale 1.1 
    888 
    889 > windowsize
    890 
    891 window size 864 682 
    892 
    893 > windowsize 1080 1080
    894 
    895 > windowsize
    896 
    897 window size 1080 682 
    898 
    899 > windowsize 864 682
    900 
    901 > windowsize 864 682
    902 
    903 > windowsize
    904 
    905 window size 864 682 
    906 
    907 > lighting shadows true
    908 
    909 > lighting shadows false
    910 
    911 > lighting shadows true
    912 
    913 > lighting shadows false
    914 
    915 > lighting shadows true
    916 
    917 > lighting simple
    918 
    919 > lighting simple
    920 
    921 > lighting simple
    922 
    923 > lighting simple
    924 
    925 > lighting simple
    926 
    927 > lighting simple
    928 
    929 > lighting shadows true
    930 
    931 > lighting shadows false
    932 
    933 > lighting simple
    934 
    935 > lighting simple
    936 
    937 > lighting simple
    938 
    939 > lighting simple
    940 
    941 > lighting simple
    942 
    943 > lighting shadows true
    944 
    945 > lighting shadows false
    946 
    947 > lighting flat
    948 
    949 > lighting flat
    950 
    951 > lighting simple
    952 
    953 > lighting flat
    954 
    955 > lighting simple
    956 
    957 > lighting simple
    958 
    959 > set silhouettes false
    960 
    961 > lighting simple
    962 
    963 > lighting simple
    964 
    965 > lighting simple
    966 
    967 > lighting simple
    968 
    969 > lighting simple
    970 
    971 > lighting simple
    972 
    973 > lighting simple
    974 
    975 > lighting shadows true
    976 
    977 > lighting shadows false
    978 
    979 > set silhouettes true
    980 
    981 > set silhouettes false
    982 
    983 > lighting simple
    984 
    985 > lighting simple
    986 
    987 > windowsize
    988 
    989 window size 864 682 
    990 
    991 > save session
    992 /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure4/DyP_2hexamer_interaction_overall.cxs
    993 
    994 > save
    995 /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure4/DyP_2hexamer_interaction_overall.png
    996 transparentBackground true supersample 3
    997 
    998 > close session
    999 
    1000 > open
    1001 /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure4/DyP_2hexamer_interaction_overall.cxs
    1002 
    1003 opened ChimeraX session 
    1004 
    1005 > save
    1006 /Users/Peter_Higgs_Mu/Downloads/Cargo/Figures/Figure4/DyP_2hexamer_interaction_overall.png
    1007 transparentBackground true supersample 3
    1008 
    1009 > windowsize
    1010 
    1011 window size 864 682 
    1012 
    1013 > close session
    1014 
    1015 
    1016 
     14Deleted log contents at user's request ticket #2903.
    101715
    101816OpenGL version: 4.1 ATI-3.5.5