| 3038 | | > color #1 green |
| 3039 | | |
| 3040 | | > color #2 tan |
| 3041 | | |
| 3042 | | > color ~C byatom |
| 3043 | | |
| 3044 | | > ~display |
| 3045 | | |
| 3046 | | > display #1:138 #2:176 |
| 3047 | | |
| 3048 | | > style stick |
| 3049 | | |
| 3050 | | Changed 4099 atom styles |
| 3051 | | |
| 3052 | | > ribbon |
| 3053 | | |
| 3054 | | > transparency 60 target r |
| 3055 | | |
| 3056 | | > view |
| 3057 | | |
| 3058 | | > size #1:138 #2:176 stickRadius 0.3 |
| 3059 | | |
| 3060 | | Changed 14 bond radii |
| 3061 | | |
| 3062 | | > ~select |
| 3063 | | |
| 3064 | | Nothing selected |
| 3065 | | |
| 3066 | | > save fig1.jpg |
| 3067 | | |
| 3068 | | > select #1@ca & #1:138@ca @< 7.5 |
| 3069 | | |
| 3070 | | 13 atoms, 1 model selected |
| 3071 | | |
| 3072 | | > select #1,2 & sel :< 2 |
| 3073 | | |
| 3074 | | 204 atoms, 197 bonds, 2 models selected |
| 3075 | | |
| 3076 | | > display sel |
| 3077 | | |
| 3078 | | > wait |
| 3079 | | |
| 3080 | | wait requires a frame count argument unless motion is in progress |
| 3081 | | |
| 3082 | | > color ~C byatom |
| 3083 | | |
| 3084 | | > style stick |
| 3085 | | |
| 3086 | | Changed 4099 atom styles |
| 3087 | | |
| 3088 | | > view #1:138 :< 5 pad -1 |
| 3089 | | |
| 3090 | | > hbonds #1:138 & #1 |
| 3091 | | |
| 3092 | | 3 hydrogen bonds found |
| 3093 | | |
| 3094 | | > hbonds #2:176 & #2 |
| 3095 | | |
| 3096 | | 4 hydrogen bonds found |
| 3097 | | |
| 3098 | | > transparency 90 target r |
| 3099 | | |
| 3100 | | > label #1:138 #2:176 offset 1,-1,1 |
| 3101 | | |
| 3102 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .92 |
| 3103 | | |
| 3104 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 3105 | | |
| 3106 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2 |
| 3107 | | > color green bgColor white |
| 3108 | | |
| 3109 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 3110 | | > color tan bgColor white |
| 3111 | | |
| 3112 | | > ~select |
| 3113 | | |
| 3114 | | Nothing selected |
| 3115 | | |
| 3116 | | > save fig2.jpg |
| 3117 | | |
| 3118 | | > ~ribbon |
| 3119 | | |
| 3120 | | > size stickRadius 0.05 |
| 3121 | | |
| 3122 | | Changed 4167 bond radii |
| 3123 | | |
| 3124 | | > size #1:138 stickRadius 0.2 |
| 3125 | | |
| 3126 | | Changed 7 bond radii |
| 3127 | | |
| 3128 | | > size #2:176 stickRadius 0.2 |
| 3129 | | |
| 3130 | | Changed 7 bond radii |
| 3131 | | |
| 3132 | | > save fig3.jpg |
| 3133 | | |
| 3134 | | > label #1:138 :< 5 & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 3135 | | |
| 3136 | | > label #2:176 :< 5 & #2 height 0.4 offset 0,1,0 color tan bgColor white |
| 3137 | | |
| 3138 | | > view #1:138 :< 5 pad -1 |
| 3139 | | |
| 3140 | | > ~select |
| 3141 | | |
| 3142 | | Nothing selected |
| 3143 | | |
| 3144 | | > save fig4.jpg |
| 3145 | | |
| 3146 | | > select #1@ca & #1:138@ca @< 7.5 |
| 3147 | | |
| 3148 | | 13 atoms, 1 model selected |
| 3149 | | |
| 3150 | | > select #1,2@ca & sel @< 1 |
| 3151 | | |
| 3152 | | 24 atoms, 2 models selected |
| 3153 | | |
| 3154 | | > align #2 & sel toAtoms #1 & sel |
| 3155 | | |
| 3156 | | Unequal number of atoms to pair, 11 and 13 |
| 3157 | | |
| 3158 | | > open "/Users/admin/Dropbox (Technion |
| 3159 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 3160 | | |
| 3161 | | > close |
| 3162 | | |
| 3163 | | > graphics bgColor white |
| 3164 | | |
| 3165 | | > open 1WMB |
| 3166 | | |
| 3167 | | 1wmb title: |
| 3168 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 3169 | | info...] |
| 3170 | | |
| 3171 | | Chain information for 1wmb #1 |
| 3172 | | --- |
| 3173 | | Chain | Description |
| 3174 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 3175 | | |
| 3176 | | Non-standard residues in 1wmb #1 |
| 3177 | | --- |
| 3178 | | CAC — cacodylate ion (dimethylarsinate) |
| 3179 | | MG — magnesium ion |
| 3180 | | |
| 3181 | | 1wmb mmCIF Assemblies |
| 3182 | | --- |
| 3183 | | 1| author_and_software_defined_assembly |
| 3184 | | |
| 3185 | | |
| 3186 | | > open 3I3O |
| 3187 | | |
| 3188 | | 3i3o title: |
| 3189 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 3190 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 3191 | | info...] |
| 3192 | | |
| 3193 | | Chain information for 3i3o #2 |
| 3194 | | --- |
| 3195 | | Chain | Description |
| 3196 | | A B C D E F G H | Short chain dehydrogenase |
| 3197 | | |
| 3198 | | Non-standard residues in 3i3o #2 |
| 3199 | | --- |
| 3200 | | CAC — cacodylate ion (dimethylarsinate) |
| 3201 | | CL — chloride ion |
| 3202 | | MG — magnesium ion |
| 3203 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 3204 | | |
| 3205 | | 3i3o mmCIF Assemblies |
| 3206 | | --- |
| 3207 | | 1| author_and_software_defined_assembly |
| 3208 | | 2| author_and_software_defined_assembly |
| 3209 | | |
| 3210 | | |
| 3211 | | > delete ~/a |
| 3212 | | |
| 3213 | | > delete solvent |
| 3214 | | |
| 3215 | | > mmaker #2 to #1 |
| 3216 | | |
| 3217 | | Parameters |
| 3218 | | --- |
| 3219 | | Chain pairing | bb |
| 3220 | | Alignment algorithm | Needleman-Wunsch |
| 3221 | | Similarity matrix | BLOSUM-62 |
| 3222 | | SS fraction | 0.3 |
| 3223 | | Gap open (HH/SS/other) | 18/18/6 |
| 3224 | | Gap extend | 1 |
| 3225 | | SS matrix | | | H | S | O |
| 3226 | | ---|---|---|--- |
| 3227 | | H | 6 | -9 | -6 |
| 3228 | | S | | 6 | -6 |
| 3229 | | O | | | 4 |
| 3230 | | Iteration cutoff | 2 |
| 3231 | | |
| 3232 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 3233 | | score = 499.7 |
| 3234 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 3235 | | 3.736) |
| 3236 | | |
| 3237 | | |
| 3238 | | > color #1 green |
| 3239 | | |
| 3240 | | > color #2 tan |
| 3241 | | |
| 3242 | | > color ~C byatom |
| 3243 | | |
| 3244 | | > ~display |
| 3245 | | |
| 3246 | | > display #1:138 #2:176 |
| 3247 | | |
| 3248 | | > style stick |
| 3249 | | |
| 3250 | | Changed 4099 atom styles |
| 3251 | | |
| 3252 | | > ribbon |
| 3253 | | |
| 3254 | | > transparency 60 target r |
| 3255 | | |
| 3256 | | > view |
| 3257 | | |
| 3258 | | > size #1:138 #2:176 stickRadius 0.3 |
| 3259 | | |
| 3260 | | Changed 14 bond radii |
| 3261 | | |
| 3262 | | > ~select |
| 3263 | | |
| 3264 | | Nothing selected |
| 3265 | | |
| 3266 | | > save fig1.jpg |
| 3267 | | |
| 3268 | | > select #1@ca & #1:138@ca @< 7.5 |
| 3269 | | |
| 3270 | | 13 atoms, 1 model selected |
| 3271 | | |
| 3272 | | > select #1,2 & sel :< 2 |
| 3273 | | |
| 3274 | | 204 atoms, 197 bonds, 2 models selected |
| 3275 | | |
| 3276 | | > display sel |
| 3277 | | |
| 3278 | | > stop |
| 3279 | | |
| 3280 | | > color ~C byatom |
| 3281 | | |
| 3282 | | > style stick |
| 3283 | | |
| 3284 | | Changed 4099 atom styles |
| 3285 | | |
| 3286 | | > view #1:138 :< 5 pad -1 |
| 3287 | | |
| 3288 | | > hbonds #1:138 & #1 |
| 3289 | | |
| 3290 | | 3 hydrogen bonds found |
| 3291 | | |
| 3292 | | > hbonds #2:176 & #2 |
| 3293 | | |
| 3294 | | 4 hydrogen bonds found |
| 3295 | | |
| 3296 | | > transparency 90 target r |
| 3297 | | |
| 3298 | | > label #1:138 #2:176 offset 1,-1,1 |
| 3299 | | |
| 3300 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .92 |
| 3301 | | |
| 3302 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 3303 | | |
| 3304 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2 |
| 3305 | | > color green bgColor white |
| 3306 | | |
| 3307 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 3308 | | > color tan bgColor white |
| 3309 | | |
| 3310 | | > ~select |
| 3311 | | |
| 3312 | | Nothing selected |
| 3313 | | |
| 3314 | | > save fig2.jpg |
| 3315 | | |
| 3316 | | > ~ribbon |
| 3317 | | |
| 3318 | | > size stickRadius 0.05 |
| 3319 | | |
| 3320 | | Changed 4167 bond radii |
| 3321 | | |
| 3322 | | > size #1:138 stickRadius 0.2 |
| 3323 | | |
| 3324 | | Changed 7 bond radii |
| 3325 | | |
| 3326 | | > size #2:176 stickRadius 0.2 |
| 3327 | | |
| 3328 | | Changed 7 bond radii |
| 3329 | | |
| 3330 | | > save fig3.jpg |
| 3331 | | |
| 3332 | | > label #1:138 :< 5 & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 3333 | | |
| 3334 | | > label #2:176 :< 5 & #2 height 0.4 offset 0,1,0 color tan bgColor white |
| 3335 | | |
| 3336 | | > view #1:138 :< 5 pad -1 |
| 3337 | | |
| 3338 | | > ~select |
| 3339 | | |
| 3340 | | Nothing selected |
| 3341 | | |
| 3342 | | > save fig4.jpg |
| 3343 | | |
| 3344 | | > select #1@ca & #1:138@ca @< 7.5 |
| 3345 | | |
| 3346 | | 13 atoms, 1 model selected |
| 3347 | | |
| 3348 | | > select #1,2@ca & sel @< 1 |
| 3349 | | |
| 3350 | | 24 atoms, 2 models selected |
| 3351 | | |
| 3352 | | > align #2 & sel toAtoms #1 & sel |
| 3353 | | |
| 3354 | | Unequal number of atoms to pair, 11 and 13 |
| 3355 | | |
| 3356 | | > close |
| 3357 | | |
| 3358 | | > open 1WMB |
| 3359 | | |
| 3360 | | 1wmb title: |
| 3361 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 3362 | | info...] |
| 3363 | | |
| 3364 | | Chain information for 1wmb #1 |
| 3365 | | --- |
| 3366 | | Chain | Description |
| 3367 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 3368 | | |
| 3369 | | Non-standard residues in 1wmb #1 |
| 3370 | | --- |
| 3371 | | CAC — cacodylate ion (dimethylarsinate) |
| 3372 | | MG — magnesium ion |
| 3373 | | |
| 3374 | | 1wmb mmCIF Assemblies |
| 3375 | | --- |
| 3376 | | 1| author_and_software_defined_assembly |
| 3377 | | |
| 3378 | | |
| 3379 | | > open 3I3O |
| 3380 | | |
| 3381 | | 3i3o title: |
| 3382 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 3383 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 3384 | | info...] |
| 3385 | | |
| 3386 | | Chain information for 3i3o #2 |
| 3387 | | --- |
| 3388 | | Chain | Description |
| 3389 | | A B C D E F G H | Short chain dehydrogenase |
| 3390 | | |
| 3391 | | Non-standard residues in 3i3o #2 |
| 3392 | | --- |
| 3393 | | CAC — cacodylate ion (dimethylarsinate) |
| 3394 | | CL — chloride ion |
| 3395 | | MG — magnesium ion |
| 3396 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 3397 | | |
| 3398 | | 3i3o mmCIF Assemblies |
| 3399 | | --- |
| 3400 | | 1| author_and_software_defined_assembly |
| 3401 | | 2| author_and_software_defined_assembly |
| 3402 | | |
| 3403 | | |
| 3404 | | > delete ~/a |
| 3405 | | |
| 3406 | | > delete solvent |
| 3407 | | |
| 3408 | | > mmaker #2 to #1 |
| 3409 | | |
| 3410 | | Parameters |
| 3411 | | --- |
| 3412 | | Chain pairing | bb |
| 3413 | | Alignment algorithm | Needleman-Wunsch |
| 3414 | | Similarity matrix | BLOSUM-62 |
| 3415 | | SS fraction | 0.3 |
| 3416 | | Gap open (HH/SS/other) | 18/18/6 |
| 3417 | | Gap extend | 1 |
| 3418 | | SS matrix | | | H | S | O |
| 3419 | | ---|---|---|--- |
| 3420 | | H | 6 | -9 | -6 |
| 3421 | | S | | 6 | -6 |
| 3422 | | O | | | 4 |
| 3423 | | Iteration cutoff | 2 |
| 3424 | | |
| 3425 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 3426 | | score = 499.7 |
| 3427 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 3428 | | 3.736) |
| 3429 | | |
| 3430 | | |
| 3431 | | > color #1 green |
| 3432 | | |
| 3433 | | > color #2 tan |
| 3434 | | |
| 3435 | | > color ~C byatom |
| 3436 | | |
| 3437 | | > ~display |
| 3438 | | |
| 3439 | | > display #1:138 #2:176 |
| 3440 | | |
| 3441 | | > style stick |
| 3442 | | |
| 3443 | | Changed 4099 atom styles |
| 3444 | | |
| 3445 | | > ribbon |
| 3446 | | |
| 3447 | | > transparency 60 target r |
| 3448 | | |
| 3449 | | > view |
| 3450 | | |
| 3451 | | > size #1:138 #2:176 stickRadius 0.3 |
| 3452 | | |
| 3453 | | Changed 14 bond radii |
| 3454 | | |
| 3455 | | > ~select |
| 3456 | | |
| 3457 | | Nothing selected |
| 3458 | | |
| 3459 | | > save fig1.jpg |
| 3460 | | |
| 3461 | | > select #1@ca & #1:138@ca @< 7.5 |
| 3462 | | |
| 3463 | | 13 atoms, 1 model selected |
| 3464 | | |
| 3465 | | > select #1,2 & sel :< 2 |
| 3466 | | |
| 3467 | | 204 atoms, 197 bonds, 2 models selected |
| 3468 | | |
| 3469 | | > display sel |
| 3470 | | |
| 3471 | | > ~ribbon |
| 3472 | | |
| 3473 | | > view |
| 3474 | | |
| 3475 | | > select clear |
| 3476 | | |
| 3477 | | > select #1@ca & #1:138@ca @< 7.5 |
| 3478 | | |
| 3479 | | 13 atoms, 1 model selected |
| 3480 | | |
| 3481 | | > style sel sphere |
| 3482 | | |
| 3483 | | Changed 13 atom styles |
| 3484 | | |
| 3485 | | > style stick |
| 3486 | | |
| 3487 | | Changed 4099 atom styles |
| 3488 | | |
| 3489 | | > label sel |
| 3490 | | |
| 3491 | | > select clear |
| 3492 | | |
| 3493 | | > label sel atoms |
| 3494 | | |
| 3495 | | > help label |
| 3496 | | |
| 3497 | | > ~label |
| 3498 | | |
| 3499 | | > select #1@ca & #1:138@ca @< 7.5 |
| 3500 | | |
| 3501 | | 13 atoms, 1 model selected |
| 3502 | | |
| 3503 | | > label sel atoms |
| 3504 | | |
| 3505 | | > select clear |
| 3506 | | |
| 3507 | | > ~display |
| 3508 | | |
| 3509 | | > select #1@ca & #1:138@ca @< 7.5 |
| 3510 | | |
| 3511 | | 13 atoms, 1 model selected |
| 3512 | | |
| 3513 | | > select #1,2 & sel :< 2 |
| 3514 | | |
| 3515 | | 204 atoms, 197 bonds, 2 models selected |
| 3516 | | |
| 3517 | | > display sel |
| 3518 | | |
| 3519 | | > select #1@ca & #1:138@ca @< 7.5 |
| 3520 | | |
| 3521 | | 13 atoms, 1 model selected |
| 3522 | | |
| 3523 | | > select #1,2@ca & sel @< 2 |
| 3524 | | |
| 3525 | | 26 atoms, 2 models selected |
| 3526 | | |
| 3527 | | > display sel-residues |
| 3528 | | |
| 3529 | | > ~display |
| 3530 | | |
| 3531 | | > display sel-residues |
| 3532 | | |
| 3533 | | > select clear |
| 3534 | | |
| 3535 | | > display sel |
| 3536 | | |
| 3537 | | > ~display |
| 3538 | | |
| 3539 | | > display sel |
| 3540 | | |
| 3541 | | > select #1@ca & #1:138@ca @< 7.5 |
| 3542 | | |
| 3543 | | 13 atoms, 1 model selected |
| 3544 | | |
| 3545 | | > select #1,2@ca & sel @< 2 |
| 3546 | | |
| 3547 | | 26 atoms, 2 models selected |
| 3548 | | |
| 3549 | | > display sel |
| 3550 | | |
| 3551 | | > display sel-res |
| 3552 | | |
| 3553 | | > show sel-res |
| 3554 | | |
| 3555 | | Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', |
| 3556 | | 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword |
| 3557 | | |
| 3558 | | > display sel-residues |
| 3559 | | |
| 3560 | | > open "/Users/admin/Dropbox (Technion |
| 3561 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 3562 | | |
| 3563 | | > close |
| 3564 | | |
| 3565 | | > graphics bgColor white |
| 3566 | | |
| 3567 | | > open 1WMB |
| 3568 | | |
| 3569 | | 1wmb title: |
| 3570 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 3571 | | info...] |
| 3572 | | |
| 3573 | | Chain information for 1wmb #1 |
| 3574 | | --- |
| 3575 | | Chain | Description |
| 3576 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 3577 | | |
| 3578 | | Non-standard residues in 1wmb #1 |
| 3579 | | --- |
| 3580 | | CAC — cacodylate ion (dimethylarsinate) |
| 3581 | | MG — magnesium ion |
| 3582 | | |
| 3583 | | 1wmb mmCIF Assemblies |
| 3584 | | --- |
| 3585 | | 1| author_and_software_defined_assembly |
| 3586 | | |
| 3587 | | |
| 3588 | | > open 3I3O |
| 3589 | | |
| 3590 | | 3i3o title: |
| 3591 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 3592 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 3593 | | info...] |
| 3594 | | |
| 3595 | | Chain information for 3i3o #2 |
| 3596 | | --- |
| 3597 | | Chain | Description |
| 3598 | | A B C D E F G H | Short chain dehydrogenase |
| 3599 | | |
| 3600 | | Non-standard residues in 3i3o #2 |
| 3601 | | --- |
| 3602 | | CAC — cacodylate ion (dimethylarsinate) |
| 3603 | | CL — chloride ion |
| 3604 | | MG — magnesium ion |
| 3605 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 3606 | | |
| 3607 | | 3i3o mmCIF Assemblies |
| 3608 | | --- |
| 3609 | | 1| author_and_software_defined_assembly |
| 3610 | | 2| author_and_software_defined_assembly |
| 3611 | | |
| 3612 | | |
| 3613 | | > delete ~/a |
| 3614 | | |
| 3615 | | > delete solvent |
| 3616 | | |
| 3617 | | > mmaker #2 to #1 |
| 3618 | | |
| 3619 | | Parameters |
| 3620 | | --- |
| 3621 | | Chain pairing | bb |
| 3622 | | Alignment algorithm | Needleman-Wunsch |
| 3623 | | Similarity matrix | BLOSUM-62 |
| 3624 | | SS fraction | 0.3 |
| 3625 | | Gap open (HH/SS/other) | 18/18/6 |
| 3626 | | Gap extend | 1 |
| 3627 | | SS matrix | | | H | S | O |
| 3628 | | ---|---|---|--- |
| 3629 | | H | 6 | -9 | -6 |
| 3630 | | S | | 6 | -6 |
| 3631 | | O | | | 4 |
| 3632 | | Iteration cutoff | 2 |
| 3633 | | |
| 3634 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 3635 | | score = 499.7 |
| 3636 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 3637 | | 3.736) |
| 3638 | | |
| 3639 | | |
| 3640 | | > color #1 green |
| 3641 | | |
| 3642 | | > color #2 tan |
| 3643 | | |
| 3644 | | > color ~C byatom |
| 3645 | | |
| 3646 | | > ~display |
| 3647 | | |
| 3648 | | > display #1:138 #2:176 |
| 3649 | | |
| 3650 | | > style stick |
| 3651 | | |
| 3652 | | Changed 4099 atom styles |
| 3653 | | |
| 3654 | | > ribbon |
| 3655 | | |
| 3656 | | > transparency 60 target r |
| 3657 | | |
| 3658 | | > view |
| 3659 | | |
| 3660 | | > size #1:138 #2:176 stickRadius 0.3 |
| 3661 | | |
| 3662 | | Changed 14 bond radii |
| 3663 | | |
| 3664 | | > ~select |
| 3665 | | |
| 3666 | | Nothing selected |
| 3667 | | |
| 3668 | | > save fig1.jpg |
| 3669 | | |
| 3670 | | > select #1@ca & #1:138@ca @< 7.5 |
| 3671 | | |
| 3672 | | 13 atoms, 1 model selected |
| 3673 | | |
| 3674 | | > select #1,2@ca & sel @< 2 |
| 3675 | | |
| 3676 | | 26 atoms, 2 models selected |
| 3677 | | |
| 3678 | | > display sel-residues |
| 3679 | | |
| 3680 | | > color ~C byatom |
| 3681 | | |
| 3682 | | > style stick |
| 3683 | | |
| 3684 | | Changed 4099 atom styles |
| 3685 | | |
| 3686 | | > view #1:138 :< 5 pad -1 |
| 3687 | | |
| 3688 | | > hbonds #1:138 & #1 |
| 3689 | | |
| 3690 | | 3 hydrogen bonds found |
| 3691 | | |
| 3692 | | > hbonds #2:176 & #2 |
| 3693 | | |
| 3694 | | 4 hydrogen bonds found |
| 3695 | | |
| 3696 | | > transparency 90 target r |
| 3697 | | |
| 3698 | | > label #1:138 #2:176 offset 1,-1,1 |
| 3699 | | |
| 3700 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .92 |
| 3701 | | |
| 3702 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 3703 | | |
| 3704 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2 |
| 3705 | | > color green bgColor white |
| 3706 | | |
| 3707 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 3708 | | > color tan bgColor white |
| 3709 | | |
| 3710 | | > ~select |
| 3711 | | |
| 3712 | | Nothing selected |
| 3713 | | |
| 3714 | | > save fig2.jpg |
| 3715 | | |
| 3716 | | > ~ribbon |
| 3717 | | |
| 3718 | | > size stickRadius 0.05 |
| 3719 | | |
| 3720 | | Changed 4167 bond radii |
| 3721 | | |
| 3722 | | > size #1:138 stickRadius 0.2 |
| 3723 | | |
| 3724 | | Changed 7 bond radii |
| 3725 | | |
| 3726 | | > size #2:176 stickRadius 0.2 |
| 3727 | | |
| 3728 | | Changed 7 bond radii |
| 3729 | | |
| 3730 | | > save fig3.jpg |
| 3731 | | |
| 3732 | | > label #1:138 :< 5 & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 3733 | | |
| 3734 | | > label #2:176 :< 5 & #2 height 0.4 offset 0,1,0 color tan bgColor white |
| 3735 | | |
| 3736 | | > view #1:138 :< 5 pad -1 |
| 3737 | | |
| 3738 | | > ~select |
| 3739 | | |
| 3740 | | Nothing selected |
| 3741 | | |
| 3742 | | > save fig4.jpg |
| 3743 | | |
| 3744 | | > select #1@ca & #1:138@ca @< 7.5 |
| 3745 | | |
| 3746 | | 13 atoms, 1 model selected |
| 3747 | | |
| 3748 | | > select #1,2@ca & sel @< 2 |
| 3749 | | |
| 3750 | | 26 atoms, 2 models selected |
| 3751 | | |
| 3752 | | > align #2 & sel toAtoms #1 & sel |
| 3753 | | |
| 3754 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 3755 | | |
| 3756 | | > ~select |
| 3757 | | |
| 3758 | | Nothing selected |
| 3759 | | |
| 3760 | | > save fig5.jpg |
| 3761 | | |
| 3762 | | > select #1@ca & #1:138@ca @< 7.5 |
| 3763 | | |
| 3764 | | 13 atoms, 1 model selected |
| 3765 | | |
| 3766 | | > select #1,2 & sel :< 2 |
| 3767 | | |
| 3768 | | 196 atoms, 189 bonds, 4 pseudobonds, 3 models selected |
| 3769 | | |
| 3770 | | > ribbon sel |
| 3771 | | |
| 3772 | | > ~select |
| 3773 | | |
| 3774 | | Nothing selected |
| 3775 | | |
| 3776 | | > save fig6.jpg |
| 3777 | | |
| 3778 | | executed script.view.cxc |
| 3779 | | |
| 3780 | | > help align |
| 3781 | | |
| 3782 | | > open "/Users/admin/Dropbox (Technion |
| 3783 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 3784 | | |
| 3785 | | > close |
| 3786 | | |
| 3787 | | > graphics bgColor white |
| 3788 | | |
| 3789 | | > open 1WMB |
| 3790 | | |
| 3791 | | 1wmb title: |
| 3792 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 3793 | | info...] |
| 3794 | | |
| 3795 | | Chain information for 1wmb #1 |
| 3796 | | --- |
| 3797 | | Chain | Description |
| 3798 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 3799 | | |
| 3800 | | Non-standard residues in 1wmb #1 |
| 3801 | | --- |
| 3802 | | CAC — cacodylate ion (dimethylarsinate) |
| 3803 | | MG — magnesium ion |
| 3804 | | |
| 3805 | | 1wmb mmCIF Assemblies |
| 3806 | | --- |
| 3807 | | 1| author_and_software_defined_assembly |
| 3808 | | |
| 3809 | | |
| 3810 | | > open 3I3O |
| 3811 | | |
| 3812 | | 3i3o title: |
| 3813 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 3814 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 3815 | | info...] |
| 3816 | | |
| 3817 | | Chain information for 3i3o #2 |
| 3818 | | --- |
| 3819 | | Chain | Description |
| 3820 | | A B C D E F G H | Short chain dehydrogenase |
| 3821 | | |
| 3822 | | Non-standard residues in 3i3o #2 |
| 3823 | | --- |
| 3824 | | CAC — cacodylate ion (dimethylarsinate) |
| 3825 | | CL — chloride ion |
| 3826 | | MG — magnesium ion |
| 3827 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 3828 | | |
| 3829 | | 3i3o mmCIF Assemblies |
| 3830 | | --- |
| 3831 | | 1| author_and_software_defined_assembly |
| 3832 | | 2| author_and_software_defined_assembly |
| 3833 | | |
| 3834 | | |
| 3835 | | > delete ~/a |
| 3836 | | |
| 3837 | | > delete solvent |
| 3838 | | |
| 3839 | | > mmaker #2 to #1 |
| 3840 | | |
| 3841 | | Parameters |
| 3842 | | --- |
| 3843 | | Chain pairing | bb |
| 3844 | | Alignment algorithm | Needleman-Wunsch |
| 3845 | | Similarity matrix | BLOSUM-62 |
| 3846 | | SS fraction | 0.3 |
| 3847 | | Gap open (HH/SS/other) | 18/18/6 |
| 3848 | | Gap extend | 1 |
| 3849 | | SS matrix | | | H | S | O |
| 3850 | | ---|---|---|--- |
| 3851 | | H | 6 | -9 | -6 |
| 3852 | | S | | 6 | -6 |
| 3853 | | O | | | 4 |
| 3854 | | Iteration cutoff | 2 |
| 3855 | | |
| 3856 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 3857 | | score = 499.7 |
| 3858 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 3859 | | 3.736) |
| 3860 | | |
| 3861 | | |
| 3862 | | > color #1 green |
| 3863 | | |
| 3864 | | > color #2 tan |
| 3865 | | |
| 3866 | | > color ~C byatom |
| 3867 | | |
| 3868 | | > ~display |
| 3869 | | |
| 3870 | | > display #1:138 #2:176 |
| 3871 | | |
| 3872 | | > style stick |
| 3873 | | |
| 3874 | | Changed 4099 atom styles |
| 3875 | | |
| 3876 | | > ribbon |
| 3877 | | |
| 3878 | | > transparency 60 target r |
| 3879 | | |
| 3880 | | > view |
| 3881 | | |
| 3882 | | > size #1:138 #2:176 stickRadius 0.3 |
| 3883 | | |
| 3884 | | Changed 14 bond radii |
| 3885 | | |
| 3886 | | > ~select |
| 3887 | | |
| 3888 | | Nothing selected |
| 3889 | | |
| 3890 | | > save fig1.jpg |
| 3891 | | |
| 3892 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 3893 | | |
| 3894 | | > sel-ca |
| 3895 | | |
| 3896 | | 13 atoms, 1 model selected |
| 3897 | | 26 atoms, 2 models selected |
| 3898 | | |
| 3899 | | > display sel-residues |
| 3900 | | |
| 3901 | | > color ~C byatom |
| 3902 | | |
| 3903 | | > style stick |
| 3904 | | |
| 3905 | | Changed 4099 atom styles |
| 3906 | | |
| 3907 | | > view #1:138 :< 5 pad -1 |
| 3908 | | |
| 3909 | | > hbonds #1:138 & #1 |
| 3910 | | |
| 3911 | | 3 hydrogen bonds found |
| 3912 | | |
| 3913 | | > hbonds #2:176 & #2 |
| 3914 | | |
| 3915 | | 4 hydrogen bonds found |
| 3916 | | |
| 3917 | | > transparency 90 target r |
| 3918 | | |
| 3919 | | > label #1:138 #2:176 offset 1,-1,1 |
| 3920 | | |
| 3921 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .92 |
| 3922 | | |
| 3923 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 3924 | | |
| 3925 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2 |
| 3926 | | > color green bgColor white |
| 3927 | | |
| 3928 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 3929 | | > color tan bgColor white |
| 3930 | | |
| 3931 | | > ~select |
| 3932 | | |
| 3933 | | Nothing selected |
| 3934 | | |
| 3935 | | > save fig2.jpg |
| 3936 | | |
| 3937 | | > ~ribbon |
| 3938 | | |
| 3939 | | > size stickRadius 0.05 |
| 3940 | | |
| 3941 | | Changed 4167 bond radii |
| 3942 | | |
| 3943 | | > size #1:138 stickRadius 0.2 |
| 3944 | | |
| 3945 | | Changed 7 bond radii |
| 3946 | | |
| 3947 | | > size #2:176 stickRadius 0.2 |
| 3948 | | |
| 3949 | | Changed 7 bond radii |
| 3950 | | |
| 3951 | | > save fig3.jpg |
| 3952 | | |
| 3953 | | > label #1:138 :< 5 & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 3954 | | |
| 3955 | | > label #2:176 :< 5 & #2 height 0.4 offset 0,1,0 color tan bgColor white |
| 3956 | | |
| 3957 | | > view #1:138 :< 5 pad -1 |
| 3958 | | |
| 3959 | | > ~select |
| 3960 | | |
| 3961 | | Nothing selected |
| 3962 | | |
| 3963 | | > save fig4.jpg |
| 3964 | | |
| 3965 | | > select #1@ca & #1:138@ca @< 7.5 |
| 3966 | | |
| 3967 | | 13 atoms, 1 model selected |
| 3968 | | |
| 3969 | | > select #1,2@ca & sel @< 2 |
| 3970 | | |
| 3971 | | 26 atoms, 2 models selected |
| 3972 | | |
| 3973 | | > align #2 & sel toAtoms #1 & sel |
| 3974 | | |
| 3975 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 3976 | | |
| 3977 | | > ~select |
| 3978 | | |
| 3979 | | Nothing selected |
| 3980 | | |
| 3981 | | > save fig5.jpg |
| 3982 | | |
| 3983 | | > select #1@ca & #1:138@ca @< 7.5 |
| 3984 | | |
| 3985 | | 13 atoms, 1 model selected |
| 3986 | | |
| 3987 | | > select #1,2 & sel :< 2 |
| 3988 | | |
| 3989 | | 196 atoms, 189 bonds, 4 pseudobonds, 3 models selected |
| 3990 | | |
| 3991 | | > ribbon sel |
| 3992 | | |
| 3993 | | > ~select |
| 3994 | | |
| 3995 | | Nothing selected |
| 3996 | | |
| 3997 | | > save fig6.jpg |
| 3998 | | |
| 3999 | | executed script.view.cxc |
| 4000 | | |
| 4001 | | > open "/Users/admin/Dropbox (Technion |
| 4002 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 4003 | | |
| 4004 | | > close |
| 4005 | | |
| 4006 | | > graphics bgColor white |
| 4007 | | |
| 4008 | | > open 1WMB |
| 4009 | | |
| 4010 | | 1wmb title: |
| 4011 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 4012 | | info...] |
| 4013 | | |
| 4014 | | Chain information for 1wmb #1 |
| 4015 | | --- |
| 4016 | | Chain | Description |
| 4017 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 4018 | | |
| 4019 | | Non-standard residues in 1wmb #1 |
| 4020 | | --- |
| 4021 | | CAC — cacodylate ion (dimethylarsinate) |
| 4022 | | MG — magnesium ion |
| 4023 | | |
| 4024 | | 1wmb mmCIF Assemblies |
| 4025 | | --- |
| 4026 | | 1| author_and_software_defined_assembly |
| 4027 | | |
| 4028 | | |
| 4029 | | > open 3I3O |
| 4030 | | |
| 4031 | | 3i3o title: |
| 4032 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 4033 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 4034 | | info...] |
| 4035 | | |
| 4036 | | Chain information for 3i3o #2 |
| 4037 | | --- |
| 4038 | | Chain | Description |
| 4039 | | A B C D E F G H | Short chain dehydrogenase |
| 4040 | | |
| 4041 | | Non-standard residues in 3i3o #2 |
| 4042 | | --- |
| 4043 | | CAC — cacodylate ion (dimethylarsinate) |
| 4044 | | CL — chloride ion |
| 4045 | | MG — magnesium ion |
| 4046 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 4047 | | |
| 4048 | | 3i3o mmCIF Assemblies |
| 4049 | | --- |
| 4050 | | 1| author_and_software_defined_assembly |
| 4051 | | 2| author_and_software_defined_assembly |
| 4052 | | |
| 4053 | | |
| 4054 | | > delete ~/a |
| 4055 | | |
| 4056 | | > delete solvent |
| 4057 | | |
| 4058 | | > mmaker #2 to #1 |
| 4059 | | |
| 4060 | | Parameters |
| 4061 | | --- |
| 4062 | | Chain pairing | bb |
| 4063 | | Alignment algorithm | Needleman-Wunsch |
| 4064 | | Similarity matrix | BLOSUM-62 |
| 4065 | | SS fraction | 0.3 |
| 4066 | | Gap open (HH/SS/other) | 18/18/6 |
| 4067 | | Gap extend | 1 |
| 4068 | | SS matrix | | | H | S | O |
| 4069 | | ---|---|---|--- |
| 4070 | | H | 6 | -9 | -6 |
| 4071 | | S | | 6 | -6 |
| 4072 | | O | | | 4 |
| 4073 | | Iteration cutoff | 2 |
| 4074 | | |
| 4075 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 4076 | | score = 499.7 |
| 4077 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 4078 | | 3.736) |
| 4079 | | |
| 4080 | | |
| 4081 | | > color #1 green |
| 4082 | | |
| 4083 | | > color #2 tan |
| 4084 | | |
| 4085 | | > color ~C byatom |
| 4086 | | |
| 4087 | | > ~display |
| 4088 | | |
| 4089 | | > display #1:138 #2:176 |
| 4090 | | |
| 4091 | | > style stick |
| 4092 | | |
| 4093 | | Changed 4099 atom styles |
| 4094 | | |
| 4095 | | > ribbon |
| 4096 | | |
| 4097 | | > transparency 60 target r |
| 4098 | | |
| 4099 | | > view |
| 4100 | | |
| 4101 | | > size #1:138 #2:176 stickRadius 0.3 |
| 4102 | | |
| 4103 | | Changed 14 bond radii |
| 4104 | | |
| 4105 | | > ~select |
| 4106 | | |
| 4107 | | Nothing selected |
| 4108 | | |
| 4109 | | > save fig1.jpg |
| 4110 | | |
| 4111 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 4112 | | |
| 4113 | | > sel-ca |
| 4114 | | |
| 4115 | | 13 atoms, 1 model selected |
| 4116 | | 26 atoms, 2 models selected |
| 4117 | | |
| 4118 | | > display sel-residues |
| 4119 | | |
| 4120 | | > color ~C byatom |
| 4121 | | |
| 4122 | | > style stick |
| 4123 | | |
| 4124 | | Changed 4099 atom styles |
| 4125 | | |
| 4126 | | > view #1:138 :< 5 pad -1 |
| 4127 | | |
| 4128 | | > hbonds #1:138 & #1 |
| 4129 | | |
| 4130 | | 3 hydrogen bonds found |
| 4131 | | |
| 4132 | | > hbonds #2:176 & #2 |
| 4133 | | |
| 4134 | | 4 hydrogen bonds found |
| 4135 | | |
| 4136 | | > transparency 90 target r |
| 4137 | | |
| 4138 | | > label #1:138 #2:176 offset 1,-1,1 |
| 4139 | | |
| 4140 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .92 |
| 4141 | | |
| 4142 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 4143 | | |
| 4144 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2 |
| 4145 | | > color green bgColor white |
| 4146 | | |
| 4147 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 4148 | | > color tan bgColor white |
| 4149 | | |
| 4150 | | > ~select |
| 4151 | | |
| 4152 | | Nothing selected |
| 4153 | | |
| 4154 | | > save fig2.jpg |
| 4155 | | |
| 4156 | | > ~ribbon |
| 4157 | | |
| 4158 | | > size stickRadius 0.05 |
| 4159 | | |
| 4160 | | Changed 4167 bond radii |
| 4161 | | |
| 4162 | | > size #1:138 stickRadius 0.2 |
| 4163 | | |
| 4164 | | Changed 7 bond radii |
| 4165 | | |
| 4166 | | > size #2:176 stickRadius 0.2 |
| 4167 | | |
| 4168 | | Changed 7 bond radii |
| 4169 | | |
| 4170 | | > save fig3.jpg |
| 4171 | | |
| 4172 | | > label #1:138 :< 5 & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 4173 | | |
| 4174 | | > label #2:176 :< 5 & #2 height 0.4 offset 0,1,0 color tan bgColor white |
| 4175 | | |
| 4176 | | > view #1:138 :< 5 pad -1 |
| 4177 | | |
| 4178 | | > ~select |
| 4179 | | |
| 4180 | | Nothing selected |
| 4181 | | |
| 4182 | | > save fig4.jpg |
| 4183 | | |
| 4184 | | > select #1@ca & #1:138@ca @< 7.5 |
| 4185 | | |
| 4186 | | 13 atoms, 1 model selected |
| 4187 | | |
| 4188 | | > select #1,2@ca & sel @< 2 |
| 4189 | | |
| 4190 | | 26 atoms, 2 models selected |
| 4191 | | |
| 4192 | | > align #2 & sel toAtoms #1 & sel |
| 4193 | | |
| 4194 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 4195 | | |
| 4196 | | > ~select |
| 4197 | | |
| 4198 | | Nothing selected |
| 4199 | | |
| 4200 | | > save fig5.jpg |
| 4201 | | |
| 4202 | | > select #1@ca & #1:138@ca @< 7.5 |
| 4203 | | |
| 4204 | | 13 atoms, 1 model selected |
| 4205 | | |
| 4206 | | > select #1,2 & sel :< 2 |
| 4207 | | |
| 4208 | | 196 atoms, 189 bonds, 4 pseudobonds, 3 models selected |
| 4209 | | |
| 4210 | | > ribbon sel |
| 4211 | | |
| 4212 | | > ~select |
| 4213 | | |
| 4214 | | Nothing selected |
| 4215 | | |
| 4216 | | > save fig6.jpg |
| 4217 | | |
| 4218 | | executed script.view.cxc |
| 4219 | | |
| 4220 | | > open "/Users/admin/Dropbox (Technion |
| 4221 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 4222 | | |
| 4223 | | > close |
| 4224 | | |
| 4225 | | > graphics bgColor white |
| 4226 | | |
| 4227 | | > open 1WMB |
| 4228 | | |
| 4229 | | 1wmb title: |
| 4230 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 4231 | | info...] |
| 4232 | | |
| 4233 | | Chain information for 1wmb #1 |
| 4234 | | --- |
| 4235 | | Chain | Description |
| 4236 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 4237 | | |
| 4238 | | Non-standard residues in 1wmb #1 |
| 4239 | | --- |
| 4240 | | CAC — cacodylate ion (dimethylarsinate) |
| 4241 | | MG — magnesium ion |
| 4242 | | |
| 4243 | | 1wmb mmCIF Assemblies |
| 4244 | | --- |
| 4245 | | 1| author_and_software_defined_assembly |
| 4246 | | |
| 4247 | | |
| 4248 | | > open 3I3O |
| 4249 | | |
| 4250 | | 3i3o title: |
| 4251 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 4252 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 4253 | | info...] |
| 4254 | | |
| 4255 | | Chain information for 3i3o #2 |
| 4256 | | --- |
| 4257 | | Chain | Description |
| 4258 | | A B C D E F G H | Short chain dehydrogenase |
| 4259 | | |
| 4260 | | Non-standard residues in 3i3o #2 |
| 4261 | | --- |
| 4262 | | CAC — cacodylate ion (dimethylarsinate) |
| 4263 | | CL — chloride ion |
| 4264 | | MG — magnesium ion |
| 4265 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 4266 | | |
| 4267 | | 3i3o mmCIF Assemblies |
| 4268 | | --- |
| 4269 | | 1| author_and_software_defined_assembly |
| 4270 | | 2| author_and_software_defined_assembly |
| 4271 | | |
| 4272 | | |
| 4273 | | > delete ~/a |
| 4274 | | |
| 4275 | | > delete solvent |
| 4276 | | |
| 4277 | | > mmaker #2 to #1 |
| 4278 | | |
| 4279 | | Parameters |
| 4280 | | --- |
| 4281 | | Chain pairing | bb |
| 4282 | | Alignment algorithm | Needleman-Wunsch |
| 4283 | | Similarity matrix | BLOSUM-62 |
| 4284 | | SS fraction | 0.3 |
| 4285 | | Gap open (HH/SS/other) | 18/18/6 |
| 4286 | | Gap extend | 1 |
| 4287 | | SS matrix | | | H | S | O |
| 4288 | | ---|---|---|--- |
| 4289 | | H | 6 | -9 | -6 |
| 4290 | | S | | 6 | -6 |
| 4291 | | O | | | 4 |
| 4292 | | Iteration cutoff | 2 |
| 4293 | | |
| 4294 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 4295 | | score = 499.7 |
| 4296 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 4297 | | 3.736) |
| 4298 | | |
| 4299 | | |
| 4300 | | > color #1 green |
| 4301 | | |
| 4302 | | > color #2 tan |
| 4303 | | |
| 4304 | | > color ~C byatom |
| 4305 | | |
| 4306 | | > ~display |
| 4307 | | |
| 4308 | | > display #1:138 #2:176 |
| 4309 | | |
| 4310 | | > style stick |
| 4311 | | |
| 4312 | | Changed 4099 atom styles |
| 4313 | | |
| 4314 | | > ribbon |
| 4315 | | |
| 4316 | | > transparency 60 target r |
| 4317 | | |
| 4318 | | > view |
| 4319 | | |
| 4320 | | > size #1:138 #2:176 stickRadius 0.3 |
| 4321 | | |
| 4322 | | Changed 14 bond radii |
| 4323 | | |
| 4324 | | > ~select |
| 4325 | | |
| 4326 | | Nothing selected |
| 4327 | | |
| 4328 | | > save fig1.jpg |
| 4329 | | |
| 4330 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 4331 | | |
| 4332 | | > sel-ca |
| 4333 | | |
| 4334 | | 13 atoms, 1 model selected |
| 4335 | | 26 atoms, 2 models selected |
| 4336 | | |
| 4337 | | > display sel-residues |
| 4338 | | |
| 4339 | | > color ~C byatom |
| 4340 | | |
| 4341 | | > style stick |
| 4342 | | |
| 4343 | | Changed 4099 atom styles |
| 4344 | | |
| 4345 | | > view #1:138 :< 5 pad -1 |
| 4346 | | |
| 4347 | | > hbonds #1:138 & #1 |
| 4348 | | |
| 4349 | | 3 hydrogen bonds found |
| 4350 | | |
| 4351 | | > hbonds #2:176 & #2 |
| 4352 | | |
| 4353 | | 4 hydrogen bonds found |
| 4354 | | |
| 4355 | | > transparency 90 target r |
| 4356 | | |
| 4357 | | > label #1:138 #2:176 offset 1,-1,1 |
| 4358 | | |
| 4359 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .92 |
| 4360 | | |
| 4361 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 4362 | | |
| 4363 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2 |
| 4364 | | > color green bgColor white |
| 4365 | | |
| 4366 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 4367 | | > color tan bgColor white |
| 4368 | | |
| 4369 | | > ~select |
| 4370 | | |
| 4371 | | Nothing selected |
| 4372 | | |
| 4373 | | > save fig2.jpg |
| 4374 | | |
| 4375 | | > ~ribbon |
| 4376 | | |
| 4377 | | > size stickRadius 0.05 |
| 4378 | | |
| 4379 | | Changed 4167 bond radii |
| 4380 | | |
| 4381 | | > size #1:138 stickRadius 0.2 |
| 4382 | | |
| 4383 | | Changed 7 bond radii |
| 4384 | | |
| 4385 | | > size #2:176 stickRadius 0.2 |
| 4386 | | |
| 4387 | | Changed 7 bond radii |
| 4388 | | |
| 4389 | | > save fig3.jpg |
| 4390 | | |
| 4391 | | > label #1:138 :< 5 & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 4392 | | |
| 4393 | | > label #2:176 :< 5 & #2 height 0.4 offset 0,1,0 color tan bgColor white |
| 4394 | | |
| 4395 | | > view #1:138 :< 5 pad -1 |
| 4396 | | |
| 4397 | | > ~select |
| 4398 | | |
| 4399 | | Nothing selected |
| 4400 | | |
| 4401 | | > save fig4.jpg |
| 4402 | | |
| 4403 | | > sel-ca |
| 4404 | | |
| 4405 | | 13 atoms, 1 model selected |
| 4406 | | 26 atoms, 2 models selected |
| 4407 | | |
| 4408 | | > align #2 & sel toAtoms #1 & sel |
| 4409 | | |
| 4410 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 4411 | | |
| 4412 | | > ~select |
| 4413 | | |
| 4414 | | Nothing selected |
| 4415 | | |
| 4416 | | > save fig5.jpg |
| 4417 | | |
| 4418 | | > sel-ca |
| 4419 | | |
| 4420 | | 13 atoms, 1 model selected |
| 4421 | | 26 atoms, 2 models selected |
| 4422 | | |
| 4423 | | > ribbon sel |
| 4424 | | |
| 4425 | | > ~select |
| 4426 | | |
| 4427 | | Nothing selected |
| 4428 | | |
| 4429 | | > save fig6.jpg |
| 4430 | | |
| 4431 | | executed script.view.cxc |
| 4432 | | |
| 4433 | | > ~ribbon |
| 4434 | | |
| 4435 | | > open "/Users/admin/Dropbox (Technion |
| 4436 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 4437 | | |
| 4438 | | > close |
| 4439 | | |
| 4440 | | > graphics bgColor white |
| 4441 | | |
| 4442 | | > open 1WMB |
| 4443 | | |
| 4444 | | 1wmb title: |
| 4445 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 4446 | | info...] |
| 4447 | | |
| 4448 | | Chain information for 1wmb #1 |
| 4449 | | --- |
| 4450 | | Chain | Description |
| 4451 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 4452 | | |
| 4453 | | Non-standard residues in 1wmb #1 |
| 4454 | | --- |
| 4455 | | CAC — cacodylate ion (dimethylarsinate) |
| 4456 | | MG — magnesium ion |
| 4457 | | |
| 4458 | | 1wmb mmCIF Assemblies |
| 4459 | | --- |
| 4460 | | 1| author_and_software_defined_assembly |
| 4461 | | |
| 4462 | | |
| 4463 | | > open 3I3O |
| 4464 | | |
| 4465 | | 3i3o title: |
| 4466 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 4467 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 4468 | | info...] |
| 4469 | | |
| 4470 | | Chain information for 3i3o #2 |
| 4471 | | --- |
| 4472 | | Chain | Description |
| 4473 | | A B C D E F G H | Short chain dehydrogenase |
| 4474 | | |
| 4475 | | Non-standard residues in 3i3o #2 |
| 4476 | | --- |
| 4477 | | CAC — cacodylate ion (dimethylarsinate) |
| 4478 | | CL — chloride ion |
| 4479 | | MG — magnesium ion |
| 4480 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 4481 | | |
| 4482 | | 3i3o mmCIF Assemblies |
| 4483 | | --- |
| 4484 | | 1| author_and_software_defined_assembly |
| 4485 | | 2| author_and_software_defined_assembly |
| 4486 | | |
| 4487 | | |
| 4488 | | > delete ~/a |
| 4489 | | |
| 4490 | | > delete solvent |
| 4491 | | |
| 4492 | | > mmaker #2 to #1 |
| 4493 | | |
| 4494 | | Parameters |
| 4495 | | --- |
| 4496 | | Chain pairing | bb |
| 4497 | | Alignment algorithm | Needleman-Wunsch |
| 4498 | | Similarity matrix | BLOSUM-62 |
| 4499 | | SS fraction | 0.3 |
| 4500 | | Gap open (HH/SS/other) | 18/18/6 |
| 4501 | | Gap extend | 1 |
| 4502 | | SS matrix | | | H | S | O |
| 4503 | | ---|---|---|--- |
| 4504 | | H | 6 | -9 | -6 |
| 4505 | | S | | 6 | -6 |
| 4506 | | O | | | 4 |
| 4507 | | Iteration cutoff | 2 |
| 4508 | | |
| 4509 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 4510 | | score = 499.7 |
| 4511 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 4512 | | 3.736) |
| 4513 | | |
| 4514 | | |
| 4515 | | > color #1 green |
| 4516 | | |
| 4517 | | > color #2 tan |
| 4518 | | |
| 4519 | | > color ~C byatom |
| 4520 | | |
| 4521 | | > ~display |
| 4522 | | |
| 4523 | | > display #1:138 #2:176 |
| 4524 | | |
| 4525 | | > style stick |
| 4526 | | |
| 4527 | | Changed 4099 atom styles |
| 4528 | | |
| 4529 | | > ribbon |
| 4530 | | |
| 4531 | | > transparency 60 target r |
| 4532 | | |
| 4533 | | > view |
| 4534 | | |
| 4535 | | > size #1:138 #2:176 stickRadius 0.3 |
| 4536 | | |
| 4537 | | Changed 14 bond radii |
| 4538 | | |
| 4539 | | > save fig1.jpg |
| 4540 | | |
| 4541 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 4542 | | |
| 4543 | | > sel-ca |
| 4544 | | |
| 4545 | | 13 atoms, 1 model selected |
| 4546 | | 26 atoms, 2 models selected |
| 4547 | | |
| 4548 | | > display sel-residues |
| 4549 | | |
| 4550 | | > color ~C byatom |
| 4551 | | |
| 4552 | | > style stick |
| 4553 | | |
| 4554 | | Changed 4099 atom styles |
| 4555 | | |
| 4556 | | > view #1:138 :< 5 pad -1 |
| 4557 | | |
| 4558 | | > hbonds #1:138 & #1 |
| 4559 | | |
| 4560 | | 3 hydrogen bonds found |
| 4561 | | |
| 4562 | | > hbonds #2:176 & #2 |
| 4563 | | |
| 4564 | | 4 hydrogen bonds found |
| 4565 | | |
| 4566 | | > transparency 90 target r |
| 4567 | | |
| 4568 | | > label #1:138 #2:176 offset 1,-1,1 |
| 4569 | | |
| 4570 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .92 |
| 4571 | | |
| 4572 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 4573 | | |
| 4574 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2 |
| 4575 | | > color green bgColor white |
| 4576 | | |
| 4577 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 4578 | | > color tan bgColor white |
| 4579 | | |
| 4580 | | > save fig2.jpg |
| 4581 | | |
| 4582 | | > ~ribbon |
| 4583 | | |
| 4584 | | > size stickRadius 0.05 |
| 4585 | | |
| 4586 | | Changed 4167 bond radii |
| 4587 | | |
| 4588 | | > size #1:138 stickRadius 0.2 |
| 4589 | | |
| 4590 | | Changed 7 bond radii |
| 4591 | | |
| 4592 | | > size #2:176 stickRadius 0.2 |
| 4593 | | |
| 4594 | | Changed 7 bond radii |
| 4595 | | |
| 4596 | | > save fig3.jpg |
| 4597 | | |
| 4598 | | > label sel-ca height 0.4 offset 0,0,0 col green bgColor white |
| 4599 | | |
| 4600 | | Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword |
| 4601 | | |
| 4602 | | > open "/Users/admin/Dropbox (Technion |
| 4603 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 4604 | | |
| 4605 | | > close |
| 4606 | | |
| 4607 | | > graphics bgColor white |
| 4608 | | |
| 4609 | | > open 1WMB |
| 4610 | | |
| 4611 | | 1wmb title: |
| 4612 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 4613 | | info...] |
| 4614 | | |
| 4615 | | Chain information for 1wmb #1 |
| 4616 | | --- |
| 4617 | | Chain | Description |
| 4618 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 4619 | | |
| 4620 | | Non-standard residues in 1wmb #1 |
| 4621 | | --- |
| 4622 | | CAC — cacodylate ion (dimethylarsinate) |
| 4623 | | MG — magnesium ion |
| 4624 | | |
| 4625 | | 1wmb mmCIF Assemblies |
| 4626 | | --- |
| 4627 | | 1| author_and_software_defined_assembly |
| 4628 | | |
| 4629 | | |
| 4630 | | > open 3I3O |
| 4631 | | |
| 4632 | | 3i3o title: |
| 4633 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 4634 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 4635 | | info...] |
| 4636 | | |
| 4637 | | Chain information for 3i3o #2 |
| 4638 | | --- |
| 4639 | | Chain | Description |
| 4640 | | A B C D E F G H | Short chain dehydrogenase |
| 4641 | | |
| 4642 | | Non-standard residues in 3i3o #2 |
| 4643 | | --- |
| 4644 | | CAC — cacodylate ion (dimethylarsinate) |
| 4645 | | CL — chloride ion |
| 4646 | | MG — magnesium ion |
| 4647 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 4648 | | |
| 4649 | | 3i3o mmCIF Assemblies |
| 4650 | | --- |
| 4651 | | 1| author_and_software_defined_assembly |
| 4652 | | 2| author_and_software_defined_assembly |
| 4653 | | |
| 4654 | | |
| 4655 | | > delete ~/a |
| 4656 | | |
| 4657 | | > delete solvent |
| 4658 | | |
| 4659 | | > mmaker #2 to #1 |
| 4660 | | |
| 4661 | | Parameters |
| 4662 | | --- |
| 4663 | | Chain pairing | bb |
| 4664 | | Alignment algorithm | Needleman-Wunsch |
| 4665 | | Similarity matrix | BLOSUM-62 |
| 4666 | | SS fraction | 0.3 |
| 4667 | | Gap open (HH/SS/other) | 18/18/6 |
| 4668 | | Gap extend | 1 |
| 4669 | | SS matrix | | | H | S | O |
| 4670 | | ---|---|---|--- |
| 4671 | | H | 6 | -9 | -6 |
| 4672 | | S | | 6 | -6 |
| 4673 | | O | | | 4 |
| 4674 | | Iteration cutoff | 2 |
| 4675 | | |
| 4676 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 4677 | | score = 499.7 |
| 4678 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 4679 | | 3.736) |
| 4680 | | |
| 4681 | | |
| 4682 | | > color #1 green |
| 4683 | | |
| 4684 | | > color #2 tan |
| 4685 | | |
| 4686 | | > color ~C byatom |
| 4687 | | |
| 4688 | | > ~display |
| 4689 | | |
| 4690 | | > display #1:138 #2:176 |
| 4691 | | |
| 4692 | | > style stick |
| 4693 | | |
| 4694 | | Changed 4099 atom styles |
| 4695 | | |
| 4696 | | > ribbon |
| 4697 | | |
| 4698 | | > transparency 60 target r |
| 4699 | | |
| 4700 | | > view |
| 4701 | | |
| 4702 | | > size #1:138 #2:176 stickRadius 0.3 |
| 4703 | | |
| 4704 | | Changed 14 bond radii |
| 4705 | | |
| 4706 | | > save fig1.jpg |
| 4707 | | |
| 4708 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 4709 | | |
| 4710 | | > sel-ca |
| 4711 | | |
| 4712 | | 13 atoms, 1 model selected |
| 4713 | | 26 atoms, 2 models selected |
| 4714 | | |
| 4715 | | > display sel-residues |
| 4716 | | |
| 4717 | | > color ~C byatom |
| 4718 | | |
| 4719 | | > style stick |
| 4720 | | |
| 4721 | | Changed 4099 atom styles |
| 4722 | | |
| 4723 | | > view #1:138 :< 5 pad -1 |
| 4724 | | |
| 4725 | | > hbonds #1:138 & #1 |
| 4726 | | |
| 4727 | | 3 hydrogen bonds found |
| 4728 | | |
| 4729 | | > hbonds #2:176 & #2 |
| 4730 | | |
| 4731 | | 4 hydrogen bonds found |
| 4732 | | |
| 4733 | | > transparency 90 target r |
| 4734 | | |
| 4735 | | > label #1:138 #2:176 offset 1,-1,1 |
| 4736 | | |
| 4737 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .92 |
| 4738 | | |
| 4739 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 4740 | | |
| 4741 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2 |
| 4742 | | > color green bgColor white |
| 4743 | | |
| 4744 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 4745 | | > color tan bgColor white |
| 4746 | | |
| 4747 | | > save fig2.jpg |
| 4748 | | |
| 4749 | | > ~ribbon |
| 4750 | | |
| 4751 | | > size stickRadius 0.05 |
| 4752 | | |
| 4753 | | Changed 4167 bond radii |
| 4754 | | |
| 4755 | | > size #1:138 stickRadius 0.2 |
| 4756 | | |
| 4757 | | Changed 7 bond radii |
| 4758 | | |
| 4759 | | > size #2:176 stickRadius 0.2 |
| 4760 | | |
| 4761 | | Changed 7 bond radii |
| 4762 | | |
| 4763 | | > save fig3.jpg |
| 4764 | | |
| 4765 | | > label sel-residues height 0.4 offset 0,0,0 color green bgColor white |
| 4766 | | |
| 4767 | | > view #1:138 :< 5 pad -1 |
| 4768 | | |
| 4769 | | > ~select |
| 4770 | | |
| 4771 | | Nothing selected |
| 4772 | | |
| 4773 | | > save fig4.jpg |
| 4774 | | |
| 4775 | | > sel-ca |
| 4776 | | |
| 4777 | | 13 atoms, 1 model selected |
| 4778 | | 26 atoms, 2 models selected |
| 4779 | | |
| 4780 | | > align #2 & sel toAtoms #1 & sel |
| 4781 | | |
| 4782 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 4783 | | |
| 4784 | | > ~select |
| 4785 | | |
| 4786 | | Nothing selected |
| 4787 | | |
| 4788 | | > save fig5.jpg |
| 4789 | | |
| 4790 | | > sel-ca |
| 4791 | | |
| 4792 | | 13 atoms, 1 model selected |
| 4793 | | 26 atoms, 2 models selected |
| 4794 | | |
| 4795 | | > ribbon sel |
| 4796 | | |
| 4797 | | > ~select |
| 4798 | | |
| 4799 | | Nothing selected |
| 4800 | | |
| 4801 | | > save fig6.jpg |
| 4802 | | |
| 4803 | | executed script.view.cxc |
| 4804 | | |
| 4805 | | > open "/Users/admin/Dropbox (Technion |
| 4806 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 4807 | | |
| 4808 | | > close |
| 4809 | | |
| 4810 | | > graphics bgColor white |
| 4811 | | |
| 4812 | | > open 1WMB |
| 4813 | | |
| 4814 | | 1wmb title: |
| 4815 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 4816 | | info...] |
| 4817 | | |
| 4818 | | Chain information for 1wmb #1 |
| 4819 | | --- |
| 4820 | | Chain | Description |
| 4821 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 4822 | | |
| 4823 | | Non-standard residues in 1wmb #1 |
| 4824 | | --- |
| 4825 | | CAC — cacodylate ion (dimethylarsinate) |
| 4826 | | MG — magnesium ion |
| 4827 | | |
| 4828 | | 1wmb mmCIF Assemblies |
| 4829 | | --- |
| 4830 | | 1| author_and_software_defined_assembly |
| 4831 | | |
| 4832 | | |
| 4833 | | > open 3I3O |
| 4834 | | |
| 4835 | | 3i3o title: |
| 4836 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 4837 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 4838 | | info...] |
| 4839 | | |
| 4840 | | Chain information for 3i3o #2 |
| 4841 | | --- |
| 4842 | | Chain | Description |
| 4843 | | A B C D E F G H | Short chain dehydrogenase |
| 4844 | | |
| 4845 | | Non-standard residues in 3i3o #2 |
| 4846 | | --- |
| 4847 | | CAC — cacodylate ion (dimethylarsinate) |
| 4848 | | CL — chloride ion |
| 4849 | | MG — magnesium ion |
| 4850 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 4851 | | |
| 4852 | | 3i3o mmCIF Assemblies |
| 4853 | | --- |
| 4854 | | 1| author_and_software_defined_assembly |
| 4855 | | 2| author_and_software_defined_assembly |
| 4856 | | |
| 4857 | | |
| 4858 | | > delete ~/a |
| 4859 | | |
| 4860 | | > delete solvent |
| 4861 | | |
| 4862 | | > mmaker #2 to #1 |
| 4863 | | |
| 4864 | | Parameters |
| 4865 | | --- |
| 4866 | | Chain pairing | bb |
| 4867 | | Alignment algorithm | Needleman-Wunsch |
| 4868 | | Similarity matrix | BLOSUM-62 |
| 4869 | | SS fraction | 0.3 |
| 4870 | | Gap open (HH/SS/other) | 18/18/6 |
| 4871 | | Gap extend | 1 |
| 4872 | | SS matrix | | | H | S | O |
| 4873 | | ---|---|---|--- |
| 4874 | | H | 6 | -9 | -6 |
| 4875 | | S | | 6 | -6 |
| 4876 | | O | | | 4 |
| 4877 | | Iteration cutoff | 2 |
| 4878 | | |
| 4879 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 4880 | | score = 499.7 |
| 4881 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 4882 | | 3.736) |
| 4883 | | |
| 4884 | | |
| 4885 | | > color #1 green |
| 4886 | | |
| 4887 | | > color #2 tan |
| 4888 | | |
| 4889 | | > color ~C byatom |
| 4890 | | |
| 4891 | | > ~display |
| 4892 | | |
| 4893 | | > display #1:138 #2:176 |
| 4894 | | |
| 4895 | | > style stick |
| 4896 | | |
| 4897 | | Changed 4099 atom styles |
| 4898 | | |
| 4899 | | > ribbon |
| 4900 | | |
| 4901 | | > transparency 60 target r |
| 4902 | | |
| 4903 | | > view |
| 4904 | | |
| 4905 | | > size #1:138 #2:176 stickRadius 0.3 |
| 4906 | | |
| 4907 | | Changed 14 bond radii |
| 4908 | | |
| 4909 | | > save fig1.jpg |
| 4910 | | |
| 4911 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 4912 | | |
| 4913 | | > sel-ca |
| 4914 | | |
| 4915 | | 13 atoms, 1 model selected |
| 4916 | | 26 atoms, 2 models selected |
| 4917 | | |
| 4918 | | > display sel-residues |
| 4919 | | |
| 4920 | | > color ~C byatom |
| 4921 | | |
| 4922 | | > style stick |
| 4923 | | |
| 4924 | | Changed 4099 atom styles |
| 4925 | | |
| 4926 | | > view #1:138 :< 5 pad -1 |
| 4927 | | |
| 4928 | | > hbonds #1:138 & #1 |
| 4929 | | |
| 4930 | | 3 hydrogen bonds found |
| 4931 | | |
| 4932 | | > hbonds #2:176 & #2 |
| 4933 | | |
| 4934 | | 4 hydrogen bonds found |
| 4935 | | |
| 4936 | | > transparency 90 target r |
| 4937 | | |
| 4938 | | > label #1:138 #2:176 offset 1,-1,1 |
| 4939 | | |
| 4940 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .92 |
| 4941 | | |
| 4942 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 4943 | | |
| 4944 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2 |
| 4945 | | > color green bgColor white |
| 4946 | | |
| 4947 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 4948 | | > color tan bgColor white |
| 4949 | | |
| 4950 | | > save fig2.jpg |
| 4951 | | |
| 4952 | | > ~ribbon |
| 4953 | | |
| 4954 | | > size stickRadius 0.05 |
| 4955 | | |
| 4956 | | Changed 4167 bond radii |
| 4957 | | |
| 4958 | | > size #1:138 stickRadius 0.2 |
| 4959 | | |
| 4960 | | Changed 7 bond radii |
| 4961 | | |
| 4962 | | > size #2:176 stickRadius 0.2 |
| 4963 | | |
| 4964 | | Changed 7 bond radii |
| 4965 | | |
| 4966 | | > save fig3.jpg |
| 4967 | | |
| 4968 | | > label sel-residues height 0.4 offset 0,0,0 color green bgColor white |
| 4969 | | |
| 4970 | | > view sel-residues pad -1 |
| 4971 | | |
| 4972 | | > save fig4.jpg |
| 4973 | | |
| 4974 | | > align #2 & sel toAtoms #1 & sel |
| 4975 | | |
| 4976 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 4977 | | |
| 4978 | | > save fig5.jpg |
| 4979 | | |
| 4980 | | > ribbon sel |
| 4981 | | |
| 4982 | | > save fig6.jpg |
| 4983 | | |
| 4984 | | executed script.view.cxc |
| 4985 | | |
| 4986 | | > open "/Users/admin/Dropbox (Technion |
| 4987 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 4988 | | |
| 4989 | | > close |
| 4990 | | |
| 4991 | | > graphics bgColor white |
| 4992 | | |
| 4993 | | > open 1WMB |
| 4994 | | |
| 4995 | | 1wmb title: |
| 4996 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 4997 | | info...] |
| 4998 | | |
| 4999 | | Chain information for 1wmb #1 |
| 5000 | | --- |
| 5001 | | Chain | Description |
| 5002 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 5003 | | |
| 5004 | | Non-standard residues in 1wmb #1 |
| 5005 | | --- |
| 5006 | | CAC — cacodylate ion (dimethylarsinate) |
| 5007 | | MG — magnesium ion |
| 5008 | | |
| 5009 | | 1wmb mmCIF Assemblies |
| 5010 | | --- |
| 5011 | | 1| author_and_software_defined_assembly |
| 5012 | | |
| 5013 | | |
| 5014 | | > open 3I3O |
| 5015 | | |
| 5016 | | 3i3o title: |
| 5017 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 5018 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 5019 | | info...] |
| 5020 | | |
| 5021 | | Chain information for 3i3o #2 |
| 5022 | | --- |
| 5023 | | Chain | Description |
| 5024 | | A B C D E F G H | Short chain dehydrogenase |
| 5025 | | |
| 5026 | | Non-standard residues in 3i3o #2 |
| 5027 | | --- |
| 5028 | | CAC — cacodylate ion (dimethylarsinate) |
| 5029 | | CL — chloride ion |
| 5030 | | MG — magnesium ion |
| 5031 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 5032 | | |
| 5033 | | 3i3o mmCIF Assemblies |
| 5034 | | --- |
| 5035 | | 1| author_and_software_defined_assembly |
| 5036 | | 2| author_and_software_defined_assembly |
| 5037 | | |
| 5038 | | |
| 5039 | | > delete ~/a |
| 5040 | | |
| 5041 | | > delete solvent |
| 5042 | | |
| 5043 | | > mmaker #2 to #1 |
| 5044 | | |
| 5045 | | Parameters |
| 5046 | | --- |
| 5047 | | Chain pairing | bb |
| 5048 | | Alignment algorithm | Needleman-Wunsch |
| 5049 | | Similarity matrix | BLOSUM-62 |
| 5050 | | SS fraction | 0.3 |
| 5051 | | Gap open (HH/SS/other) | 18/18/6 |
| 5052 | | Gap extend | 1 |
| 5053 | | SS matrix | | | H | S | O |
| 5054 | | ---|---|---|--- |
| 5055 | | H | 6 | -9 | -6 |
| 5056 | | S | | 6 | -6 |
| 5057 | | O | | | 4 |
| 5058 | | Iteration cutoff | 2 |
| 5059 | | |
| 5060 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 5061 | | score = 499.7 |
| 5062 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 5063 | | 3.736) |
| 5064 | | |
| 5065 | | |
| 5066 | | > color #1 green |
| 5067 | | |
| 5068 | | > color #2 tan |
| 5069 | | |
| 5070 | | > color ~C byatom |
| 5071 | | |
| 5072 | | > ~display |
| 5073 | | |
| 5074 | | > display #1:138 #2:176 |
| 5075 | | |
| 5076 | | > style stick |
| 5077 | | |
| 5078 | | Changed 4099 atom styles |
| 5079 | | |
| 5080 | | > ribbon |
| 5081 | | |
| 5082 | | > transparency 60 target r |
| 5083 | | |
| 5084 | | > view |
| 5085 | | |
| 5086 | | > size #1:138 #2:176 stickRadius 0.3 |
| 5087 | | |
| 5088 | | Changed 14 bond radii |
| 5089 | | |
| 5090 | | > save fig1.jpg |
| 5091 | | |
| 5092 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 5093 | | |
| 5094 | | > sel-ca |
| 5095 | | |
| 5096 | | 13 atoms, 1 model selected |
| 5097 | | 26 atoms, 2 models selected |
| 5098 | | |
| 5099 | | > display sel-residues |
| 5100 | | |
| 5101 | | > color ~C byatom |
| 5102 | | |
| 5103 | | > style stick |
| 5104 | | |
| 5105 | | Changed 4099 atom styles |
| 5106 | | |
| 5107 | | > view #1:138 :< 5 pad -1 |
| 5108 | | |
| 5109 | | > hbonds #1:138 & #1 |
| 5110 | | |
| 5111 | | 3 hydrogen bonds found |
| 5112 | | |
| 5113 | | > hbonds #2:176 & #2 |
| 5114 | | |
| 5115 | | 4 hydrogen bonds found |
| 5116 | | |
| 5117 | | > transparency 90 target r |
| 5118 | | |
| 5119 | | > label #1:138 #2:176 offset 1,-1,1 |
| 5120 | | |
| 5121 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .92 |
| 5122 | | |
| 5123 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 5124 | | |
| 5125 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2 |
| 5126 | | > color green bgColor white |
| 5127 | | |
| 5128 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 5129 | | > color tan bgColor white |
| 5130 | | |
| 5131 | | > save fig2.jpg |
| 5132 | | |
| 5133 | | > ~ribbon |
| 5134 | | |
| 5135 | | > size stickRadius 0.05 |
| 5136 | | |
| 5137 | | Changed 4167 bond radii |
| 5138 | | |
| 5139 | | > size #1:138 stickRadius 0.2 |
| 5140 | | |
| 5141 | | Changed 7 bond radii |
| 5142 | | |
| 5143 | | > size #2:176 stickRadius 0.2 |
| 5144 | | |
| 5145 | | Changed 7 bond radii |
| 5146 | | |
| 5147 | | > save fig3.jpg |
| 5148 | | |
| 5149 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 5150 | | |
| 5151 | | > view sel-residues pad -1 |
| 5152 | | |
| 5153 | | > save fig4.jpg |
| 5154 | | |
| 5155 | | > align #2 & sel toAtoms #1 & sel |
| 5156 | | |
| 5157 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 5158 | | |
| 5159 | | > save fig5.jpg |
| 5160 | | |
| 5161 | | > ribbon sel |
| 5162 | | |
| 5163 | | > save fig6.jpg |
| 5164 | | |
| 5165 | | executed script.view.cxc |
| 5166 | | |
| 5167 | | > open "/Users/admin/Dropbox (Technion |
| 5168 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 5169 | | |
| 5170 | | > close |
| 5171 | | |
| 5172 | | > graphics bgColor white |
| 5173 | | |
| 5174 | | > open 1WMB |
| 5175 | | |
| 5176 | | 1wmb title: |
| 5177 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 5178 | | info...] |
| 5179 | | |
| 5180 | | Chain information for 1wmb #1 |
| 5181 | | --- |
| 5182 | | Chain | Description |
| 5183 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 5184 | | |
| 5185 | | Non-standard residues in 1wmb #1 |
| 5186 | | --- |
| 5187 | | CAC — cacodylate ion (dimethylarsinate) |
| 5188 | | MG — magnesium ion |
| 5189 | | |
| 5190 | | 1wmb mmCIF Assemblies |
| 5191 | | --- |
| 5192 | | 1| author_and_software_defined_assembly |
| 5193 | | |
| 5194 | | |
| 5195 | | > open 3I3O |
| 5196 | | |
| 5197 | | 3i3o title: |
| 5198 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 5199 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 5200 | | info...] |
| 5201 | | |
| 5202 | | Chain information for 3i3o #2 |
| 5203 | | --- |
| 5204 | | Chain | Description |
| 5205 | | A B C D E F G H | Short chain dehydrogenase |
| 5206 | | |
| 5207 | | Non-standard residues in 3i3o #2 |
| 5208 | | --- |
| 5209 | | CAC — cacodylate ion (dimethylarsinate) |
| 5210 | | CL — chloride ion |
| 5211 | | MG — magnesium ion |
| 5212 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 5213 | | |
| 5214 | | 3i3o mmCIF Assemblies |
| 5215 | | --- |
| 5216 | | 1| author_and_software_defined_assembly |
| 5217 | | 2| author_and_software_defined_assembly |
| 5218 | | |
| 5219 | | |
| 5220 | | > delete ~/a |
| 5221 | | |
| 5222 | | > delete solvent |
| 5223 | | |
| 5224 | | > mmaker #2 to #1 |
| 5225 | | |
| 5226 | | Parameters |
| 5227 | | --- |
| 5228 | | Chain pairing | bb |
| 5229 | | Alignment algorithm | Needleman-Wunsch |
| 5230 | | Similarity matrix | BLOSUM-62 |
| 5231 | | SS fraction | 0.3 |
| 5232 | | Gap open (HH/SS/other) | 18/18/6 |
| 5233 | | Gap extend | 1 |
| 5234 | | SS matrix | | | H | S | O |
| 5235 | | ---|---|---|--- |
| 5236 | | H | 6 | -9 | -6 |
| 5237 | | S | | 6 | -6 |
| 5238 | | O | | | 4 |
| 5239 | | Iteration cutoff | 2 |
| 5240 | | |
| 5241 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 5242 | | score = 499.7 |
| 5243 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 5244 | | 3.736) |
| 5245 | | |
| 5246 | | |
| 5247 | | > color #1 green |
| 5248 | | |
| 5249 | | > color #2 tan |
| 5250 | | |
| 5251 | | > color ~C byatom |
| 5252 | | |
| 5253 | | > ~display |
| 5254 | | |
| 5255 | | > display #1:138 #2:176 |
| 5256 | | |
| 5257 | | > style stick |
| 5258 | | |
| 5259 | | Changed 4099 atom styles |
| 5260 | | |
| 5261 | | > ribbon |
| 5262 | | |
| 5263 | | > transparency 60 target r |
| 5264 | | |
| 5265 | | > view |
| 5266 | | |
| 5267 | | > size #1:138 #2:176 stickRadius 0.3 |
| 5268 | | |
| 5269 | | Changed 14 bond radii |
| 5270 | | |
| 5271 | | > save fig1.jpg |
| 5272 | | |
| 5273 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 5274 | | |
| 5275 | | > sel-ca |
| 5276 | | |
| 5277 | | 13 atoms, 1 model selected |
| 5278 | | 26 atoms, 2 models selected |
| 5279 | | |
| 5280 | | > display sel-residues |
| 5281 | | |
| 5282 | | > color ~C byatom |
| 5283 | | |
| 5284 | | > style stick |
| 5285 | | |
| 5286 | | Changed 4099 atom styles |
| 5287 | | |
| 5288 | | > view #1:138 :< 5 pad -1 |
| 5289 | | |
| 5290 | | > hbonds #1:138 & #1 |
| 5291 | | |
| 5292 | | 3 hydrogen bonds found |
| 5293 | | |
| 5294 | | > hbonds #2:176 & #2 |
| 5295 | | |
| 5296 | | 4 hydrogen bonds found |
| 5297 | | |
| 5298 | | > transparency 90 target r |
| 5299 | | |
| 5300 | | > label #1:138 #2:176 offset 1,-1,1 |
| 5301 | | |
| 5302 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .92 |
| 5303 | | |
| 5304 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 5305 | | |
| 5306 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2 |
| 5307 | | > color green bgColor white |
| 5308 | | |
| 5309 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 5310 | | > color tan bgColor white |
| 5311 | | |
| 5312 | | > save fig2.jpg |
| 5313 | | |
| 5314 | | > ~ribbon |
| 5315 | | |
| 5316 | | > size stickRadius 0.05 |
| 5317 | | |
| 5318 | | Changed 4167 bond radii |
| 5319 | | |
| 5320 | | > size #1:138 stickRadius 0.2 |
| 5321 | | |
| 5322 | | Changed 7 bond radii |
| 5323 | | |
| 5324 | | > size #2:176 stickRadius 0.2 |
| 5325 | | |
| 5326 | | Changed 7 bond radii |
| 5327 | | |
| 5328 | | > save fig3.jpg |
| 5329 | | |
| 5330 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 5331 | | |
| 5332 | | > label sel-residues & #2 height 0.4 offset 0,0,0 color tan bgColor white |
| 5333 | | |
| 5334 | | > view sel-residues pad -1 |
| 5335 | | |
| 5336 | | > save fig4.jpg |
| 5337 | | |
| 5338 | | > align #2 & sel toAtoms #1 & sel |
| 5339 | | |
| 5340 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 5341 | | |
| 5342 | | > save fig5.jpg |
| 5343 | | |
| 5344 | | > ribbon sel |
| 5345 | | |
| 5346 | | > save fig6.jpg |
| 5347 | | |
| 5348 | | executed script.view.cxc |
| 5349 | | |
| 5350 | | > open "/Users/admin/Dropbox (Technion |
| 5351 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 5352 | | |
| 5353 | | > close |
| 5354 | | |
| 5355 | | > graphics bgColor white |
| 5356 | | |
| 5357 | | > open 1WMB |
| 5358 | | |
| 5359 | | 1wmb title: |
| 5360 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 5361 | | info...] |
| 5362 | | |
| 5363 | | Chain information for 1wmb #1 |
| 5364 | | --- |
| 5365 | | Chain | Description |
| 5366 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 5367 | | |
| 5368 | | Non-standard residues in 1wmb #1 |
| 5369 | | --- |
| 5370 | | CAC — cacodylate ion (dimethylarsinate) |
| 5371 | | MG — magnesium ion |
| 5372 | | |
| 5373 | | 1wmb mmCIF Assemblies |
| 5374 | | --- |
| 5375 | | 1| author_and_software_defined_assembly |
| 5376 | | |
| 5377 | | |
| 5378 | | > open 3I3O |
| 5379 | | |
| 5380 | | 3i3o title: |
| 5381 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 5382 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 5383 | | info...] |
| 5384 | | |
| 5385 | | Chain information for 3i3o #2 |
| 5386 | | --- |
| 5387 | | Chain | Description |
| 5388 | | A B C D E F G H | Short chain dehydrogenase |
| 5389 | | |
| 5390 | | Non-standard residues in 3i3o #2 |
| 5391 | | --- |
| 5392 | | CAC — cacodylate ion (dimethylarsinate) |
| 5393 | | CL — chloride ion |
| 5394 | | MG — magnesium ion |
| 5395 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 5396 | | |
| 5397 | | 3i3o mmCIF Assemblies |
| 5398 | | --- |
| 5399 | | 1| author_and_software_defined_assembly |
| 5400 | | 2| author_and_software_defined_assembly |
| 5401 | | |
| 5402 | | |
| 5403 | | > delete ~/a |
| 5404 | | |
| 5405 | | > delete solvent |
| 5406 | | |
| 5407 | | > mmaker #2 to #1 |
| 5408 | | |
| 5409 | | Parameters |
| 5410 | | --- |
| 5411 | | Chain pairing | bb |
| 5412 | | Alignment algorithm | Needleman-Wunsch |
| 5413 | | Similarity matrix | BLOSUM-62 |
| 5414 | | SS fraction | 0.3 |
| 5415 | | Gap open (HH/SS/other) | 18/18/6 |
| 5416 | | Gap extend | 1 |
| 5417 | | SS matrix | | | H | S | O |
| 5418 | | ---|---|---|--- |
| 5419 | | H | 6 | -9 | -6 |
| 5420 | | S | | 6 | -6 |
| 5421 | | O | | | 4 |
| 5422 | | Iteration cutoff | 2 |
| 5423 | | |
| 5424 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 5425 | | score = 499.7 |
| 5426 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 5427 | | 3.736) |
| 5428 | | |
| 5429 | | |
| 5430 | | > color #1 green |
| 5431 | | |
| 5432 | | > color #2 tan |
| 5433 | | |
| 5434 | | > color ~C byatom |
| 5435 | | |
| 5436 | | > ~display |
| 5437 | | |
| 5438 | | > display #1:138 #2:176 |
| 5439 | | |
| 5440 | | > style stick |
| 5441 | | |
| 5442 | | Changed 4099 atom styles |
| 5443 | | |
| 5444 | | > ribbon |
| 5445 | | |
| 5446 | | > transparency 60 target r |
| 5447 | | |
| 5448 | | > view |
| 5449 | | |
| 5450 | | > size #1:138 #2:176 stickRadius 0.3 |
| 5451 | | |
| 5452 | | Changed 14 bond radii |
| 5453 | | |
| 5454 | | > save fig1.jpg |
| 5455 | | |
| 5456 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 5457 | | |
| 5458 | | > sel-ca |
| 5459 | | |
| 5460 | | 13 atoms, 1 model selected |
| 5461 | | 26 atoms, 2 models selected |
| 5462 | | |
| 5463 | | > display sel-residues |
| 5464 | | |
| 5465 | | > color ~C byatom |
| 5466 | | |
| 5467 | | > style stick |
| 5468 | | |
| 5469 | | Changed 4099 atom styles |
| 5470 | | |
| 5471 | | > view #1:138 :< 5 pad -1 |
| 5472 | | |
| 5473 | | > hbonds #1:138 & #1 |
| 5474 | | |
| 5475 | | 3 hydrogen bonds found |
| 5476 | | |
| 5477 | | > hbonds #2:176 & #2 |
| 5478 | | |
| 5479 | | 4 hydrogen bonds found |
| 5480 | | |
| 5481 | | > transparency 90 target r |
| 5482 | | |
| 5483 | | > label #1:138 #2:176 offset 1,-1,1 |
| 5484 | | |
| 5485 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .92 |
| 5486 | | |
| 5487 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 5488 | | |
| 5489 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2 |
| 5490 | | > color green bgColor white |
| 5491 | | |
| 5492 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 5493 | | > color tan bgColor white |
| 5494 | | |
| 5495 | | > ~select |
| 5496 | | |
| 5497 | | Nothing selected |
| 5498 | | |
| 5499 | | > save fig2.jpg |
| 5500 | | |
| 5501 | | > ~ribbon |
| 5502 | | |
| 5503 | | > size stickRadius 0.05 |
| 5504 | | |
| 5505 | | Changed 4167 bond radii |
| 5506 | | |
| 5507 | | > size #1:138 stickRadius 0.2 |
| 5508 | | |
| 5509 | | Changed 7 bond radii |
| 5510 | | |
| 5511 | | > size #2:176 stickRadius 0.2 |
| 5512 | | |
| 5513 | | Changed 7 bond radii |
| 5514 | | |
| 5515 | | > save fig3.jpg |
| 5516 | | |
| 5517 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 5518 | | |
| 5519 | | > label sel-residues & #2 height 0.4 offset 0,0,0 color tan bgColor white |
| 5520 | | |
| 5521 | | > view sel-residues pad -1 |
| 5522 | | |
| 5523 | | No objects specified. |
| 5524 | | |
| 5525 | | > open "/Users/admin/Dropbox (Technion |
| 5526 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 5527 | | |
| 5528 | | > close |
| 5529 | | |
| 5530 | | > graphics bgColor white |
| 5531 | | |
| 5532 | | > open 1WMB |
| 5533 | | |
| 5534 | | 1wmb title: |
| 5535 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 5536 | | info...] |
| 5537 | | |
| 5538 | | Chain information for 1wmb #1 |
| 5539 | | --- |
| 5540 | | Chain | Description |
| 5541 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 5542 | | |
| 5543 | | Non-standard residues in 1wmb #1 |
| 5544 | | --- |
| 5545 | | CAC — cacodylate ion (dimethylarsinate) |
| 5546 | | MG — magnesium ion |
| 5547 | | |
| 5548 | | 1wmb mmCIF Assemblies |
| 5549 | | --- |
| 5550 | | 1| author_and_software_defined_assembly |
| 5551 | | |
| 5552 | | |
| 5553 | | > open 3I3O |
| 5554 | | |
| 5555 | | 3i3o title: |
| 5556 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 5557 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 5558 | | info...] |
| 5559 | | |
| 5560 | | Chain information for 3i3o #2 |
| 5561 | | --- |
| 5562 | | Chain | Description |
| 5563 | | A B C D E F G H | Short chain dehydrogenase |
| 5564 | | |
| 5565 | | Non-standard residues in 3i3o #2 |
| 5566 | | --- |
| 5567 | | CAC — cacodylate ion (dimethylarsinate) |
| 5568 | | CL — chloride ion |
| 5569 | | MG — magnesium ion |
| 5570 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 5571 | | |
| 5572 | | 3i3o mmCIF Assemblies |
| 5573 | | --- |
| 5574 | | 1| author_and_software_defined_assembly |
| 5575 | | 2| author_and_software_defined_assembly |
| 5576 | | |
| 5577 | | |
| 5578 | | > delete ~/a |
| 5579 | | |
| 5580 | | > delete solvent |
| 5581 | | |
| 5582 | | > mmaker #2 to #1 |
| 5583 | | |
| 5584 | | Parameters |
| 5585 | | --- |
| 5586 | | Chain pairing | bb |
| 5587 | | Alignment algorithm | Needleman-Wunsch |
| 5588 | | Similarity matrix | BLOSUM-62 |
| 5589 | | SS fraction | 0.3 |
| 5590 | | Gap open (HH/SS/other) | 18/18/6 |
| 5591 | | Gap extend | 1 |
| 5592 | | SS matrix | | | H | S | O |
| 5593 | | ---|---|---|--- |
| 5594 | | H | 6 | -9 | -6 |
| 5595 | | S | | 6 | -6 |
| 5596 | | O | | | 4 |
| 5597 | | Iteration cutoff | 2 |
| 5598 | | |
| 5599 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 5600 | | score = 499.7 |
| 5601 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 5602 | | 3.736) |
| 5603 | | |
| 5604 | | |
| 5605 | | > color #1 green |
| 5606 | | |
| 5607 | | > color #2 tan |
| 5608 | | |
| 5609 | | > color ~C byatom |
| 5610 | | |
| 5611 | | > ~display |
| 5612 | | |
| 5613 | | > display #1:138 #2:176 |
| 5614 | | |
| 5615 | | > style stick |
| 5616 | | |
| 5617 | | Changed 4099 atom styles |
| 5618 | | |
| 5619 | | > ribbon |
| 5620 | | |
| 5621 | | > transparency 60 target r |
| 5622 | | |
| 5623 | | > view |
| 5624 | | |
| 5625 | | > size #1:138 #2:176 stickRadius 0.3 |
| 5626 | | |
| 5627 | | Changed 14 bond radii |
| 5628 | | |
| 5629 | | > save fig1.jpg |
| 5630 | | |
| 5631 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 5632 | | |
| 5633 | | > sel-ca |
| 5634 | | |
| 5635 | | 13 atoms, 1 model selected |
| 5636 | | 26 atoms, 2 models selected |
| 5637 | | |
| 5638 | | > display sel-residues |
| 5639 | | |
| 5640 | | > color ~C byatom |
| 5641 | | |
| 5642 | | > style stick |
| 5643 | | |
| 5644 | | Changed 4099 atom styles |
| 5645 | | |
| 5646 | | > view #1:138 :< 5 pad -1 |
| 5647 | | |
| 5648 | | > hbonds #1:138 & #1 |
| 5649 | | |
| 5650 | | 3 hydrogen bonds found |
| 5651 | | |
| 5652 | | > hbonds #2:176 & #2 |
| 5653 | | |
| 5654 | | 4 hydrogen bonds found |
| 5655 | | |
| 5656 | | > transparency 90 target r |
| 5657 | | |
| 5658 | | > label #1:138 #2:176 offset 1,-1,1 |
| 5659 | | |
| 5660 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .92 |
| 5661 | | |
| 5662 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 5663 | | |
| 5664 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2 |
| 5665 | | > color green bgColor white |
| 5666 | | |
| 5667 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 5668 | | > color tan bgColor white |
| 5669 | | |
| 5670 | | > ~select |
| 5671 | | |
| 5672 | | Nothing selected |
| 5673 | | |
| 5674 | | > save fig2.jpg |
| 5675 | | |
| 5676 | | > sel-ca |
| 5677 | | |
| 5678 | | 13 atoms, 1 model selected |
| 5679 | | 26 atoms, 2 models selected |
| 5680 | | |
| 5681 | | > ~ribbon |
| 5682 | | |
| 5683 | | > size stickRadius 0.05 |
| 5684 | | |
| 5685 | | Changed 4167 bond radii |
| 5686 | | |
| 5687 | | > size #1:138 stickRadius 0.2 |
| 5688 | | |
| 5689 | | Changed 7 bond radii |
| 5690 | | |
| 5691 | | > size #2:176 stickRadius 0.2 |
| 5692 | | |
| 5693 | | Changed 7 bond radii |
| 5694 | | |
| 5695 | | > ~select |
| 5696 | | |
| 5697 | | Nothing selected |
| 5698 | | |
| 5699 | | > save fig3.jpg |
| 5700 | | |
| 5701 | | > sel-ca |
| 5702 | | |
| 5703 | | 13 atoms, 1 model selected |
| 5704 | | 26 atoms, 2 models selected |
| 5705 | | |
| 5706 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 5707 | | |
| 5708 | | > label sel-residues & #2 height 0.4 offset 0,0,0 color tan bgColor white |
| 5709 | | |
| 5710 | | > view sel-residues pad -1 |
| 5711 | | |
| 5712 | | > ~select |
| 5713 | | |
| 5714 | | Nothing selected |
| 5715 | | |
| 5716 | | > save fig4.jpg |
| 5717 | | |
| 5718 | | > sel-ca |
| 5719 | | |
| 5720 | | 13 atoms, 1 model selected |
| 5721 | | 26 atoms, 2 models selected |
| 5722 | | |
| 5723 | | > align #2 & sel toAtoms #1 & sel |
| 5724 | | |
| 5725 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 5726 | | |
| 5727 | | > ~select |
| 5728 | | |
| 5729 | | Nothing selected |
| 5730 | | |
| 5731 | | > save fig5.jpg |
| 5732 | | |
| 5733 | | > sel-ca |
| 5734 | | |
| 5735 | | 13 atoms, 1 model selected |
| 5736 | | 26 atoms, 2 models selected |
| 5737 | | |
| 5738 | | > ribbon sel |
| 5739 | | |
| 5740 | | > ~select |
| 5741 | | |
| 5742 | | Nothing selected |
| 5743 | | |
| 5744 | | > save fig6.jpg |
| 5745 | | |
| 5746 | | executed script.view.cxc |
| 5747 | | |
| 5748 | | > open "/Users/admin/Dropbox (Technion |
| 5749 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 5750 | | |
| 5751 | | > close |
| 5752 | | |
| 5753 | | > graphics bgColor white |
| 5754 | | |
| 5755 | | > open 1WMB |
| 5756 | | |
| 5757 | | 1wmb title: |
| 5758 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 5759 | | info...] |
| 5760 | | |
| 5761 | | Chain information for 1wmb #1 |
| 5762 | | --- |
| 5763 | | Chain | Description |
| 5764 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 5765 | | |
| 5766 | | Non-standard residues in 1wmb #1 |
| 5767 | | --- |
| 5768 | | CAC — cacodylate ion (dimethylarsinate) |
| 5769 | | MG — magnesium ion |
| 5770 | | |
| 5771 | | 1wmb mmCIF Assemblies |
| 5772 | | --- |
| 5773 | | 1| author_and_software_defined_assembly |
| 5774 | | |
| 5775 | | |
| 5776 | | > open 3I3O |
| 5777 | | |
| 5778 | | 3i3o title: |
| 5779 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 5780 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 5781 | | info...] |
| 5782 | | |
| 5783 | | Chain information for 3i3o #2 |
| 5784 | | --- |
| 5785 | | Chain | Description |
| 5786 | | A B C D E F G H | Short chain dehydrogenase |
| 5787 | | |
| 5788 | | Non-standard residues in 3i3o #2 |
| 5789 | | --- |
| 5790 | | CAC — cacodylate ion (dimethylarsinate) |
| 5791 | | CL — chloride ion |
| 5792 | | MG — magnesium ion |
| 5793 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 5794 | | |
| 5795 | | 3i3o mmCIF Assemblies |
| 5796 | | --- |
| 5797 | | 1| author_and_software_defined_assembly |
| 5798 | | 2| author_and_software_defined_assembly |
| 5799 | | |
| 5800 | | |
| 5801 | | > delete ~/a |
| 5802 | | |
| 5803 | | > delete solvent |
| 5804 | | |
| 5805 | | > mmaker #2 to #1 |
| 5806 | | |
| 5807 | | Parameters |
| 5808 | | --- |
| 5809 | | Chain pairing | bb |
| 5810 | | Alignment algorithm | Needleman-Wunsch |
| 5811 | | Similarity matrix | BLOSUM-62 |
| 5812 | | SS fraction | 0.3 |
| 5813 | | Gap open (HH/SS/other) | 18/18/6 |
| 5814 | | Gap extend | 1 |
| 5815 | | SS matrix | | | H | S | O |
| 5816 | | ---|---|---|--- |
| 5817 | | H | 6 | -9 | -6 |
| 5818 | | S | | 6 | -6 |
| 5819 | | O | | | 4 |
| 5820 | | Iteration cutoff | 2 |
| 5821 | | |
| 5822 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 5823 | | score = 499.7 |
| 5824 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 5825 | | 3.736) |
| 5826 | | |
| 5827 | | |
| 5828 | | > color #1 green |
| 5829 | | |
| 5830 | | > color #2 tan |
| 5831 | | |
| 5832 | | > color ~C byatom |
| 5833 | | |
| 5834 | | > ~display |
| 5835 | | |
| 5836 | | > display #1:138 #2:176 |
| 5837 | | |
| 5838 | | > style stick |
| 5839 | | |
| 5840 | | Changed 4099 atom styles |
| 5841 | | |
| 5842 | | > ribbon |
| 5843 | | |
| 5844 | | > transparency 60 target r |
| 5845 | | |
| 5846 | | > view |
| 5847 | | |
| 5848 | | > size #1:138 #2:176 stickRadius 0.3 |
| 5849 | | |
| 5850 | | Changed 14 bond radii |
| 5851 | | |
| 5852 | | > save fig1.jpg |
| 5853 | | |
| 5854 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 5855 | | |
| 5856 | | > sel-ca |
| 5857 | | |
| 5858 | | 13 atoms, 1 model selected |
| 5859 | | 26 atoms, 2 models selected |
| 5860 | | |
| 5861 | | > display sel-residues |
| 5862 | | |
| 5863 | | > color ~C byatom |
| 5864 | | |
| 5865 | | > style stick |
| 5866 | | |
| 5867 | | Changed 4099 atom styles |
| 5868 | | |
| 5869 | | > view #1:138 :< 5 pad -1 |
| 5870 | | |
| 5871 | | > hbonds #1:138 & #1 |
| 5872 | | |
| 5873 | | 3 hydrogen bonds found |
| 5874 | | |
| 5875 | | > hbonds #2:176 & #2 |
| 5876 | | |
| 5877 | | 4 hydrogen bonds found |
| 5878 | | |
| 5879 | | > transparency 90 target r |
| 5880 | | |
| 5881 | | > label #1:138 #2:176 offset 1,-1,1 |
| 5882 | | |
| 5883 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .92 |
| 5884 | | |
| 5885 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 5886 | | |
| 5887 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2 |
| 5888 | | > color green bgColor white |
| 5889 | | |
| 5890 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 5891 | | > color tan bgColor white |
| 5892 | | |
| 5893 | | > ~select |
| 5894 | | |
| 5895 | | Nothing selected |
| 5896 | | |
| 5897 | | > save fig2.jpg |
| 5898 | | |
| 5899 | | > sel-ca |
| 5900 | | |
| 5901 | | 13 atoms, 1 model selected |
| 5902 | | 26 atoms, 2 models selected |
| 5903 | | |
| 5904 | | > ~ribbon |
| 5905 | | |
| 5906 | | > size stickRadius 0.05 |
| 5907 | | |
| 5908 | | Changed 4167 bond radii |
| 5909 | | |
| 5910 | | > size #1:138 stickRadius 0.2 |
| 5911 | | |
| 5912 | | Changed 7 bond radii |
| 5913 | | |
| 5914 | | > size #2:176 stickRadius 0.2 |
| 5915 | | |
| 5916 | | Changed 7 bond radii |
| 5917 | | |
| 5918 | | > ~select |
| 5919 | | |
| 5920 | | Nothing selected |
| 5921 | | |
| 5922 | | > save fig3.jpg |
| 5923 | | |
| 5924 | | > sel-ca |
| 5925 | | |
| 5926 | | 13 atoms, 1 model selected |
| 5927 | | 26 atoms, 2 models selected |
| 5928 | | |
| 5929 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 5930 | | |
| 5931 | | > label sel-residues & #2 height 0.4 offset 0,0,0 color tan bgColor white |
| 5932 | | |
| 5933 | | > view sel-residues pad -1 |
| 5934 | | |
| 5935 | | > sel-ca |
| 5936 | | |
| 5937 | | 13 atoms, 1 model selected |
| 5938 | | 26 atoms, 2 models selected |
| 5939 | | |
| 5940 | | > align #2 & sel toAtoms #1 & sel |
| 5941 | | |
| 5942 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 5943 | | |
| 5944 | | > ~select |
| 5945 | | |
| 5946 | | Nothing selected |
| 5947 | | |
| 5948 | | > save fig4.jpg |
| 5949 | | |
| 5950 | | > sel-ca |
| 5951 | | |
| 5952 | | 13 atoms, 1 model selected |
| 5953 | | 26 atoms, 2 models selected |
| 5954 | | |
| 5955 | | > ribbon sel |
| 5956 | | |
| 5957 | | > ~select |
| 5958 | | |
| 5959 | | Nothing selected |
| 5960 | | |
| 5961 | | > save fig5.jpg |
| 5962 | | |
| 5963 | | executed script.view.cxc |
| 5964 | | |
| 5965 | | > open "/Users/admin/Dropbox (Technion |
| 5966 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 5967 | | |
| 5968 | | > close |
| 5969 | | |
| 5970 | | > graphics bgColor white |
| 5971 | | |
| 5972 | | > open 1WMB |
| 5973 | | |
| 5974 | | 1wmb title: |
| 5975 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 5976 | | info...] |
| 5977 | | |
| 5978 | | Chain information for 1wmb #1 |
| 5979 | | --- |
| 5980 | | Chain | Description |
| 5981 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 5982 | | |
| 5983 | | Non-standard residues in 1wmb #1 |
| 5984 | | --- |
| 5985 | | CAC — cacodylate ion (dimethylarsinate) |
| 5986 | | MG — magnesium ion |
| 5987 | | |
| 5988 | | 1wmb mmCIF Assemblies |
| 5989 | | --- |
| 5990 | | 1| author_and_software_defined_assembly |
| 5991 | | |
| 5992 | | |
| 5993 | | > open 3I3O |
| 5994 | | |
| 5995 | | 3i3o title: |
| 5996 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 5997 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 5998 | | info...] |
| 5999 | | |
| 6000 | | Chain information for 3i3o #2 |
| 6001 | | --- |
| 6002 | | Chain | Description |
| 6003 | | A B C D E F G H | Short chain dehydrogenase |
| 6004 | | |
| 6005 | | Non-standard residues in 3i3o #2 |
| 6006 | | --- |
| 6007 | | CAC — cacodylate ion (dimethylarsinate) |
| 6008 | | CL — chloride ion |
| 6009 | | MG — magnesium ion |
| 6010 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 6011 | | |
| 6012 | | 3i3o mmCIF Assemblies |
| 6013 | | --- |
| 6014 | | 1| author_and_software_defined_assembly |
| 6015 | | 2| author_and_software_defined_assembly |
| 6016 | | |
| 6017 | | |
| 6018 | | > delete ~/a |
| 6019 | | |
| 6020 | | > delete solvent |
| 6021 | | |
| 6022 | | > mmaker #2 to #1 |
| 6023 | | |
| 6024 | | Parameters |
| 6025 | | --- |
| 6026 | | Chain pairing | bb |
| 6027 | | Alignment algorithm | Needleman-Wunsch |
| 6028 | | Similarity matrix | BLOSUM-62 |
| 6029 | | SS fraction | 0.3 |
| 6030 | | Gap open (HH/SS/other) | 18/18/6 |
| 6031 | | Gap extend | 1 |
| 6032 | | SS matrix | | | H | S | O |
| 6033 | | ---|---|---|--- |
| 6034 | | H | 6 | -9 | -6 |
| 6035 | | S | | 6 | -6 |
| 6036 | | O | | | 4 |
| 6037 | | Iteration cutoff | 2 |
| 6038 | | |
| 6039 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 6040 | | score = 499.7 |
| 6041 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 6042 | | 3.736) |
| 6043 | | |
| 6044 | | |
| 6045 | | > color #1 green |
| 6046 | | |
| 6047 | | > color #2 tan |
| 6048 | | |
| 6049 | | > color ~C byatom |
| 6050 | | |
| 6051 | | > ~display |
| 6052 | | |
| 6053 | | > display #1:138 #2:176 |
| 6054 | | |
| 6055 | | > style stick |
| 6056 | | |
| 6057 | | Changed 4099 atom styles |
| 6058 | | |
| 6059 | | > ribbon |
| 6060 | | |
| 6061 | | > transparency 60 target r |
| 6062 | | |
| 6063 | | > view |
| 6064 | | |
| 6065 | | > size #1:138 #2:176 stickRadius 0.3 |
| 6066 | | |
| 6067 | | Changed 14 bond radii |
| 6068 | | |
| 6069 | | > save fig1.jpg |
| 6070 | | |
| 6071 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 6072 | | |
| 6073 | | > sel-ca |
| 6074 | | |
| 6075 | | 13 atoms, 1 model selected |
| 6076 | | 26 atoms, 2 models selected |
| 6077 | | |
| 6078 | | > display sel-residues |
| 6079 | | |
| 6080 | | > color ~C byatom |
| 6081 | | |
| 6082 | | > style stick |
| 6083 | | |
| 6084 | | Changed 4099 atom styles |
| 6085 | | |
| 6086 | | > view #1:138 :< 5 pad -1 |
| 6087 | | |
| 6088 | | > hbonds #1:138 & #1 |
| 6089 | | |
| 6090 | | 3 hydrogen bonds found |
| 6091 | | |
| 6092 | | > hbonds #2:176 & #2 |
| 6093 | | |
| 6094 | | 4 hydrogen bonds found |
| 6095 | | |
| 6096 | | > transparency 90 target r |
| 6097 | | |
| 6098 | | > label #1:138 #2:176 offset 1,-1,1 |
| 6099 | | |
| 6100 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .92 |
| 6101 | | |
| 6102 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 6103 | | |
| 6104 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2 |
| 6105 | | > color green bgColor white |
| 6106 | | |
| 6107 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 6108 | | > color tan bgColor white |
| 6109 | | |
| 6110 | | > ~select |
| 6111 | | |
| 6112 | | Nothing selected |
| 6113 | | |
| 6114 | | > save fig2.jpg |
| 6115 | | |
| 6116 | | > sel-ca |
| 6117 | | |
| 6118 | | 13 atoms, 1 model selected |
| 6119 | | 26 atoms, 2 models selected |
| 6120 | | |
| 6121 | | > ~ribbon |
| 6122 | | |
| 6123 | | > size stickRadius 0.05 |
| 6124 | | |
| 6125 | | Changed 4167 bond radii |
| 6126 | | |
| 6127 | | > size #1:138 stickRadius 0.2 |
| 6128 | | |
| 6129 | | Changed 7 bond radii |
| 6130 | | |
| 6131 | | > size #2:176 stickRadius 0.2 |
| 6132 | | |
| 6133 | | Changed 7 bond radii |
| 6134 | | |
| 6135 | | > view sel-residues pad -1 |
| 6136 | | |
| 6137 | | > ~select |
| 6138 | | |
| 6139 | | Nothing selected |
| 6140 | | |
| 6141 | | > save fig3.jpg |
| 6142 | | |
| 6143 | | > sel-ca |
| 6144 | | |
| 6145 | | 13 atoms, 1 model selected |
| 6146 | | 26 atoms, 2 models selected |
| 6147 | | |
| 6148 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 6149 | | |
| 6150 | | > label sel-residues & #2 height 0.4 offset 0,0,0 color tan bgColor white |
| 6151 | | |
| 6152 | | > view sel-residues pad -1 |
| 6153 | | |
| 6154 | | > sel-ca |
| 6155 | | |
| 6156 | | 13 atoms, 1 model selected |
| 6157 | | 26 atoms, 2 models selected |
| 6158 | | |
| 6159 | | > align #2 & sel toAtoms #1 & sel |
| 6160 | | |
| 6161 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 6162 | | |
| 6163 | | > ~select |
| 6164 | | |
| 6165 | | Nothing selected |
| 6166 | | |
| 6167 | | > save fig4.jpg |
| 6168 | | |
| 6169 | | > sel-ca |
| 6170 | | |
| 6171 | | 13 atoms, 1 model selected |
| 6172 | | 26 atoms, 2 models selected |
| 6173 | | |
| 6174 | | > ribbon sel |
| 6175 | | |
| 6176 | | > ~select |
| 6177 | | |
| 6178 | | Nothing selected |
| 6179 | | |
| 6180 | | > save fig5.jpg |
| 6181 | | |
| 6182 | | executed script.view.cxc |
| 6183 | | |
| 6184 | | > hide #3 models |
| 6185 | | |
| 6186 | | > show #3 models |
| 6187 | | |
| 6188 | | > hide #!1 models |
| 6189 | | |
| 6190 | | > show #!1 models |
| 6191 | | |
| 6192 | | > hide #!1 models |
| 6193 | | |
| 6194 | | > show #!1 models |
| 6195 | | |
| 6196 | | > open "/Users/admin/Dropbox (Technion |
| 6197 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 6198 | | |
| 6199 | | > close |
| 6200 | | |
| 6201 | | > graphics bgColor white |
| 6202 | | |
| 6203 | | > open 1WMB |
| 6204 | | |
| 6205 | | 1wmb title: |
| 6206 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 6207 | | info...] |
| 6208 | | |
| 6209 | | Chain information for 1wmb #1 |
| 6210 | | --- |
| 6211 | | Chain | Description |
| 6212 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 6213 | | |
| 6214 | | Non-standard residues in 1wmb #1 |
| 6215 | | --- |
| 6216 | | CAC — cacodylate ion (dimethylarsinate) |
| 6217 | | MG — magnesium ion |
| 6218 | | |
| 6219 | | 1wmb mmCIF Assemblies |
| 6220 | | --- |
| 6221 | | 1| author_and_software_defined_assembly |
| 6222 | | |
| 6223 | | |
| 6224 | | > open 3I3O |
| 6225 | | |
| 6226 | | 3i3o title: |
| 6227 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 6228 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 6229 | | info...] |
| 6230 | | |
| 6231 | | Chain information for 3i3o #2 |
| 6232 | | --- |
| 6233 | | Chain | Description |
| 6234 | | A B C D E F G H | Short chain dehydrogenase |
| 6235 | | |
| 6236 | | Non-standard residues in 3i3o #2 |
| 6237 | | --- |
| 6238 | | CAC — cacodylate ion (dimethylarsinate) |
| 6239 | | CL — chloride ion |
| 6240 | | MG — magnesium ion |
| 6241 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 6242 | | |
| 6243 | | 3i3o mmCIF Assemblies |
| 6244 | | --- |
| 6245 | | 1| author_and_software_defined_assembly |
| 6246 | | 2| author_and_software_defined_assembly |
| 6247 | | |
| 6248 | | |
| 6249 | | > delete ~/a |
| 6250 | | |
| 6251 | | > delete solvent |
| 6252 | | |
| 6253 | | > mmaker #2 to #1 |
| 6254 | | |
| 6255 | | Parameters |
| 6256 | | --- |
| 6257 | | Chain pairing | bb |
| 6258 | | Alignment algorithm | Needleman-Wunsch |
| 6259 | | Similarity matrix | BLOSUM-62 |
| 6260 | | SS fraction | 0.3 |
| 6261 | | Gap open (HH/SS/other) | 18/18/6 |
| 6262 | | Gap extend | 1 |
| 6263 | | SS matrix | | | H | S | O |
| 6264 | | ---|---|---|--- |
| 6265 | | H | 6 | -9 | -6 |
| 6266 | | S | | 6 | -6 |
| 6267 | | O | | | 4 |
| 6268 | | Iteration cutoff | 2 |
| 6269 | | |
| 6270 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 6271 | | score = 499.7 |
| 6272 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 6273 | | 3.736) |
| 6274 | | |
| 6275 | | |
| 6276 | | > color #1 green |
| 6277 | | |
| 6278 | | > color #2 tan |
| 6279 | | |
| 6280 | | > color ~C byatom |
| 6281 | | |
| 6282 | | > ~display |
| 6283 | | |
| 6284 | | > display #1:138 #2:176 |
| 6285 | | |
| 6286 | | > style stick |
| 6287 | | |
| 6288 | | Changed 4099 atom styles |
| 6289 | | |
| 6290 | | > ribbon |
| 6291 | | |
| 6292 | | > transparency 60 target r |
| 6293 | | |
| 6294 | | > view |
| 6295 | | |
| 6296 | | > size #1:138 #2:176 stickRadius 0.3 |
| 6297 | | |
| 6298 | | Changed 14 bond radii |
| 6299 | | |
| 6300 | | > save fig1.jpg |
| 6301 | | |
| 6302 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 6303 | | |
| 6304 | | > sel-ca |
| 6305 | | |
| 6306 | | 13 atoms, 1 model selected |
| 6307 | | 26 atoms, 2 models selected |
| 6308 | | |
| 6309 | | > display sel-residues |
| 6310 | | |
| 6311 | | > color ~C byatom |
| 6312 | | |
| 6313 | | > style stick |
| 6314 | | |
| 6315 | | Changed 4099 atom styles |
| 6316 | | |
| 6317 | | > view #1:138 :< 5 pad -1 |
| 6318 | | |
| 6319 | | > hbonds #1:138 & #1 color green |
| 6320 | | |
| 6321 | | 3 hydrogen bonds found |
| 6322 | | |
| 6323 | | > hbonds #2:176 & #2 color tan |
| 6324 | | |
| 6325 | | 4 hydrogen bonds found |
| 6326 | | |
| 6327 | | > transparency 90 target r |
| 6328 | | |
| 6329 | | > label #1:138 #2:176 offset 1,-1,1 |
| 6330 | | |
| 6331 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .92 |
| 6332 | | |
| 6333 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 6334 | | |
| 6335 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2 |
| 6336 | | > color green bgColor white |
| 6337 | | |
| 6338 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 6339 | | > color tan bgColor white |
| 6340 | | |
| 6341 | | > ~select |
| 6342 | | |
| 6343 | | Nothing selected |
| 6344 | | |
| 6345 | | > save fig2.jpg |
| 6346 | | |
| 6347 | | > sel-ca |
| 6348 | | |
| 6349 | | 13 atoms, 1 model selected |
| 6350 | | 26 atoms, 2 models selected |
| 6351 | | |
| 6352 | | > ~ribbon |
| 6353 | | |
| 6354 | | > size stickRadius 0.05 |
| 6355 | | |
| 6356 | | Changed 4167 bond radii |
| 6357 | | |
| 6358 | | > size #1:138 stickRadius 0.2 |
| 6359 | | |
| 6360 | | Changed 7 bond radii |
| 6361 | | |
| 6362 | | > size #2:176 stickRadius 0.2 |
| 6363 | | |
| 6364 | | Changed 7 bond radii |
| 6365 | | |
| 6366 | | > view sel-residues pad -1 |
| 6367 | | |
| 6368 | | > ~select |
| 6369 | | |
| 6370 | | Nothing selected |
| 6371 | | |
| 6372 | | > save fig3.jpg |
| 6373 | | |
| 6374 | | > sel-ca |
| 6375 | | |
| 6376 | | 13 atoms, 1 model selected |
| 6377 | | 26 atoms, 2 models selected |
| 6378 | | |
| 6379 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 6380 | | |
| 6381 | | > label sel-residues & #2 height 0.4 offset 0,0,0 color tan bgColor white |
| 6382 | | |
| 6383 | | > view sel-residues pad -1 |
| 6384 | | |
| 6385 | | > sel-ca |
| 6386 | | |
| 6387 | | 13 atoms, 1 model selected |
| 6388 | | 26 atoms, 2 models selected |
| 6389 | | |
| 6390 | | > align #2 & sel toAtoms #1 & sel |
| 6391 | | |
| 6392 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 6393 | | |
| 6394 | | > ~select |
| 6395 | | |
| 6396 | | Nothing selected |
| 6397 | | |
| 6398 | | > save fig4.jpg |
| 6399 | | |
| 6400 | | > sel-ca |
| 6401 | | |
| 6402 | | 13 atoms, 1 model selected |
| 6403 | | 26 atoms, 2 models selected |
| 6404 | | |
| 6405 | | > ribbon sel |
| 6406 | | |
| 6407 | | > ~select |
| 6408 | | |
| 6409 | | Nothing selected |
| 6410 | | |
| 6411 | | > save fig5.jpg |
| 6412 | | |
| 6413 | | executed script.view.cxc |
| 6414 | | |
| 6415 | | > open "/Users/admin/Dropbox (Technion |
| 6416 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 6417 | | |
| 6418 | | > close |
| 6419 | | |
| 6420 | | > graphics bgColor white |
| 6421 | | |
| 6422 | | > open 1WMB |
| 6423 | | |
| 6424 | | 1wmb title: |
| 6425 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 6426 | | info...] |
| 6427 | | |
| 6428 | | Chain information for 1wmb #1 |
| 6429 | | --- |
| 6430 | | Chain | Description |
| 6431 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 6432 | | |
| 6433 | | Non-standard residues in 1wmb #1 |
| 6434 | | --- |
| 6435 | | CAC — cacodylate ion (dimethylarsinate) |
| 6436 | | MG — magnesium ion |
| 6437 | | |
| 6438 | | 1wmb mmCIF Assemblies |
| 6439 | | --- |
| 6440 | | 1| author_and_software_defined_assembly |
| 6441 | | |
| 6442 | | |
| 6443 | | > open 3I3O |
| 6444 | | |
| 6445 | | 3i3o title: |
| 6446 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 6447 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 6448 | | info...] |
| 6449 | | |
| 6450 | | Chain information for 3i3o #2 |
| 6451 | | --- |
| 6452 | | Chain | Description |
| 6453 | | A B C D E F G H | Short chain dehydrogenase |
| 6454 | | |
| 6455 | | Non-standard residues in 3i3o #2 |
| 6456 | | --- |
| 6457 | | CAC — cacodylate ion (dimethylarsinate) |
| 6458 | | CL — chloride ion |
| 6459 | | MG — magnesium ion |
| 6460 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 6461 | | |
| 6462 | | 3i3o mmCIF Assemblies |
| 6463 | | --- |
| 6464 | | 1| author_and_software_defined_assembly |
| 6465 | | 2| author_and_software_defined_assembly |
| 6466 | | |
| 6467 | | |
| 6468 | | > delete ~/a |
| 6469 | | |
| 6470 | | > delete solvent |
| 6471 | | |
| 6472 | | > mmaker #2 to #1 |
| 6473 | | |
| 6474 | | Parameters |
| 6475 | | --- |
| 6476 | | Chain pairing | bb |
| 6477 | | Alignment algorithm | Needleman-Wunsch |
| 6478 | | Similarity matrix | BLOSUM-62 |
| 6479 | | SS fraction | 0.3 |
| 6480 | | Gap open (HH/SS/other) | 18/18/6 |
| 6481 | | Gap extend | 1 |
| 6482 | | SS matrix | | | H | S | O |
| 6483 | | ---|---|---|--- |
| 6484 | | H | 6 | -9 | -6 |
| 6485 | | S | | 6 | -6 |
| 6486 | | O | | | 4 |
| 6487 | | Iteration cutoff | 2 |
| 6488 | | |
| 6489 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 6490 | | score = 499.7 |
| 6491 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 6492 | | 3.736) |
| 6493 | | |
| 6494 | | |
| 6495 | | > color #1 green |
| 6496 | | |
| 6497 | | > color #2 tan |
| 6498 | | |
| 6499 | | > color ~C byatom |
| 6500 | | |
| 6501 | | > ~display |
| 6502 | | |
| 6503 | | > display #1:138 #2:176 |
| 6504 | | |
| 6505 | | > style stick |
| 6506 | | |
| 6507 | | Changed 4099 atom styles |
| 6508 | | |
| 6509 | | > ribbon |
| 6510 | | |
| 6511 | | > transparency 60 target r |
| 6512 | | |
| 6513 | | > view |
| 6514 | | |
| 6515 | | > size #1:138 #2:176 stickRadius 0.3 |
| 6516 | | |
| 6517 | | Changed 14 bond radii |
| 6518 | | |
| 6519 | | > save fig1.jpg |
| 6520 | | |
| 6521 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 6522 | | |
| 6523 | | > sel-ca |
| 6524 | | |
| 6525 | | 13 atoms, 1 model selected |
| 6526 | | 26 atoms, 2 models selected |
| 6527 | | |
| 6528 | | > display sel-residues |
| 6529 | | |
| 6530 | | > color ~C byatom |
| 6531 | | |
| 6532 | | > style stick |
| 6533 | | |
| 6534 | | Changed 4099 atom styles |
| 6535 | | |
| 6536 | | > view #1:138 :< 5 pad -1 |
| 6537 | | |
| 6538 | | > hbonds #1:138 #1 name hb1 color green |
| 6539 | | |
| 6540 | | 607 hydrogen bonds found |
| 6541 | | |
| 6542 | | > hbonds #2:176 #2 name hb2 color tan |
| 6543 | | |
| 6544 | | 666 hydrogen bonds found |
| 6545 | | |
| 6546 | | > transparency 90 target r |
| 6547 | | |
| 6548 | | > label #1:138 #2:176 offset 1,-1,1 |
| 6549 | | |
| 6550 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .92 |
| 6551 | | |
| 6552 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 6553 | | |
| 6554 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2 |
| 6555 | | > color green bgColor white |
| 6556 | | |
| 6557 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 6558 | | > color tan bgColor white |
| 6559 | | |
| 6560 | | > ~select |
| 6561 | | |
| 6562 | | Nothing selected |
| 6563 | | |
| 6564 | | > save fig2.jpg |
| 6565 | | |
| 6566 | | > sel-ca |
| 6567 | | |
| 6568 | | 13 atoms, 1 model selected |
| 6569 | | 26 atoms, 2 models selected |
| 6570 | | |
| 6571 | | > ~ribbon |
| 6572 | | |
| 6573 | | > size stickRadius 0.05 |
| 6574 | | |
| 6575 | | Changed 4167 bond radii |
| 6576 | | |
| 6577 | | > size #1:138 stickRadius 0.2 |
| 6578 | | |
| 6579 | | Changed 7 bond radii |
| 6580 | | |
| 6581 | | > size #2:176 stickRadius 0.2 |
| 6582 | | |
| 6583 | | Changed 7 bond radii |
| 6584 | | |
| 6585 | | > view sel-residues pad -1 |
| 6586 | | |
| 6587 | | > ~select |
| 6588 | | |
| 6589 | | Nothing selected |
| 6590 | | |
| 6591 | | > save fig3.jpg |
| 6592 | | |
| 6593 | | > sel-ca |
| 6594 | | |
| 6595 | | 13 atoms, 1 model selected |
| 6596 | | 26 atoms, 2 models selected |
| 6597 | | |
| 6598 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 6599 | | |
| 6600 | | > label sel-residues & #2 height 0.4 offset 0,0,0 color tan bgColor white |
| 6601 | | |
| 6602 | | > view sel-residues pad -1 |
| 6603 | | |
| 6604 | | > sel-ca |
| 6605 | | |
| 6606 | | 13 atoms, 1 model selected |
| 6607 | | 26 atoms, 2 models selected |
| 6608 | | |
| 6609 | | > align #2 & sel toAtoms #1 & sel |
| 6610 | | |
| 6611 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 6612 | | |
| 6613 | | > ~select |
| 6614 | | |
| 6615 | | Nothing selected |
| 6616 | | |
| 6617 | | > save fig4.jpg |
| 6618 | | |
| 6619 | | > sel-ca |
| 6620 | | |
| 6621 | | 13 atoms, 1 model selected |
| 6622 | | 26 atoms, 2 models selected |
| 6623 | | |
| 6624 | | > ribbon sel |
| 6625 | | |
| 6626 | | > ~select |
| 6627 | | |
| 6628 | | Nothing selected |
| 6629 | | |
| 6630 | | > save fig5.jpg |
| 6631 | | |
| 6632 | | executed script.view.cxc |
| 6633 | | |
| 6634 | | > open "/Users/admin/Dropbox (Technion |
| 6635 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 6636 | | |
| 6637 | | > close |
| 6638 | | |
| 6639 | | > graphics bgColor white |
| 6640 | | |
| 6641 | | > open 1WMB |
| 6642 | | |
| 6643 | | 1wmb title: |
| 6644 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 6645 | | info...] |
| 6646 | | |
| 6647 | | Chain information for 1wmb #1 |
| 6648 | | --- |
| 6649 | | Chain | Description |
| 6650 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 6651 | | |
| 6652 | | Non-standard residues in 1wmb #1 |
| 6653 | | --- |
| 6654 | | CAC — cacodylate ion (dimethylarsinate) |
| 6655 | | MG — magnesium ion |
| 6656 | | |
| 6657 | | 1wmb mmCIF Assemblies |
| 6658 | | --- |
| 6659 | | 1| author_and_software_defined_assembly |
| 6660 | | |
| 6661 | | |
| 6662 | | > open 3I3O |
| 6663 | | |
| 6664 | | 3i3o title: |
| 6665 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 6666 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 6667 | | info...] |
| 6668 | | |
| 6669 | | Chain information for 3i3o #2 |
| 6670 | | --- |
| 6671 | | Chain | Description |
| 6672 | | A B C D E F G H | Short chain dehydrogenase |
| 6673 | | |
| 6674 | | Non-standard residues in 3i3o #2 |
| 6675 | | --- |
| 6676 | | CAC — cacodylate ion (dimethylarsinate) |
| 6677 | | CL — chloride ion |
| 6678 | | MG — magnesium ion |
| 6679 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 6680 | | |
| 6681 | | 3i3o mmCIF Assemblies |
| 6682 | | --- |
| 6683 | | 1| author_and_software_defined_assembly |
| 6684 | | 2| author_and_software_defined_assembly |
| 6685 | | |
| 6686 | | |
| 6687 | | > delete ~/a |
| 6688 | | |
| 6689 | | > delete solvent |
| 6690 | | |
| 6691 | | > mmaker #2 to #1 |
| 6692 | | |
| 6693 | | Parameters |
| 6694 | | --- |
| 6695 | | Chain pairing | bb |
| 6696 | | Alignment algorithm | Needleman-Wunsch |
| 6697 | | Similarity matrix | BLOSUM-62 |
| 6698 | | SS fraction | 0.3 |
| 6699 | | Gap open (HH/SS/other) | 18/18/6 |
| 6700 | | Gap extend | 1 |
| 6701 | | SS matrix | | | H | S | O |
| 6702 | | ---|---|---|--- |
| 6703 | | H | 6 | -9 | -6 |
| 6704 | | S | | 6 | -6 |
| 6705 | | O | | | 4 |
| 6706 | | Iteration cutoff | 2 |
| 6707 | | |
| 6708 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 6709 | | score = 499.7 |
| 6710 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 6711 | | 3.736) |
| 6712 | | |
| 6713 | | |
| 6714 | | > color #1 green |
| 6715 | | |
| 6716 | | > color #2 tan |
| 6717 | | |
| 6718 | | > color ~C byatom |
| 6719 | | |
| 6720 | | > ~display |
| 6721 | | |
| 6722 | | > display #1:138 #2:176 |
| 6723 | | |
| 6724 | | > style stick |
| 6725 | | |
| 6726 | | Changed 4099 atom styles |
| 6727 | | |
| 6728 | | > ribbon |
| 6729 | | |
| 6730 | | > transparency 60 target r |
| 6731 | | |
| 6732 | | > view |
| 6733 | | |
| 6734 | | > size #1:138 #2:176 stickRadius 0.3 |
| 6735 | | |
| 6736 | | Changed 14 bond radii |
| 6737 | | |
| 6738 | | > save fig1.jpg |
| 6739 | | |
| 6740 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 6741 | | |
| 6742 | | > sel-ca |
| 6743 | | |
| 6744 | | 13 atoms, 1 model selected |
| 6745 | | 26 atoms, 2 models selected |
| 6746 | | |
| 6747 | | > display sel-residues |
| 6748 | | |
| 6749 | | > color ~C byatom |
| 6750 | | |
| 6751 | | > style stick |
| 6752 | | |
| 6753 | | Changed 4099 atom styles |
| 6754 | | |
| 6755 | | > view #1:138 :< 5 pad -1 |
| 6756 | | |
| 6757 | | > hbonds #1:138 & #1 name hb1 color green |
| 6758 | | |
| 6759 | | 3 hydrogen bonds found |
| 6760 | | |
| 6761 | | > hbonds #2:176 & #2 name hb2 color tan |
| 6762 | | |
| 6763 | | 4 hydrogen bonds found |
| 6764 | | |
| 6765 | | > transparency 90 target r |
| 6766 | | |
| 6767 | | > label #1:138 #2:176 offset 1,-1,1 |
| 6768 | | |
| 6769 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .92 |
| 6770 | | |
| 6771 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 6772 | | |
| 6773 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1.5,2 |
| 6774 | | > color green bgColor white |
| 6775 | | |
| 6776 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 6777 | | > color tan bgColor white |
| 6778 | | |
| 6779 | | > ~select |
| 6780 | | |
| 6781 | | Nothing selected |
| 6782 | | |
| 6783 | | > save fig2.jpg |
| 6784 | | |
| 6785 | | > sel-ca |
| 6786 | | |
| 6787 | | 13 atoms, 1 model selected |
| 6788 | | 26 atoms, 2 models selected |
| 6789 | | |
| 6790 | | > ~ribbon |
| 6791 | | |
| 6792 | | > size stickRadius 0.05 |
| 6793 | | |
| 6794 | | Changed 4167 bond radii |
| 6795 | | |
| 6796 | | > size #1:138 stickRadius 0.2 |
| 6797 | | |
| 6798 | | Changed 7 bond radii |
| 6799 | | |
| 6800 | | > size #2:176 stickRadius 0.2 |
| 6801 | | |
| 6802 | | Changed 7 bond radii |
| 6803 | | |
| 6804 | | > view sel-residues pad -1 |
| 6805 | | |
| 6806 | | > ~select |
| 6807 | | |
| 6808 | | Nothing selected |
| 6809 | | |
| 6810 | | > save fig3.jpg |
| 6811 | | |
| 6812 | | > sel-ca |
| 6813 | | |
| 6814 | | 13 atoms, 1 model selected |
| 6815 | | 26 atoms, 2 models selected |
| 6816 | | |
| 6817 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 6818 | | |
| 6819 | | > label sel-residues & #2 height 0.4 offset 0,0,0 color tan bgColor white |
| 6820 | | |
| 6821 | | > view sel-residues pad -1 |
| 6822 | | |
| 6823 | | > sel-ca |
| 6824 | | |
| 6825 | | 13 atoms, 1 model selected |
| 6826 | | 26 atoms, 2 models selected |
| 6827 | | |
| 6828 | | > align #2 & sel toAtoms #1 & sel |
| 6829 | | |
| 6830 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 6831 | | |
| 6832 | | > ~select |
| 6833 | | |
| 6834 | | Nothing selected |
| 6835 | | |
| 6836 | | > save fig4.jpg |
| 6837 | | |
| 6838 | | > sel-ca |
| 6839 | | |
| 6840 | | 13 atoms, 1 model selected |
| 6841 | | 26 atoms, 2 models selected |
| 6842 | | |
| 6843 | | > ribbon sel |
| 6844 | | |
| 6845 | | > ~select |
| 6846 | | |
| 6847 | | Nothing selected |
| 6848 | | |
| 6849 | | > save fig5.jpg |
| 6850 | | |
| 6851 | | executed script.view.cxc |
| 6852 | | |
| 6853 | | > hide #!1 models |
| 6854 | | |
| 6855 | | > show #!1 models |
| 6856 | | |
| 6857 | | > hide #!2 models |
| 6858 | | |
| 6859 | | > show #!2 models |
| 6860 | | |
| 6861 | | > open "/Users/admin/Dropbox (Technion |
| 6862 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 6863 | | |
| 6864 | | > close |
| 6865 | | |
| 6866 | | > graphics bgColor white |
| 6867 | | |
| 6868 | | > open 1WMB |
| 6869 | | |
| 6870 | | 1wmb title: |
| 6871 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 6872 | | info...] |
| 6873 | | |
| 6874 | | Chain information for 1wmb #1 |
| 6875 | | --- |
| 6876 | | Chain | Description |
| 6877 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 6878 | | |
| 6879 | | Non-standard residues in 1wmb #1 |
| 6880 | | --- |
| 6881 | | CAC — cacodylate ion (dimethylarsinate) |
| 6882 | | MG — magnesium ion |
| 6883 | | |
| 6884 | | 1wmb mmCIF Assemblies |
| 6885 | | --- |
| 6886 | | 1| author_and_software_defined_assembly |
| 6887 | | |
| 6888 | | |
| 6889 | | > open 3I3O |
| 6890 | | |
| 6891 | | 3i3o title: |
| 6892 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 6893 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 6894 | | info...] |
| 6895 | | |
| 6896 | | Chain information for 3i3o #2 |
| 6897 | | --- |
| 6898 | | Chain | Description |
| 6899 | | A B C D E F G H | Short chain dehydrogenase |
| 6900 | | |
| 6901 | | Non-standard residues in 3i3o #2 |
| 6902 | | --- |
| 6903 | | CAC — cacodylate ion (dimethylarsinate) |
| 6904 | | CL — chloride ion |
| 6905 | | MG — magnesium ion |
| 6906 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 6907 | | |
| 6908 | | 3i3o mmCIF Assemblies |
| 6909 | | --- |
| 6910 | | 1| author_and_software_defined_assembly |
| 6911 | | 2| author_and_software_defined_assembly |
| 6912 | | |
| 6913 | | |
| 6914 | | > delete ~/a |
| 6915 | | |
| 6916 | | > delete solvent |
| 6917 | | |
| 6918 | | > mmaker #2 to #1 |
| 6919 | | |
| 6920 | | Parameters |
| 6921 | | --- |
| 6922 | | Chain pairing | bb |
| 6923 | | Alignment algorithm | Needleman-Wunsch |
| 6924 | | Similarity matrix | BLOSUM-62 |
| 6925 | | SS fraction | 0.3 |
| 6926 | | Gap open (HH/SS/other) | 18/18/6 |
| 6927 | | Gap extend | 1 |
| 6928 | | SS matrix | | | H | S | O |
| 6929 | | ---|---|---|--- |
| 6930 | | H | 6 | -9 | -6 |
| 6931 | | S | | 6 | -6 |
| 6932 | | O | | | 4 |
| 6933 | | Iteration cutoff | 2 |
| 6934 | | |
| 6935 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 6936 | | score = 499.7 |
| 6937 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 6938 | | 3.736) |
| 6939 | | |
| 6940 | | |
| 6941 | | > color #1 green |
| 6942 | | |
| 6943 | | > color #2 tan |
| 6944 | | |
| 6945 | | > color ~C byatom |
| 6946 | | |
| 6947 | | > ~display |
| 6948 | | |
| 6949 | | > display #1:138 #2:176 |
| 6950 | | |
| 6951 | | > style stick |
| 6952 | | |
| 6953 | | Changed 4099 atom styles |
| 6954 | | |
| 6955 | | > ribbon |
| 6956 | | |
| 6957 | | > transparency 60 target r |
| 6958 | | |
| 6959 | | > view |
| 6960 | | |
| 6961 | | > size #1:138 #2:176 stickRadius 0.3 |
| 6962 | | |
| 6963 | | Changed 14 bond radii |
| 6964 | | |
| 6965 | | > save fig1.jpg |
| 6966 | | |
| 6967 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 6968 | | |
| 6969 | | > sel-ca |
| 6970 | | |
| 6971 | | 13 atoms, 1 model selected |
| 6972 | | 26 atoms, 2 models selected |
| 6973 | | |
| 6974 | | > display sel-residues |
| 6975 | | |
| 6976 | | > color ~C byatom |
| 6977 | | |
| 6978 | | > style stick |
| 6979 | | |
| 6980 | | Changed 4099 atom styles |
| 6981 | | |
| 6982 | | > view #1:138 :< 5 pad -1 |
| 6983 | | |
| 6984 | | > hbonds #1:138 & #1 name hb1 color green |
| 6985 | | |
| 6986 | | 3 hydrogen bonds found |
| 6987 | | |
| 6988 | | > hbonds #2:176 & #2 name hb2 color tan |
| 6989 | | |
| 6990 | | 4 hydrogen bonds found |
| 6991 | | |
| 6992 | | > transparency 90 target r |
| 6993 | | |
| 6994 | | > label #1:138 #2:176 offset 1,-1,1 |
| 6995 | | |
| 6996 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .90 |
| 6997 | | |
| 6998 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 6999 | | |
| 7000 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset |
| 7001 | | > 1.5,1.5,2 color green bgColor white |
| 7002 | | |
| 7003 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 7004 | | > color tan bgColor white |
| 7005 | | |
| 7006 | | > ~select |
| 7007 | | |
| 7008 | | Nothing selected |
| 7009 | | |
| 7010 | | > save fig2.jpg |
| 7011 | | |
| 7012 | | > sel-ca |
| 7013 | | |
| 7014 | | 13 atoms, 1 model selected |
| 7015 | | 26 atoms, 2 models selected |
| 7016 | | |
| 7017 | | > ~ribbon |
| 7018 | | |
| 7019 | | > size stickRadius 0.05 |
| 7020 | | |
| 7021 | | Changed 4167 bond radii |
| 7022 | | |
| 7023 | | > size #1:138 stickRadius 0.2 |
| 7024 | | |
| 7025 | | Changed 7 bond radii |
| 7026 | | |
| 7027 | | > size #2:176 stickRadius 0.2 |
| 7028 | | |
| 7029 | | Changed 7 bond radii |
| 7030 | | |
| 7031 | | > view sel-residues pad -1 |
| 7032 | | |
| 7033 | | > ~select |
| 7034 | | |
| 7035 | | Nothing selected |
| 7036 | | |
| 7037 | | > save fig3.jpg |
| 7038 | | |
| 7039 | | > sel-ca |
| 7040 | | |
| 7041 | | 13 atoms, 1 model selected |
| 7042 | | 26 atoms, 2 models selected |
| 7043 | | |
| 7044 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 7045 | | |
| 7046 | | > label sel-residues & #2 height 0.4 offset 0,0,0 color tan bgColor white |
| 7047 | | |
| 7048 | | > view sel-residues pad -1 |
| 7049 | | |
| 7050 | | > sel-ca |
| 7051 | | |
| 7052 | | 13 atoms, 1 model selected |
| 7053 | | 26 atoms, 2 models selected |
| 7054 | | |
| 7055 | | > align #2 & sel toAtoms #1 & sel |
| 7056 | | |
| 7057 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 7058 | | |
| 7059 | | > ~select |
| 7060 | | |
| 7061 | | Nothing selected |
| 7062 | | |
| 7063 | | > save fig4.jpg |
| 7064 | | |
| 7065 | | > sel-ca |
| 7066 | | |
| 7067 | | 13 atoms, 1 model selected |
| 7068 | | 26 atoms, 2 models selected |
| 7069 | | |
| 7070 | | > ribbon sel |
| 7071 | | |
| 7072 | | > ~select |
| 7073 | | |
| 7074 | | Nothing selected |
| 7075 | | |
| 7076 | | > save fig5.jpg |
| 7077 | | |
| 7078 | | executed script.view.cxc |
| 7079 | | |
| 7080 | | > open "/Users/admin/Dropbox (Technion |
| 7081 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 7082 | | |
| 7083 | | > close |
| 7084 | | |
| 7085 | | > graphics bgColor white |
| 7086 | | |
| 7087 | | > open 1WMB |
| 7088 | | |
| 7089 | | 1wmb title: |
| 7090 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 7091 | | info...] |
| 7092 | | |
| 7093 | | Chain information for 1wmb #1 |
| 7094 | | --- |
| 7095 | | Chain | Description |
| 7096 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 7097 | | |
| 7098 | | Non-standard residues in 1wmb #1 |
| 7099 | | --- |
| 7100 | | CAC — cacodylate ion (dimethylarsinate) |
| 7101 | | MG — magnesium ion |
| 7102 | | |
| 7103 | | 1wmb mmCIF Assemblies |
| 7104 | | --- |
| 7105 | | 1| author_and_software_defined_assembly |
| 7106 | | |
| 7107 | | |
| 7108 | | > open 3I3O |
| 7109 | | |
| 7110 | | 3i3o title: |
| 7111 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 7112 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 7113 | | info...] |
| 7114 | | |
| 7115 | | Chain information for 3i3o #2 |
| 7116 | | --- |
| 7117 | | Chain | Description |
| 7118 | | A B C D E F G H | Short chain dehydrogenase |
| 7119 | | |
| 7120 | | Non-standard residues in 3i3o #2 |
| 7121 | | --- |
| 7122 | | CAC — cacodylate ion (dimethylarsinate) |
| 7123 | | CL — chloride ion |
| 7124 | | MG — magnesium ion |
| 7125 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 7126 | | |
| 7127 | | 3i3o mmCIF Assemblies |
| 7128 | | --- |
| 7129 | | 1| author_and_software_defined_assembly |
| 7130 | | 2| author_and_software_defined_assembly |
| 7131 | | |
| 7132 | | |
| 7133 | | > delete ~/a |
| 7134 | | |
| 7135 | | > delete solvent |
| 7136 | | |
| 7137 | | > mmaker #2 to #1 |
| 7138 | | |
| 7139 | | Parameters |
| 7140 | | --- |
| 7141 | | Chain pairing | bb |
| 7142 | | Alignment algorithm | Needleman-Wunsch |
| 7143 | | Similarity matrix | BLOSUM-62 |
| 7144 | | SS fraction | 0.3 |
| 7145 | | Gap open (HH/SS/other) | 18/18/6 |
| 7146 | | Gap extend | 1 |
| 7147 | | SS matrix | | | H | S | O |
| 7148 | | ---|---|---|--- |
| 7149 | | H | 6 | -9 | -6 |
| 7150 | | S | | 6 | -6 |
| 7151 | | O | | | 4 |
| 7152 | | Iteration cutoff | 2 |
| 7153 | | |
| 7154 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 7155 | | score = 499.7 |
| 7156 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 7157 | | 3.736) |
| 7158 | | |
| 7159 | | |
| 7160 | | > color #1 green |
| 7161 | | |
| 7162 | | > color #2 tan |
| 7163 | | |
| 7164 | | > color ~C byatom |
| 7165 | | |
| 7166 | | > ~display |
| 7167 | | |
| 7168 | | > display #1:138 #2:176 |
| 7169 | | |
| 7170 | | > style stick |
| 7171 | | |
| 7172 | | Changed 4099 atom styles |
| 7173 | | |
| 7174 | | > ribbon |
| 7175 | | |
| 7176 | | > transparency 60 target r |
| 7177 | | |
| 7178 | | > view |
| 7179 | | |
| 7180 | | > size #1:138 #2:176 stickRadius 0.3 |
| 7181 | | |
| 7182 | | Changed 14 bond radii |
| 7183 | | |
| 7184 | | > save fig1.jpg |
| 7185 | | |
| 7186 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 7187 | | |
| 7188 | | > sel-ca |
| 7189 | | |
| 7190 | | 13 atoms, 1 model selected |
| 7191 | | 26 atoms, 2 models selected |
| 7192 | | |
| 7193 | | > display sel-residues |
| 7194 | | |
| 7195 | | > color ~C byatom |
| 7196 | | |
| 7197 | | > style stick |
| 7198 | | |
| 7199 | | Changed 4099 atom styles |
| 7200 | | |
| 7201 | | > view #1:138 :< 5 pad -1 |
| 7202 | | |
| 7203 | | > hbonds #1:138 & #1 name hb1 color green |
| 7204 | | |
| 7205 | | 3 hydrogen bonds found |
| 7206 | | |
| 7207 | | > hbonds #2:176 & #2 name hb2 color tan |
| 7208 | | |
| 7209 | | 4 hydrogen bonds found |
| 7210 | | |
| 7211 | | > transparency 90 target r |
| 7212 | | |
| 7213 | | > label #1:138 #2:176 offset 1,-1,1 |
| 7214 | | |
| 7215 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .90 |
| 7216 | | |
| 7217 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 7218 | | |
| 7219 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset |
| 7220 | | > 222222222222222222222,1.5,2 color green bgColor white |
| 7221 | | |
| 7222 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 7223 | | > color tan bgColor white |
| 7224 | | |
| 7225 | | > ~select |
| 7226 | | |
| 7227 | | Nothing selected |
| 7228 | | |
| 7229 | | > save fig2.jpg |
| 7230 | | |
| 7231 | | /Applications/ChimeraX-1.0 |
| 7232 | | copy.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- |
| 7233 | | packages/chimerax/geometry/bounds.py:53: RuntimeWarning: overflow encountered |
| 7234 | | in multiply |
| 7235 | | r = 0.5*sqrt((size*size).sum()) |
| 7236 | | |
| 7237 | | > sel-ca |
| 7238 | | |
| 7239 | | 13 atoms, 1 model selected |
| 7240 | | 26 atoms, 2 models selected |
| 7241 | | |
| 7242 | | > ~ribbon |
| 7243 | | |
| 7244 | | > size stickRadius 0.05 |
| 7245 | | |
| 7246 | | Changed 4167 bond radii |
| 7247 | | |
| 7248 | | > size #1:138 stickRadius 0.2 |
| 7249 | | |
| 7250 | | Changed 7 bond radii |
| 7251 | | |
| 7252 | | > size #2:176 stickRadius 0.2 |
| 7253 | | |
| 7254 | | Changed 7 bond radii |
| 7255 | | |
| 7256 | | > view sel-residues pad -1 |
| 7257 | | |
| 7258 | | > ~select |
| 7259 | | |
| 7260 | | Nothing selected |
| 7261 | | |
| 7262 | | > save fig3.jpg |
| 7263 | | |
| 7264 | | > sel-ca |
| 7265 | | |
| 7266 | | 13 atoms, 1 model selected |
| 7267 | | 26 atoms, 2 models selected |
| 7268 | | |
| 7269 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 7270 | | |
| 7271 | | > label sel-residues & #2 height 0.4 offset 0,0,0 color tan bgColor white |
| 7272 | | |
| 7273 | | > view sel-residues pad -1 |
| 7274 | | |
| 7275 | | > sel-ca |
| 7276 | | |
| 7277 | | 13 atoms, 1 model selected |
| 7278 | | 26 atoms, 2 models selected |
| 7279 | | |
| 7280 | | > align #2 & sel toAtoms #1 & sel |
| 7281 | | |
| 7282 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 7283 | | |
| 7284 | | > ~select |
| 7285 | | |
| 7286 | | Nothing selected |
| 7287 | | |
| 7288 | | > save fig4.jpg |
| 7289 | | |
| 7290 | | > sel-ca |
| 7291 | | |
| 7292 | | 13 atoms, 1 model selected |
| 7293 | | 26 atoms, 2 models selected |
| 7294 | | |
| 7295 | | > ribbon sel |
| 7296 | | |
| 7297 | | > ~select |
| 7298 | | |
| 7299 | | Nothing selected |
| 7300 | | |
| 7301 | | > save fig5.jpg |
| 7302 | | |
| 7303 | | executed script.view.cxc |
| 7304 | | |
| 7305 | | > open "/Users/admin/Dropbox (Technion |
| 7306 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 7307 | | |
| 7308 | | > close |
| 7309 | | |
| 7310 | | > graphics bgColor white |
| 7311 | | |
| 7312 | | > open 1WMB |
| 7313 | | |
| 7314 | | 1wmb title: |
| 7315 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 7316 | | info...] |
| 7317 | | |
| 7318 | | Chain information for 1wmb #1 |
| 7319 | | --- |
| 7320 | | Chain | Description |
| 7321 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 7322 | | |
| 7323 | | Non-standard residues in 1wmb #1 |
| 7324 | | --- |
| 7325 | | CAC — cacodylate ion (dimethylarsinate) |
| 7326 | | MG — magnesium ion |
| 7327 | | |
| 7328 | | 1wmb mmCIF Assemblies |
| 7329 | | --- |
| 7330 | | 1| author_and_software_defined_assembly |
| 7331 | | |
| 7332 | | |
| 7333 | | > open 3I3O |
| 7334 | | |
| 7335 | | 3i3o title: |
| 7336 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 7337 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 7338 | | info...] |
| 7339 | | |
| 7340 | | Chain information for 3i3o #2 |
| 7341 | | --- |
| 7342 | | Chain | Description |
| 7343 | | A B C D E F G H | Short chain dehydrogenase |
| 7344 | | |
| 7345 | | Non-standard residues in 3i3o #2 |
| 7346 | | --- |
| 7347 | | CAC — cacodylate ion (dimethylarsinate) |
| 7348 | | CL — chloride ion |
| 7349 | | MG — magnesium ion |
| 7350 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 7351 | | |
| 7352 | | 3i3o mmCIF Assemblies |
| 7353 | | --- |
| 7354 | | 1| author_and_software_defined_assembly |
| 7355 | | 2| author_and_software_defined_assembly |
| 7356 | | |
| 7357 | | |
| 7358 | | > delete ~/a |
| 7359 | | |
| 7360 | | > delete solvent |
| 7361 | | |
| 7362 | | > mmaker #2 to #1 |
| 7363 | | |
| 7364 | | Parameters |
| 7365 | | --- |
| 7366 | | Chain pairing | bb |
| 7367 | | Alignment algorithm | Needleman-Wunsch |
| 7368 | | Similarity matrix | BLOSUM-62 |
| 7369 | | SS fraction | 0.3 |
| 7370 | | Gap open (HH/SS/other) | 18/18/6 |
| 7371 | | Gap extend | 1 |
| 7372 | | SS matrix | | | H | S | O |
| 7373 | | ---|---|---|--- |
| 7374 | | H | 6 | -9 | -6 |
| 7375 | | S | | 6 | -6 |
| 7376 | | O | | | 4 |
| 7377 | | Iteration cutoff | 2 |
| 7378 | | |
| 7379 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 7380 | | score = 499.7 |
| 7381 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 7382 | | 3.736) |
| 7383 | | |
| 7384 | | |
| 7385 | | > color #1 green |
| 7386 | | |
| 7387 | | > color #2 tan |
| 7388 | | |
| 7389 | | > color ~C byatom |
| 7390 | | |
| 7391 | | > ~display |
| 7392 | | |
| 7393 | | > display #1:138 #2:176 |
| 7394 | | |
| 7395 | | > style stick |
| 7396 | | |
| 7397 | | Changed 4099 atom styles |
| 7398 | | |
| 7399 | | > ribbon |
| 7400 | | |
| 7401 | | > transparency 60 target r |
| 7402 | | |
| 7403 | | > view |
| 7404 | | |
| 7405 | | > size #1:138 #2:176 stickRadius 0.3 |
| 7406 | | |
| 7407 | | Changed 14 bond radii |
| 7408 | | |
| 7409 | | > save fig1.jpg |
| 7410 | | |
| 7411 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 7412 | | |
| 7413 | | > sel-ca |
| 7414 | | |
| 7415 | | 13 atoms, 1 model selected |
| 7416 | | 26 atoms, 2 models selected |
| 7417 | | |
| 7418 | | > display sel-residues |
| 7419 | | |
| 7420 | | > color ~C byatom |
| 7421 | | |
| 7422 | | > style stick |
| 7423 | | |
| 7424 | | Changed 4099 atom styles |
| 7425 | | |
| 7426 | | > view #1:138 :< 5 pad -1 |
| 7427 | | |
| 7428 | | > hbonds #1:138 & #1 name hb1 color green |
| 7429 | | |
| 7430 | | 3 hydrogen bonds found |
| 7431 | | |
| 7432 | | > hbonds #2:176 & #2 name hb2 color tan |
| 7433 | | |
| 7434 | | 4 hydrogen bonds found |
| 7435 | | |
| 7436 | | > transparency 90 target r |
| 7437 | | |
| 7438 | | > label #1:138 #2:176 offset 1,-1,1 |
| 7439 | | |
| 7440 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .90 |
| 7441 | | |
| 7442 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 7443 | | |
| 7444 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 3,3,2 |
| 7445 | | > color green bgColor white |
| 7446 | | |
| 7447 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 7448 | | > color tan bgColor white |
| 7449 | | |
| 7450 | | > ~select |
| 7451 | | |
| 7452 | | Nothing selected |
| 7453 | | |
| 7454 | | > save fig2.jpg |
| 7455 | | |
| 7456 | | > sel-ca |
| 7457 | | |
| 7458 | | 13 atoms, 1 model selected |
| 7459 | | 26 atoms, 2 models selected |
| 7460 | | |
| 7461 | | > ~ribbon |
| 7462 | | |
| 7463 | | > size stickRadius 0.05 |
| 7464 | | |
| 7465 | | Changed 4167 bond radii |
| 7466 | | |
| 7467 | | > size #1:138 stickRadius 0.2 |
| 7468 | | |
| 7469 | | Changed 7 bond radii |
| 7470 | | |
| 7471 | | > size #2:176 stickRadius 0.2 |
| 7472 | | |
| 7473 | | Changed 7 bond radii |
| 7474 | | |
| 7475 | | > view sel-residues pad -1 |
| 7476 | | |
| 7477 | | > ~select |
| 7478 | | |
| 7479 | | Nothing selected |
| 7480 | | |
| 7481 | | > save fig3.jpg |
| 7482 | | |
| 7483 | | > sel-ca |
| 7484 | | |
| 7485 | | 13 atoms, 1 model selected |
| 7486 | | 26 atoms, 2 models selected |
| 7487 | | |
| 7488 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 7489 | | |
| 7490 | | > label sel-residues & #2 height 0.4 offset 0,0,0 color tan bgColor white |
| 7491 | | |
| 7492 | | > view sel-residues pad -1 |
| 7493 | | |
| 7494 | | > sel-ca |
| 7495 | | |
| 7496 | | 13 atoms, 1 model selected |
| 7497 | | 26 atoms, 2 models selected |
| 7498 | | |
| 7499 | | > align #2 & sel toAtoms #1 & sel |
| 7500 | | |
| 7501 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 7502 | | |
| 7503 | | > ~select |
| 7504 | | |
| 7505 | | Nothing selected |
| 7506 | | |
| 7507 | | > save fig4.jpg |
| 7508 | | |
| 7509 | | > sel-ca |
| 7510 | | |
| 7511 | | 13 atoms, 1 model selected |
| 7512 | | 26 atoms, 2 models selected |
| 7513 | | |
| 7514 | | > ribbon sel |
| 7515 | | |
| 7516 | | > ~select |
| 7517 | | |
| 7518 | | Nothing selected |
| 7519 | | |
| 7520 | | > save fig5.jpg |
| 7521 | | |
| 7522 | | executed script.view.cxc |
| 7523 | | |
| 7524 | | > open "/Users/admin/Dropbox (Technion |
| 7525 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 7526 | | |
| 7527 | | > close |
| 7528 | | |
| 7529 | | > graphics bgColor white |
| 7530 | | |
| 7531 | | > open 1WMB |
| 7532 | | |
| 7533 | | 1wmb title: |
| 7534 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 7535 | | info...] |
| 7536 | | |
| 7537 | | Chain information for 1wmb #1 |
| 7538 | | --- |
| 7539 | | Chain | Description |
| 7540 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 7541 | | |
| 7542 | | Non-standard residues in 1wmb #1 |
| 7543 | | --- |
| 7544 | | CAC — cacodylate ion (dimethylarsinate) |
| 7545 | | MG — magnesium ion |
| 7546 | | |
| 7547 | | 1wmb mmCIF Assemblies |
| 7548 | | --- |
| 7549 | | 1| author_and_software_defined_assembly |
| 7550 | | |
| 7551 | | |
| 7552 | | > open 3I3O |
| 7553 | | |
| 7554 | | 3i3o title: |
| 7555 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 7556 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 7557 | | info...] |
| 7558 | | |
| 7559 | | Chain information for 3i3o #2 |
| 7560 | | --- |
| 7561 | | Chain | Description |
| 7562 | | A B C D E F G H | Short chain dehydrogenase |
| 7563 | | |
| 7564 | | Non-standard residues in 3i3o #2 |
| 7565 | | --- |
| 7566 | | CAC — cacodylate ion (dimethylarsinate) |
| 7567 | | CL — chloride ion |
| 7568 | | MG — magnesium ion |
| 7569 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 7570 | | |
| 7571 | | 3i3o mmCIF Assemblies |
| 7572 | | --- |
| 7573 | | 1| author_and_software_defined_assembly |
| 7574 | | 2| author_and_software_defined_assembly |
| 7575 | | |
| 7576 | | |
| 7577 | | > delete ~/a |
| 7578 | | |
| 7579 | | > delete solvent |
| 7580 | | |
| 7581 | | > mmaker #2 to #1 |
| 7582 | | |
| 7583 | | Parameters |
| 7584 | | --- |
| 7585 | | Chain pairing | bb |
| 7586 | | Alignment algorithm | Needleman-Wunsch |
| 7587 | | Similarity matrix | BLOSUM-62 |
| 7588 | | SS fraction | 0.3 |
| 7589 | | Gap open (HH/SS/other) | 18/18/6 |
| 7590 | | Gap extend | 1 |
| 7591 | | SS matrix | | | H | S | O |
| 7592 | | ---|---|---|--- |
| 7593 | | H | 6 | -9 | -6 |
| 7594 | | S | | 6 | -6 |
| 7595 | | O | | | 4 |
| 7596 | | Iteration cutoff | 2 |
| 7597 | | |
| 7598 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 7599 | | score = 499.7 |
| 7600 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 7601 | | 3.736) |
| 7602 | | |
| 7603 | | |
| 7604 | | > color #1 green |
| 7605 | | |
| 7606 | | > color #2 tan |
| 7607 | | |
| 7608 | | > color ~C byatom |
| 7609 | | |
| 7610 | | > ~display |
| 7611 | | |
| 7612 | | > display #1:138 #2:176 |
| 7613 | | |
| 7614 | | > style stick |
| 7615 | | |
| 7616 | | Changed 4099 atom styles |
| 7617 | | |
| 7618 | | > ribbon |
| 7619 | | |
| 7620 | | > transparency 60 target r |
| 7621 | | |
| 7622 | | > view |
| 7623 | | |
| 7624 | | > size #1:138 #2:176 stickRadius 0.3 |
| 7625 | | |
| 7626 | | Changed 14 bond radii |
| 7627 | | |
| 7628 | | > save fig1.jpg |
| 7629 | | |
| 7630 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 7631 | | |
| 7632 | | > sel-ca |
| 7633 | | |
| 7634 | | 13 atoms, 1 model selected |
| 7635 | | 26 atoms, 2 models selected |
| 7636 | | |
| 7637 | | > display sel-residues |
| 7638 | | |
| 7639 | | > color ~C byatom |
| 7640 | | |
| 7641 | | > style stick |
| 7642 | | |
| 7643 | | Changed 4099 atom styles |
| 7644 | | |
| 7645 | | > view #1:138 :< 5 pad -1 |
| 7646 | | |
| 7647 | | > hbonds #1:138 & #1 name hb1 color green |
| 7648 | | |
| 7649 | | 3 hydrogen bonds found |
| 7650 | | |
| 7651 | | > hbonds #2:176 & #2 name hb2 color tan |
| 7652 | | |
| 7653 | | 4 hydrogen bonds found |
| 7654 | | |
| 7655 | | > transparency 90 target r |
| 7656 | | |
| 7657 | | > label #1:138 #2:176 offset 1,-1,1 |
| 7658 | | |
| 7659 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .90 |
| 7660 | | |
| 7661 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 7662 | | |
| 7663 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 3,3,2 |
| 7664 | | > color green bgColor white |
| 7665 | | |
| 7666 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 7667 | | > color tan bgColor white |
| 7668 | | |
| 7669 | | > ~select |
| 7670 | | |
| 7671 | | Nothing selected |
| 7672 | | |
| 7673 | | > save fig2.jpg |
| 7674 | | |
| 7675 | | > sel-ca |
| 7676 | | |
| 7677 | | 13 atoms, 1 model selected |
| 7678 | | 26 atoms, 2 models selected |
| 7679 | | |
| 7680 | | > ~ribbon |
| 7681 | | |
| 7682 | | > size stickRadius 0.05 |
| 7683 | | |
| 7684 | | Changed 4167 bond radii |
| 7685 | | |
| 7686 | | > size #1:138 stickRadius 0.2 |
| 7687 | | |
| 7688 | | Changed 7 bond radii |
| 7689 | | |
| 7690 | | > size #2:176 stickRadius 0.2 |
| 7691 | | |
| 7692 | | Changed 7 bond radii |
| 7693 | | |
| 7694 | | > view sel-residues pad -1 |
| 7695 | | |
| 7696 | | > ~select |
| 7697 | | |
| 7698 | | Nothing selected |
| 7699 | | |
| 7700 | | > save fig3.jpg |
| 7701 | | |
| 7702 | | > sel-ca |
| 7703 | | |
| 7704 | | 13 atoms, 1 model selected |
| 7705 | | 26 atoms, 2 models selected |
| 7706 | | |
| 7707 | | > label sel-residues & #1 height 0.4 offset 0,1,0 color green bgColor white |
| 7708 | | |
| 7709 | | > label sel-residues & #2 height 0.4 offset 0,0,0 color tan bgColor white |
| 7710 | | |
| 7711 | | > view sel-residues pad -1 |
| 7712 | | |
| 7713 | | > sel-ca |
| 7714 | | |
| 7715 | | 13 atoms, 1 model selected |
| 7716 | | 26 atoms, 2 models selected |
| 7717 | | |
| 7718 | | > align #2 & sel toAtoms #1 & sel |
| 7719 | | |
| 7720 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 7721 | | |
| 7722 | | > ~select |
| 7723 | | |
| 7724 | | Nothing selected |
| 7725 | | |
| 7726 | | > save fig4.jpg |
| 7727 | | |
| 7728 | | > sel-ca |
| 7729 | | |
| 7730 | | 13 atoms, 1 model selected |
| 7731 | | 26 atoms, 2 models selected |
| 7732 | | |
| 7733 | | > ribbon sel |
| 7734 | | |
| 7735 | | > ~select |
| 7736 | | |
| 7737 | | Nothing selected |
| 7738 | | |
| 7739 | | > save fig5.jpg |
| 7740 | | |
| 7741 | | executed script.view.cxc |
| 7742 | | |
| 7743 | | > open "/Users/admin/Dropbox (Technion |
| 7744 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 7745 | | |
| 7746 | | > close |
| 7747 | | |
| 7748 | | > graphics bgColor white |
| 7749 | | |
| 7750 | | > open 1WMB |
| 7751 | | |
| 7752 | | 1wmb title: |
| 7753 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 7754 | | info...] |
| 7755 | | |
| 7756 | | Chain information for 1wmb #1 |
| 7757 | | --- |
| 7758 | | Chain | Description |
| 7759 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 7760 | | |
| 7761 | | Non-standard residues in 1wmb #1 |
| 7762 | | --- |
| 7763 | | CAC — cacodylate ion (dimethylarsinate) |
| 7764 | | MG — magnesium ion |
| 7765 | | |
| 7766 | | 1wmb mmCIF Assemblies |
| 7767 | | --- |
| 7768 | | 1| author_and_software_defined_assembly |
| 7769 | | |
| 7770 | | |
| 7771 | | > open 3I3O |
| 7772 | | |
| 7773 | | 3i3o title: |
| 7774 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 7775 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 7776 | | info...] |
| 7777 | | |
| 7778 | | Chain information for 3i3o #2 |
| 7779 | | --- |
| 7780 | | Chain | Description |
| 7781 | | A B C D E F G H | Short chain dehydrogenase |
| 7782 | | |
| 7783 | | Non-standard residues in 3i3o #2 |
| 7784 | | --- |
| 7785 | | CAC — cacodylate ion (dimethylarsinate) |
| 7786 | | CL — chloride ion |
| 7787 | | MG — magnesium ion |
| 7788 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 7789 | | |
| 7790 | | 3i3o mmCIF Assemblies |
| 7791 | | --- |
| 7792 | | 1| author_and_software_defined_assembly |
| 7793 | | 2| author_and_software_defined_assembly |
| 7794 | | |
| 7795 | | |
| 7796 | | > delete ~/a |
| 7797 | | |
| 7798 | | > delete solvent |
| 7799 | | |
| 7800 | | > mmaker #2 to #1 |
| 7801 | | |
| 7802 | | Parameters |
| 7803 | | --- |
| 7804 | | Chain pairing | bb |
| 7805 | | Alignment algorithm | Needleman-Wunsch |
| 7806 | | Similarity matrix | BLOSUM-62 |
| 7807 | | SS fraction | 0.3 |
| 7808 | | Gap open (HH/SS/other) | 18/18/6 |
| 7809 | | Gap extend | 1 |
| 7810 | | SS matrix | | | H | S | O |
| 7811 | | ---|---|---|--- |
| 7812 | | H | 6 | -9 | -6 |
| 7813 | | S | | 6 | -6 |
| 7814 | | O | | | 4 |
| 7815 | | Iteration cutoff | 2 |
| 7816 | | |
| 7817 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 7818 | | score = 499.7 |
| 7819 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 7820 | | 3.736) |
| 7821 | | |
| 7822 | | |
| 7823 | | > color #1 green |
| 7824 | | |
| 7825 | | > color #2 tan |
| 7826 | | |
| 7827 | | > color ~C byatom |
| 7828 | | |
| 7829 | | > ~display |
| 7830 | | |
| 7831 | | > display #1:138 #2:176 |
| 7832 | | |
| 7833 | | > style stick |
| 7834 | | |
| 7835 | | Changed 4099 atom styles |
| 7836 | | |
| 7837 | | > ribbon |
| 7838 | | |
| 7839 | | > transparency 60 target r |
| 7840 | | |
| 7841 | | > view |
| 7842 | | |
| 7843 | | > size #1:138 #2:176 stickRadius 0.3 |
| 7844 | | |
| 7845 | | Changed 14 bond radii |
| 7846 | | |
| 7847 | | > save fig1.jpg |
| 7848 | | |
| 7849 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 7850 | | |
| 7851 | | > sel-ca |
| 7852 | | |
| 7853 | | 13 atoms, 1 model selected |
| 7854 | | 26 atoms, 2 models selected |
| 7855 | | |
| 7856 | | > display sel-residues |
| 7857 | | |
| 7858 | | > color ~C byatom |
| 7859 | | |
| 7860 | | > style stick |
| 7861 | | |
| 7862 | | Changed 4099 atom styles |
| 7863 | | |
| 7864 | | > view #1:138 :< 5 pad -1 |
| 7865 | | |
| 7866 | | > hbonds #1:138 & #1 name hb1 color green |
| 7867 | | |
| 7868 | | 3 hydrogen bonds found |
| 7869 | | |
| 7870 | | > hbonds #2:176 & #2 name hb2 color tan |
| 7871 | | |
| 7872 | | 4 hydrogen bonds found |
| 7873 | | |
| 7874 | | > transparency 90 target r |
| 7875 | | |
| 7876 | | > label #1:138 #2:176 offset 1,-1,1 |
| 7877 | | |
| 7878 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .90 |
| 7879 | | |
| 7880 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 7881 | | |
| 7882 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 3,3,2 |
| 7883 | | > color green bgColor white |
| 7884 | | |
| 7885 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 offset 1,1,1 |
| 7886 | | > color tan bgColor white |
| 7887 | | |
| 7888 | | > ~select |
| 7889 | | |
| 7890 | | Nothing selected |
| 7891 | | |
| 7892 | | > save fig2.jpg |
| 7893 | | |
| 7894 | | > sel-ca |
| 7895 | | |
| 7896 | | 13 atoms, 1 model selected |
| 7897 | | 26 atoms, 2 models selected |
| 7898 | | |
| 7899 | | > ~ribbon |
| 7900 | | |
| 7901 | | > size stickRadius 0.05 |
| 7902 | | |
| 7903 | | Changed 4167 bond radii |
| 7904 | | |
| 7905 | | > size #1:138 stickRadius 0.2 |
| 7906 | | |
| 7907 | | Changed 7 bond radii |
| 7908 | | |
| 7909 | | > size #2:176 stickRadius 0.2 |
| 7910 | | |
| 7911 | | Changed 7 bond radii |
| 7912 | | |
| 7913 | | > view sel-residues pad -1 |
| 7914 | | |
| 7915 | | > ~select |
| 7916 | | |
| 7917 | | Nothing selected |
| 7918 | | |
| 7919 | | > save fig3.jpg |
| 7920 | | |
| 7921 | | > sel-ca |
| 7922 | | |
| 7923 | | 13 atoms, 1 model selected |
| 7924 | | 26 atoms, 2 models selected |
| 7925 | | |
| 7926 | | > label sel-residues & #1 height 0.4 offset 0,0.5,0 color green bgColor white |
| 7927 | | |
| 7928 | | > label sel-residues & #2 height 0.4 offset 0,0,0 color tan bgColor white |
| 7929 | | |
| 7930 | | > view sel-residues pad -1 |
| 7931 | | |
| 7932 | | > sel-ca |
| 7933 | | |
| 7934 | | 13 atoms, 1 model selected |
| 7935 | | 26 atoms, 2 models selected |
| 7936 | | |
| 7937 | | > align #2 & sel toAtoms #1 & sel |
| 7938 | | |
| 7939 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 7940 | | |
| 7941 | | > ~select |
| 7942 | | |
| 7943 | | Nothing selected |
| 7944 | | |
| 7945 | | > save fig4.jpg |
| 7946 | | |
| 7947 | | > sel-ca |
| 7948 | | |
| 7949 | | 13 atoms, 1 model selected |
| 7950 | | 26 atoms, 2 models selected |
| 7951 | | |
| 7952 | | > ribbon sel |
| 7953 | | |
| 7954 | | > ~select |
| 7955 | | |
| 7956 | | Nothing selected |
| 7957 | | |
| 7958 | | > save fig5.jpg |
| 7959 | | |
| 7960 | | executed script.view.cxc |
| 7961 | | |
| 7962 | | > open "/Users/admin/Dropbox (Technion |
| 7963 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 7964 | | |
| 7965 | | > close |
| 7966 | | |
| 7967 | | > graphics bgColor white |
| 7968 | | |
| 7969 | | > open 1WMB |
| 7970 | | |
| 7971 | | 1wmb title: |
| 7972 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 7973 | | info...] |
| 7974 | | |
| 7975 | | Chain information for 1wmb #1 |
| 7976 | | --- |
| 7977 | | Chain | Description |
| 7978 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 7979 | | |
| 7980 | | Non-standard residues in 1wmb #1 |
| 7981 | | --- |
| 7982 | | CAC — cacodylate ion (dimethylarsinate) |
| 7983 | | MG — magnesium ion |
| 7984 | | |
| 7985 | | 1wmb mmCIF Assemblies |
| 7986 | | --- |
| 7987 | | 1| author_and_software_defined_assembly |
| 7988 | | |
| 7989 | | |
| 7990 | | > open 3I3O |
| 7991 | | |
| 7992 | | 3i3o title: |
| 7993 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 7994 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 7995 | | info...] |
| 7996 | | |
| 7997 | | Chain information for 3i3o #2 |
| 7998 | | --- |
| 7999 | | Chain | Description |
| 8000 | | A B C D E F G H | Short chain dehydrogenase |
| 8001 | | |
| 8002 | | Non-standard residues in 3i3o #2 |
| 8003 | | --- |
| 8004 | | CAC — cacodylate ion (dimethylarsinate) |
| 8005 | | CL — chloride ion |
| 8006 | | MG — magnesium ion |
| 8007 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 8008 | | |
| 8009 | | 3i3o mmCIF Assemblies |
| 8010 | | --- |
| 8011 | | 1| author_and_software_defined_assembly |
| 8012 | | 2| author_and_software_defined_assembly |
| 8013 | | |
| 8014 | | |
| 8015 | | > delete ~/a |
| 8016 | | |
| 8017 | | > delete solvent |
| 8018 | | |
| 8019 | | > mmaker #2 to #1 |
| 8020 | | |
| 8021 | | Parameters |
| 8022 | | --- |
| 8023 | | Chain pairing | bb |
| 8024 | | Alignment algorithm | Needleman-Wunsch |
| 8025 | | Similarity matrix | BLOSUM-62 |
| 8026 | | SS fraction | 0.3 |
| 8027 | | Gap open (HH/SS/other) | 18/18/6 |
| 8028 | | Gap extend | 1 |
| 8029 | | SS matrix | | | H | S | O |
| 8030 | | ---|---|---|--- |
| 8031 | | H | 6 | -9 | -6 |
| 8032 | | S | | 6 | -6 |
| 8033 | | O | | | 4 |
| 8034 | | Iteration cutoff | 2 |
| 8035 | | |
| 8036 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 8037 | | score = 499.7 |
| 8038 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 8039 | | 3.736) |
| 8040 | | |
| 8041 | | |
| 8042 | | > color #1 green |
| 8043 | | |
| 8044 | | > color #2 tan |
| 8045 | | |
| 8046 | | > color ~C byatom |
| 8047 | | |
| 8048 | | > ~display |
| 8049 | | |
| 8050 | | > display #1:138 #2:176 |
| 8051 | | |
| 8052 | | > style stick |
| 8053 | | |
| 8054 | | Changed 4099 atom styles |
| 8055 | | |
| 8056 | | > ribbon |
| 8057 | | |
| 8058 | | > transparency 60 target r |
| 8059 | | |
| 8060 | | > view |
| 8061 | | |
| 8062 | | > size #1:138 #2:176 stickRadius 0.3 |
| 8063 | | |
| 8064 | | Changed 14 bond radii |
| 8065 | | |
| 8066 | | > save fig1.jpg |
| 8067 | | |
| 8068 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 8069 | | |
| 8070 | | > sel-ca |
| 8071 | | |
| 8072 | | 13 atoms, 1 model selected |
| 8073 | | 26 atoms, 2 models selected |
| 8074 | | |
| 8075 | | > display sel-residues |
| 8076 | | |
| 8077 | | > color ~C byatom |
| 8078 | | |
| 8079 | | > style stick |
| 8080 | | |
| 8081 | | Changed 4099 atom styles |
| 8082 | | |
| 8083 | | > view #1:138 :< 5 pad -1 |
| 8084 | | |
| 8085 | | > hbonds #1:138 & #1 name hb1 color green |
| 8086 | | |
| 8087 | | 3 hydrogen bonds found |
| 8088 | | |
| 8089 | | > hbonds #2:176 & #2 name hb2 color tan |
| 8090 | | |
| 8091 | | 4 hydrogen bonds found |
| 8092 | | |
| 8093 | | > transparency 90 target r |
| 8094 | | |
| 8095 | | > label #1:138 #2:176 offset 1,-1,1 |
| 8096 | | |
| 8097 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .90 |
| 8098 | | |
| 8099 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 8100 | | |
| 8101 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color offset |
| 8102 | | > 0,0.7,0 green bgColor white |
| 8103 | | |
| 8104 | | Invalid "color" argument: Expected 'default' or a color |
| 8105 | | |
| 8106 | | > open "/Users/admin/Dropbox (Technion |
| 8107 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 8108 | | |
| 8109 | | > close |
| 8110 | | |
| 8111 | | > graphics bgColor white |
| 8112 | | |
| 8113 | | > open 1WMB |
| 8114 | | |
| 8115 | | 1wmb title: |
| 8116 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 8117 | | info...] |
| 8118 | | |
| 8119 | | Chain information for 1wmb #1 |
| 8120 | | --- |
| 8121 | | Chain | Description |
| 8122 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 8123 | | |
| 8124 | | Non-standard residues in 1wmb #1 |
| 8125 | | --- |
| 8126 | | CAC — cacodylate ion (dimethylarsinate) |
| 8127 | | MG — magnesium ion |
| 8128 | | |
| 8129 | | 1wmb mmCIF Assemblies |
| 8130 | | --- |
| 8131 | | 1| author_and_software_defined_assembly |
| 8132 | | |
| 8133 | | |
| 8134 | | > open 3I3O |
| 8135 | | |
| 8136 | | 3i3o title: |
| 8137 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 8138 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 8139 | | info...] |
| 8140 | | |
| 8141 | | Chain information for 3i3o #2 |
| 8142 | | --- |
| 8143 | | Chain | Description |
| 8144 | | A B C D E F G H | Short chain dehydrogenase |
| 8145 | | |
| 8146 | | Non-standard residues in 3i3o #2 |
| 8147 | | --- |
| 8148 | | CAC — cacodylate ion (dimethylarsinate) |
| 8149 | | CL — chloride ion |
| 8150 | | MG — magnesium ion |
| 8151 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 8152 | | |
| 8153 | | 3i3o mmCIF Assemblies |
| 8154 | | --- |
| 8155 | | 1| author_and_software_defined_assembly |
| 8156 | | 2| author_and_software_defined_assembly |
| 8157 | | |
| 8158 | | |
| 8159 | | > delete ~/a |
| 8160 | | |
| 8161 | | > delete solvent |
| 8162 | | |
| 8163 | | > mmaker #2 to #1 |
| 8164 | | |
| 8165 | | Parameters |
| 8166 | | --- |
| 8167 | | Chain pairing | bb |
| 8168 | | Alignment algorithm | Needleman-Wunsch |
| 8169 | | Similarity matrix | BLOSUM-62 |
| 8170 | | SS fraction | 0.3 |
| 8171 | | Gap open (HH/SS/other) | 18/18/6 |
| 8172 | | Gap extend | 1 |
| 8173 | | SS matrix | | | H | S | O |
| 8174 | | ---|---|---|--- |
| 8175 | | H | 6 | -9 | -6 |
| 8176 | | S | | 6 | -6 |
| 8177 | | O | | | 4 |
| 8178 | | Iteration cutoff | 2 |
| 8179 | | |
| 8180 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 8181 | | score = 499.7 |
| 8182 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 8183 | | 3.736) |
| 8184 | | |
| 8185 | | |
| 8186 | | > color #1 green |
| 8187 | | |
| 8188 | | > color #2 tan |
| 8189 | | |
| 8190 | | > color ~C byatom |
| 8191 | | |
| 8192 | | > ~display |
| 8193 | | |
| 8194 | | > display #1:138 #2:176 |
| 8195 | | |
| 8196 | | > style stick |
| 8197 | | |
| 8198 | | Changed 4099 atom styles |
| 8199 | | |
| 8200 | | > ribbon |
| 8201 | | |
| 8202 | | > transparency 60 target r |
| 8203 | | |
| 8204 | | > view |
| 8205 | | |
| 8206 | | > size #1:138 #2:176 stickRadius 0.3 |
| 8207 | | |
| 8208 | | Changed 14 bond radii |
| 8209 | | |
| 8210 | | > save fig1.jpg |
| 8211 | | |
| 8212 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 8213 | | |
| 8214 | | > sel-ca |
| 8215 | | |
| 8216 | | 13 atoms, 1 model selected |
| 8217 | | 26 atoms, 2 models selected |
| 8218 | | |
| 8219 | | > display sel-residues |
| 8220 | | |
| 8221 | | > color ~C byatom |
| 8222 | | |
| 8223 | | > style stick |
| 8224 | | |
| 8225 | | Changed 4099 atom styles |
| 8226 | | |
| 8227 | | > view #1:138 :< 5 pad -1 |
| 8228 | | |
| 8229 | | > hbonds #1:138 & #1 name hb1 color green |
| 8230 | | |
| 8231 | | 3 hydrogen bonds found |
| 8232 | | |
| 8233 | | > hbonds #2:176 & #2 name hb2 color tan |
| 8234 | | |
| 8235 | | 4 hydrogen bonds found |
| 8236 | | |
| 8237 | | > transparency 90 target r |
| 8238 | | |
| 8239 | | > label #1:138 #2:176 offset 1,-1,1 |
| 8240 | | |
| 8241 | | > 2dlabels text 1WMB color green size 50 xpos .03 ypos .90 |
| 8242 | | |
| 8243 | | > 2dlabels text 3I3O color tan size 50 xpos .03 ypos .82 |
| 8244 | | |
| 8245 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 8246 | | > bgColor white offset 0,0,0 |
| 8247 | | |
| 8248 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 8249 | | > bgColor white offset 0,0.7,0 |
| 8250 | | |
| 8251 | | > ~select |
| 8252 | | |
| 8253 | | Nothing selected |
| 8254 | | |
| 8255 | | > save fig2.jpg |
| 8256 | | |
| 8257 | | > sel-ca |
| 8258 | | |
| 8259 | | 13 atoms, 1 model selected |
| 8260 | | 26 atoms, 2 models selected |
| 8261 | | |
| 8262 | | > ~ribbon |
| 8263 | | |
| 8264 | | > size stickRadius 0.05 |
| 8265 | | |
| 8266 | | Changed 4167 bond radii |
| 8267 | | |
| 8268 | | > size #1:138 stickRadius 0.2 |
| 8269 | | |
| 8270 | | Changed 7 bond radii |
| 8271 | | |
| 8272 | | > size #2:176 stickRadius 0.2 |
| 8273 | | |
| 8274 | | Changed 7 bond radii |
| 8275 | | |
| 8276 | | > view sel-residues pad -1 |
| 8277 | | |
| 8278 | | > ~select |
| 8279 | | |
| 8280 | | Nothing selected |
| 8281 | | |
| 8282 | | > save fig3.jpg |
| 8283 | | |
| 8284 | | > sel-ca |
| 8285 | | |
| 8286 | | 13 atoms, 1 model selected |
| 8287 | | 26 atoms, 2 models selected |
| 8288 | | |
| 8289 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 8290 | | |
| 8291 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 8292 | | |
| 8293 | | > view sel-residues pad -1 |
| 8294 | | |
| 8295 | | > sel-ca |
| 8296 | | |
| 8297 | | 13 atoms, 1 model selected |
| 8298 | | 26 atoms, 2 models selected |
| 8299 | | |
| 8300 | | > align #2 & sel toAtoms #1 & sel |
| 8301 | | |
| 8302 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 8303 | | |
| 8304 | | > ~select |
| 8305 | | |
| 8306 | | Nothing selected |
| 8307 | | |
| 8308 | | > save fig4.jpg |
| 8309 | | |
| 8310 | | > sel-ca |
| 8311 | | |
| 8312 | | 13 atoms, 1 model selected |
| 8313 | | 26 atoms, 2 models selected |
| 8314 | | |
| 8315 | | > ribbon sel |
| 8316 | | |
| 8317 | | > ~select |
| 8318 | | |
| 8319 | | Nothing selected |
| 8320 | | |
| 8321 | | > save fig5.jpg |
| 8322 | | |
| 8323 | | executed script.view.cxc |
| 8324 | | |
| 8325 | | > open "/Users/admin/Dropbox (Technion |
| 8326 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 8327 | | |
| 8328 | | > close |
| 8329 | | |
| 8330 | | > graphics bgColor white |
| 8331 | | |
| 8332 | | > open 1WMB |
| 8333 | | |
| 8334 | | 1wmb title: |
| 8335 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 8336 | | info...] |
| 8337 | | |
| 8338 | | Chain information for 1wmb #1 |
| 8339 | | --- |
| 8340 | | Chain | Description |
| 8341 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 8342 | | |
| 8343 | | Non-standard residues in 1wmb #1 |
| 8344 | | --- |
| 8345 | | CAC — cacodylate ion (dimethylarsinate) |
| 8346 | | MG — magnesium ion |
| 8347 | | |
| 8348 | | 1wmb mmCIF Assemblies |
| 8349 | | --- |
| 8350 | | 1| author_and_software_defined_assembly |
| 8351 | | |
| 8352 | | |
| 8353 | | > open 3I3O |
| 8354 | | |
| 8355 | | 3i3o title: |
| 8356 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 8357 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 8358 | | info...] |
| 8359 | | |
| 8360 | | Chain information for 3i3o #2 |
| 8361 | | --- |
| 8362 | | Chain | Description |
| 8363 | | A B C D E F G H | Short chain dehydrogenase |
| 8364 | | |
| 8365 | | Non-standard residues in 3i3o #2 |
| 8366 | | --- |
| 8367 | | CAC — cacodylate ion (dimethylarsinate) |
| 8368 | | CL — chloride ion |
| 8369 | | MG — magnesium ion |
| 8370 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 8371 | | |
| 8372 | | 3i3o mmCIF Assemblies |
| 8373 | | --- |
| 8374 | | 1| author_and_software_defined_assembly |
| 8375 | | 2| author_and_software_defined_assembly |
| 8376 | | |
| 8377 | | |
| 8378 | | > delete ~/a |
| 8379 | | |
| 8380 | | > delete solvent |
| 8381 | | |
| 8382 | | > mmaker #2 to #1 |
| 8383 | | |
| 8384 | | Parameters |
| 8385 | | --- |
| 8386 | | Chain pairing | bb |
| 8387 | | Alignment algorithm | Needleman-Wunsch |
| 8388 | | Similarity matrix | BLOSUM-62 |
| 8389 | | SS fraction | 0.3 |
| 8390 | | Gap open (HH/SS/other) | 18/18/6 |
| 8391 | | Gap extend | 1 |
| 8392 | | SS matrix | | | H | S | O |
| 8393 | | ---|---|---|--- |
| 8394 | | H | 6 | -9 | -6 |
| 8395 | | S | | 6 | -6 |
| 8396 | | O | | | 4 |
| 8397 | | Iteration cutoff | 2 |
| 8398 | | |
| 8399 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 8400 | | score = 499.7 |
| 8401 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 8402 | | 3.736) |
| 8403 | | |
| 8404 | | |
| 8405 | | > color #1 green |
| 8406 | | |
| 8407 | | > color #2 tan |
| 8408 | | |
| 8409 | | > color ~C byatom |
| 8410 | | |
| 8411 | | > ~display |
| 8412 | | |
| 8413 | | > display #1:138 #2:176 |
| 8414 | | |
| 8415 | | > style stick |
| 8416 | | |
| 8417 | | Changed 4099 atom styles |
| 8418 | | |
| 8419 | | > ribbon |
| 8420 | | |
| 8421 | | > transparency 60 target r |
| 8422 | | |
| 8423 | | > view |
| 8424 | | |
| 8425 | | > size #1:138 #2:176 stickRadius 0.3 |
| 8426 | | |
| 8427 | | Changed 14 bond radii |
| 8428 | | |
| 8429 | | > save fig1.jpg |
| 8430 | | |
| 8431 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 8432 | | |
| 8433 | | > sel-ca |
| 8434 | | |
| 8435 | | 13 atoms, 1 model selected |
| 8436 | | 26 atoms, 2 models selected |
| 8437 | | |
| 8438 | | > display sel-residues |
| 8439 | | |
| 8440 | | > color ~C byatom |
| 8441 | | |
| 8442 | | > style stick |
| 8443 | | |
| 8444 | | Changed 4099 atom styles |
| 8445 | | |
| 8446 | | > view #1:138 :< 5 pad -1 |
| 8447 | | |
| 8448 | | > hbonds #1:138 & #1 name hb1 color green |
| 8449 | | |
| 8450 | | 3 hydrogen bonds found |
| 8451 | | |
| 8452 | | > hbonds #2:176 & #2 name hb2 color tan |
| 8453 | | |
| 8454 | | 4 hydrogen bonds found |
| 8455 | | |
| 8456 | | > transparency 90 target r |
| 8457 | | |
| 8458 | | > label #1:138 #2:176 offset 1,-1,1 |
| 8459 | | |
| 8460 | | > 2dlabels text "1WMB - {0.phi:.1f},{0.psi:.1f}" color green size 40 xpos .03 |
| 8461 | | > ypos .90 |
| 8462 | | |
| 8463 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 8464 | | |
| 8465 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 8466 | | > bgColor white offset 0,0,0 |
| 8467 | | |
| 8468 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 8469 | | > bgColor white offset 0,0.7,0 |
| 8470 | | |
| 8471 | | > ~select |
| 8472 | | |
| 8473 | | Nothing selected |
| 8474 | | |
| 8475 | | > save fig2.jpg |
| 8476 | | |
| 8477 | | > sel-ca |
| 8478 | | |
| 8479 | | 13 atoms, 1 model selected |
| 8480 | | 26 atoms, 2 models selected |
| 8481 | | |
| 8482 | | > ~ribbon |
| 8483 | | |
| 8484 | | > size stickRadius 0.05 |
| 8485 | | |
| 8486 | | Changed 4167 bond radii |
| 8487 | | |
| 8488 | | > size #1:138 stickRadius 0.2 |
| 8489 | | |
| 8490 | | Changed 7 bond radii |
| 8491 | | |
| 8492 | | > size #2:176 stickRadius 0.2 |
| 8493 | | |
| 8494 | | Changed 7 bond radii |
| 8495 | | |
| 8496 | | > view sel-residues pad -1 |
| 8497 | | |
| 8498 | | > ~select |
| 8499 | | |
| 8500 | | Nothing selected |
| 8501 | | |
| 8502 | | > save fig3.jpg |
| 8503 | | |
| 8504 | | > sel-ca |
| 8505 | | |
| 8506 | | 13 atoms, 1 model selected |
| 8507 | | 26 atoms, 2 models selected |
| 8508 | | |
| 8509 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 8510 | | |
| 8511 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 8512 | | |
| 8513 | | > view sel-residues pad -1 |
| 8514 | | |
| 8515 | | > sel-ca |
| 8516 | | |
| 8517 | | 13 atoms, 1 model selected |
| 8518 | | 26 atoms, 2 models selected |
| 8519 | | |
| 8520 | | > align #2 & sel toAtoms #1 & sel |
| 8521 | | |
| 8522 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 8523 | | |
| 8524 | | > ~select |
| 8525 | | |
| 8526 | | Nothing selected |
| 8527 | | |
| 8528 | | > save fig4.jpg |
| 8529 | | |
| 8530 | | > sel-ca |
| 8531 | | |
| 8532 | | 13 atoms, 1 model selected |
| 8533 | | 26 atoms, 2 models selected |
| 8534 | | |
| 8535 | | > ribbon sel |
| 8536 | | |
| 8537 | | > ~select |
| 8538 | | |
| 8539 | | Nothing selected |
| 8540 | | |
| 8541 | | > save fig5.jpg |
| 8542 | | |
| 8543 | | executed script.view.cxc |
| 8544 | | |
| 8545 | | > open "/Users/admin/Dropbox (Technion |
| 8546 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 8547 | | |
| 8548 | | > close |
| 8549 | | |
| 8550 | | > graphics bgColor white |
| 8551 | | |
| 8552 | | > open 1WMB |
| 8553 | | |
| 8554 | | 1wmb title: |
| 8555 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 8556 | | info...] |
| 8557 | | |
| 8558 | | Chain information for 1wmb #1 |
| 8559 | | --- |
| 8560 | | Chain | Description |
| 8561 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 8562 | | |
| 8563 | | Non-standard residues in 1wmb #1 |
| 8564 | | --- |
| 8565 | | CAC — cacodylate ion (dimethylarsinate) |
| 8566 | | MG — magnesium ion |
| 8567 | | |
| 8568 | | 1wmb mmCIF Assemblies |
| 8569 | | --- |
| 8570 | | 1| author_and_software_defined_assembly |
| 8571 | | |
| 8572 | | |
| 8573 | | > open 3I3O |
| 8574 | | |
| 8575 | | 3i3o title: |
| 8576 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 8577 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 8578 | | info...] |
| 8579 | | |
| 8580 | | Chain information for 3i3o #2 |
| 8581 | | --- |
| 8582 | | Chain | Description |
| 8583 | | A B C D E F G H | Short chain dehydrogenase |
| 8584 | | |
| 8585 | | Non-standard residues in 3i3o #2 |
| 8586 | | --- |
| 8587 | | CAC — cacodylate ion (dimethylarsinate) |
| 8588 | | CL — chloride ion |
| 8589 | | MG — magnesium ion |
| 8590 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 8591 | | |
| 8592 | | 3i3o mmCIF Assemblies |
| 8593 | | --- |
| 8594 | | 1| author_and_software_defined_assembly |
| 8595 | | 2| author_and_software_defined_assembly |
| 8596 | | |
| 8597 | | |
| 8598 | | > delete ~/a |
| 8599 | | |
| 8600 | | > delete solvent |
| 8601 | | |
| 8602 | | > mmaker #2 to #1 |
| 8603 | | |
| 8604 | | Parameters |
| 8605 | | --- |
| 8606 | | Chain pairing | bb |
| 8607 | | Alignment algorithm | Needleman-Wunsch |
| 8608 | | Similarity matrix | BLOSUM-62 |
| 8609 | | SS fraction | 0.3 |
| 8610 | | Gap open (HH/SS/other) | 18/18/6 |
| 8611 | | Gap extend | 1 |
| 8612 | | SS matrix | | | H | S | O |
| 8613 | | ---|---|---|--- |
| 8614 | | H | 6 | -9 | -6 |
| 8615 | | S | | 6 | -6 |
| 8616 | | O | | | 4 |
| 8617 | | Iteration cutoff | 2 |
| 8618 | | |
| 8619 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 8620 | | score = 499.7 |
| 8621 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 8622 | | 3.736) |
| 8623 | | |
| 8624 | | |
| 8625 | | > color #1 green |
| 8626 | | |
| 8627 | | > color #2 tan |
| 8628 | | |
| 8629 | | > color ~C byatom |
| 8630 | | |
| 8631 | | > ~display |
| 8632 | | |
| 8633 | | > display #1:138 #2:176 |
| 8634 | | |
| 8635 | | > style stick |
| 8636 | | |
| 8637 | | Changed 4099 atom styles |
| 8638 | | |
| 8639 | | > ribbon |
| 8640 | | |
| 8641 | | > transparency 60 target r |
| 8642 | | |
| 8643 | | > view |
| 8644 | | |
| 8645 | | > size #1:138 #2:176 stickRadius 0.3 |
| 8646 | | |
| 8647 | | Changed 14 bond radii |
| 8648 | | |
| 8649 | | > save fig1.jpg |
| 8650 | | |
| 8651 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 8652 | | |
| 8653 | | > sel-ca |
| 8654 | | |
| 8655 | | 13 atoms, 1 model selected |
| 8656 | | 26 atoms, 2 models selected |
| 8657 | | |
| 8658 | | > display sel-residues |
| 8659 | | |
| 8660 | | > color ~C byatom |
| 8661 | | |
| 8662 | | > style stick |
| 8663 | | |
| 8664 | | Changed 4099 atom styles |
| 8665 | | |
| 8666 | | > view #1:138 :< 5 pad -1 |
| 8667 | | |
| 8668 | | > hbonds #1:138 & #1 name hb1 color green |
| 8669 | | |
| 8670 | | 3 hydrogen bonds found |
| 8671 | | |
| 8672 | | > hbonds #2:176 & #2 name hb2 color tan |
| 8673 | | |
| 8674 | | 4 hydrogen bonds found |
| 8675 | | |
| 8676 | | > transparency 90 target r |
| 8677 | | |
| 8678 | | > label #1:138 #2:176 offset 1,-1,1 |
| 8679 | | |
| 8680 | | > 2dlabels text "1WMB - #1:138 residues text "{0.phi:.1f},{0.psi:.1f}"" color |
| 8681 | | > green size 40 xpos .03 ypos .90 |
| 8682 | | |
| 8683 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 8684 | | |
| 8685 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 8686 | | > bgColor white offset 0,0,0 |
| 8687 | | |
| 8688 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 8689 | | > bgColor white offset 0,0.7,0 |
| 8690 | | |
| 8691 | | > ~select |
| 8692 | | |
| 8693 | | Nothing selected |
| 8694 | | |
| 8695 | | > save fig2.jpg |
| 8696 | | |
| 8697 | | > sel-ca |
| 8698 | | |
| 8699 | | 13 atoms, 1 model selected |
| 8700 | | 26 atoms, 2 models selected |
| 8701 | | |
| 8702 | | > ~ribbon |
| 8703 | | |
| 8704 | | > size stickRadius 0.05 |
| 8705 | | |
| 8706 | | Changed 4167 bond radii |
| 8707 | | |
| 8708 | | > size #1:138 stickRadius 0.2 |
| 8709 | | |
| 8710 | | Changed 7 bond radii |
| 8711 | | |
| 8712 | | > size #2:176 stickRadius 0.2 |
| 8713 | | |
| 8714 | | Changed 7 bond radii |
| 8715 | | |
| 8716 | | > view sel-residues pad -1 |
| 8717 | | |
| 8718 | | > ~select |
| 8719 | | |
| 8720 | | Nothing selected |
| 8721 | | |
| 8722 | | > save fig3.jpg |
| 8723 | | |
| 8724 | | > sel-ca |
| 8725 | | |
| 8726 | | 13 atoms, 1 model selected |
| 8727 | | 26 atoms, 2 models selected |
| 8728 | | |
| 8729 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 8730 | | |
| 8731 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 8732 | | |
| 8733 | | > view sel-residues pad -1 |
| 8734 | | |
| 8735 | | > sel-ca |
| 8736 | | |
| 8737 | | 13 atoms, 1 model selected |
| 8738 | | 26 atoms, 2 models selected |
| 8739 | | |
| 8740 | | > align #2 & sel toAtoms #1 & sel |
| 8741 | | |
| 8742 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 8743 | | |
| 8744 | | > ~select |
| 8745 | | |
| 8746 | | Nothing selected |
| 8747 | | |
| 8748 | | > save fig4.jpg |
| 8749 | | |
| 8750 | | > sel-ca |
| 8751 | | |
| 8752 | | 13 atoms, 1 model selected |
| 8753 | | 26 atoms, 2 models selected |
| 8754 | | |
| 8755 | | > ribbon sel |
| 8756 | | |
| 8757 | | > ~select |
| 8758 | | |
| 8759 | | Nothing selected |
| 8760 | | |
| 8761 | | > save fig5.jpg |
| 8762 | | |
| 8763 | | executed script.view.cxc |
| 8764 | | |
| 8765 | | > open "/Users/admin/Dropbox (Technion |
| 8766 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 8767 | | |
| 8768 | | > close |
| 8769 | | |
| 8770 | | > graphics bgColor white |
| 8771 | | |
| 8772 | | > open 1WMB |
| 8773 | | |
| 8774 | | 1wmb title: |
| 8775 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 8776 | | info...] |
| 8777 | | |
| 8778 | | Chain information for 1wmb #1 |
| 8779 | | --- |
| 8780 | | Chain | Description |
| 8781 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 8782 | | |
| 8783 | | Non-standard residues in 1wmb #1 |
| 8784 | | --- |
| 8785 | | CAC — cacodylate ion (dimethylarsinate) |
| 8786 | | MG — magnesium ion |
| 8787 | | |
| 8788 | | 1wmb mmCIF Assemblies |
| 8789 | | --- |
| 8790 | | 1| author_and_software_defined_assembly |
| 8791 | | |
| 8792 | | |
| 8793 | | > open 3I3O |
| 8794 | | |
| 8795 | | 3i3o title: |
| 8796 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 8797 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 8798 | | info...] |
| 8799 | | |
| 8800 | | Chain information for 3i3o #2 |
| 8801 | | --- |
| 8802 | | Chain | Description |
| 8803 | | A B C D E F G H | Short chain dehydrogenase |
| 8804 | | |
| 8805 | | Non-standard residues in 3i3o #2 |
| 8806 | | --- |
| 8807 | | CAC — cacodylate ion (dimethylarsinate) |
| 8808 | | CL — chloride ion |
| 8809 | | MG — magnesium ion |
| 8810 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 8811 | | |
| 8812 | | 3i3o mmCIF Assemblies |
| 8813 | | --- |
| 8814 | | 1| author_and_software_defined_assembly |
| 8815 | | 2| author_and_software_defined_assembly |
| 8816 | | |
| 8817 | | |
| 8818 | | > delete ~/a |
| 8819 | | |
| 8820 | | > delete solvent |
| 8821 | | |
| 8822 | | > mmaker #2 to #1 |
| 8823 | | |
| 8824 | | Parameters |
| 8825 | | --- |
| 8826 | | Chain pairing | bb |
| 8827 | | Alignment algorithm | Needleman-Wunsch |
| 8828 | | Similarity matrix | BLOSUM-62 |
| 8829 | | SS fraction | 0.3 |
| 8830 | | Gap open (HH/SS/other) | 18/18/6 |
| 8831 | | Gap extend | 1 |
| 8832 | | SS matrix | | | H | S | O |
| 8833 | | ---|---|---|--- |
| 8834 | | H | 6 | -9 | -6 |
| 8835 | | S | | 6 | -6 |
| 8836 | | O | | | 4 |
| 8837 | | Iteration cutoff | 2 |
| 8838 | | |
| 8839 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 8840 | | score = 499.7 |
| 8841 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 8842 | | 3.736) |
| 8843 | | |
| 8844 | | |
| 8845 | | > color #1 green |
| 8846 | | |
| 8847 | | > color #2 tan |
| 8848 | | |
| 8849 | | > color ~C byatom |
| 8850 | | |
| 8851 | | > ~display |
| 8852 | | |
| 8853 | | > display #1:138 #2:176 |
| 8854 | | |
| 8855 | | > style stick |
| 8856 | | |
| 8857 | | Changed 4099 atom styles |
| 8858 | | |
| 8859 | | > ribbon |
| 8860 | | |
| 8861 | | > transparency 60 target r |
| 8862 | | |
| 8863 | | > view |
| 8864 | | |
| 8865 | | > size #1:138 #2:176 stickRadius 0.3 |
| 8866 | | |
| 8867 | | Changed 14 bond radii |
| 8868 | | |
| 8869 | | > save fig1.jpg |
| 8870 | | |
| 8871 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 8872 | | |
| 8873 | | > sel-ca |
| 8874 | | |
| 8875 | | 13 atoms, 1 model selected |
| 8876 | | 26 atoms, 2 models selected |
| 8877 | | |
| 8878 | | > display sel-residues |
| 8879 | | |
| 8880 | | > color ~C byatom |
| 8881 | | |
| 8882 | | > style stick |
| 8883 | | |
| 8884 | | Changed 4099 atom styles |
| 8885 | | |
| 8886 | | > view #1:138 :< 5 pad -1 |
| 8887 | | |
| 8888 | | > hbonds #1:138 & #1 name hb1 color green |
| 8889 | | |
| 8890 | | 3 hydrogen bonds found |
| 8891 | | |
| 8892 | | > hbonds #2:176 & #2 name hb2 color tan |
| 8893 | | |
| 8894 | | 4 hydrogen bonds found |
| 8895 | | |
| 8896 | | > transparency 90 target r |
| 8897 | | |
| 8898 | | > label #1:138 #2:176 offset 1,-1,1 |
| 8899 | | |
| 8900 | | > 2dlabels text "1WMB - label #1:138 residues text "{0.phi:.1f},{0.psi:.1f}"" |
| 8901 | | > color green size 40 xpos .03 ypos .90 |
| 8902 | | |
| 8903 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 8904 | | |
| 8905 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 8906 | | > bgColor white offset 0,0,0 |
| 8907 | | |
| 8908 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 8909 | | > bgColor white offset 0,0.7,0 |
| 8910 | | |
| 8911 | | > ~select |
| 8912 | | |
| 8913 | | Nothing selected |
| 8914 | | |
| 8915 | | > save fig2.jpg |
| 8916 | | |
| 8917 | | > sel-ca |
| 8918 | | |
| 8919 | | 13 atoms, 1 model selected |
| 8920 | | 26 atoms, 2 models selected |
| 8921 | | |
| 8922 | | > ~ribbon |
| 8923 | | |
| 8924 | | > size stickRadius 0.05 |
| 8925 | | |
| 8926 | | Changed 4167 bond radii |
| 8927 | | |
| 8928 | | > size #1:138 stickRadius 0.2 |
| 8929 | | |
| 8930 | | Changed 7 bond radii |
| 8931 | | |
| 8932 | | > size #2:176 stickRadius 0.2 |
| 8933 | | |
| 8934 | | Changed 7 bond radii |
| 8935 | | |
| 8936 | | > view sel-residues pad -1 |
| 8937 | | |
| 8938 | | > ~select |
| 8939 | | |
| 8940 | | Nothing selected |
| 8941 | | |
| 8942 | | > save fig3.jpg |
| 8943 | | |
| 8944 | | > sel-ca |
| 8945 | | |
| 8946 | | 13 atoms, 1 model selected |
| 8947 | | 26 atoms, 2 models selected |
| 8948 | | |
| 8949 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 8950 | | |
| 8951 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 8952 | | |
| 8953 | | > view sel-residues pad -1 |
| 8954 | | |
| 8955 | | > sel-ca |
| 8956 | | |
| 8957 | | 13 atoms, 1 model selected |
| 8958 | | 26 atoms, 2 models selected |
| 8959 | | |
| 8960 | | > align #2 & sel toAtoms #1 & sel |
| 8961 | | |
| 8962 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 8963 | | |
| 8964 | | > ~select |
| 8965 | | |
| 8966 | | Nothing selected |
| 8967 | | |
| 8968 | | > save fig4.jpg |
| 8969 | | |
| 8970 | | > sel-ca |
| 8971 | | |
| 8972 | | 13 atoms, 1 model selected |
| 8973 | | 26 atoms, 2 models selected |
| 8974 | | |
| 8975 | | > ribbon sel |
| 8976 | | |
| 8977 | | > ~select |
| 8978 | | |
| 8979 | | Nothing selected |
| 8980 | | |
| 8981 | | > save fig5.jpg |
| 8982 | | |
| 8983 | | executed script.view.cxc |
| 8984 | | |
| 8985 | | > open "/Users/admin/Dropbox (Technion |
| 8986 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 8987 | | |
| 8988 | | > close |
| 8989 | | |
| 8990 | | > graphics bgColor white |
| 8991 | | |
| 8992 | | > open 1WMB |
| 8993 | | |
| 8994 | | 1wmb title: |
| 8995 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 8996 | | info...] |
| 8997 | | |
| 8998 | | Chain information for 1wmb #1 |
| 8999 | | --- |
| 9000 | | Chain | Description |
| 9001 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 9002 | | |
| 9003 | | Non-standard residues in 1wmb #1 |
| 9004 | | --- |
| 9005 | | CAC — cacodylate ion (dimethylarsinate) |
| 9006 | | MG — magnesium ion |
| 9007 | | |
| 9008 | | 1wmb mmCIF Assemblies |
| 9009 | | --- |
| 9010 | | 1| author_and_software_defined_assembly |
| 9011 | | |
| 9012 | | |
| 9013 | | > open 3I3O |
| 9014 | | |
| 9015 | | 3i3o title: |
| 9016 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 9017 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 9018 | | info...] |
| 9019 | | |
| 9020 | | Chain information for 3i3o #2 |
| 9021 | | --- |
| 9022 | | Chain | Description |
| 9023 | | A B C D E F G H | Short chain dehydrogenase |
| 9024 | | |
| 9025 | | Non-standard residues in 3i3o #2 |
| 9026 | | --- |
| 9027 | | CAC — cacodylate ion (dimethylarsinate) |
| 9028 | | CL — chloride ion |
| 9029 | | MG — magnesium ion |
| 9030 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 9031 | | |
| 9032 | | 3i3o mmCIF Assemblies |
| 9033 | | --- |
| 9034 | | 1| author_and_software_defined_assembly |
| 9035 | | 2| author_and_software_defined_assembly |
| 9036 | | |
| 9037 | | |
| 9038 | | > delete ~/a |
| 9039 | | |
| 9040 | | > delete solvent |
| 9041 | | |
| 9042 | | > mmaker #2 to #1 |
| 9043 | | |
| 9044 | | Parameters |
| 9045 | | --- |
| 9046 | | Chain pairing | bb |
| 9047 | | Alignment algorithm | Needleman-Wunsch |
| 9048 | | Similarity matrix | BLOSUM-62 |
| 9049 | | SS fraction | 0.3 |
| 9050 | | Gap open (HH/SS/other) | 18/18/6 |
| 9051 | | Gap extend | 1 |
| 9052 | | SS matrix | | | H | S | O |
| 9053 | | ---|---|---|--- |
| 9054 | | H | 6 | -9 | -6 |
| 9055 | | S | | 6 | -6 |
| 9056 | | O | | | 4 |
| 9057 | | Iteration cutoff | 2 |
| 9058 | | |
| 9059 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 9060 | | score = 499.7 |
| 9061 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 9062 | | 3.736) |
| 9063 | | |
| 9064 | | |
| 9065 | | > color #1 green |
| 9066 | | |
| 9067 | | > color #2 tan |
| 9068 | | |
| 9069 | | > color ~C byatom |
| 9070 | | |
| 9071 | | > ~display |
| 9072 | | |
| 9073 | | > display #1:138 #2:176 |
| 9074 | | |
| 9075 | | > style stick |
| 9076 | | |
| 9077 | | Changed 4099 atom styles |
| 9078 | | |
| 9079 | | > ribbon |
| 9080 | | |
| 9081 | | > transparency 60 target r |
| 9082 | | |
| 9083 | | > view |
| 9084 | | |
| 9085 | | > size #1:138 #2:176 stickRadius 0.3 |
| 9086 | | |
| 9087 | | Changed 14 bond radii |
| 9088 | | |
| 9089 | | > save fig1.jpg |
| 9090 | | |
| 9091 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 9092 | | |
| 9093 | | > sel-ca |
| 9094 | | |
| 9095 | | 13 atoms, 1 model selected |
| 9096 | | 26 atoms, 2 models selected |
| 9097 | | |
| 9098 | | > display sel-residues |
| 9099 | | |
| 9100 | | > color ~C byatom |
| 9101 | | |
| 9102 | | > style stick |
| 9103 | | |
| 9104 | | Changed 4099 atom styles |
| 9105 | | |
| 9106 | | > view #1:138 :< 5 pad -1 |
| 9107 | | |
| 9108 | | > hbonds #1:138 & #1 name hb1 color green |
| 9109 | | |
| 9110 | | 3 hydrogen bonds found |
| 9111 | | |
| 9112 | | > hbonds #2:176 & #2 name hb2 color tan |
| 9113 | | |
| 9114 | | 4 hydrogen bonds found |
| 9115 | | |
| 9116 | | > transparency 90 target r |
| 9117 | | |
| 9118 | | > label #1:138 #2:176 offset 1,-1,1 |
| 9119 | | |
| 9120 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 9121 | | |
| 9122 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 9123 | | |
| 9124 | | > label #1:138 residues text "attr number {0.phi:.1f},{0.psi:.1f}" height 0.5 |
| 9125 | | > color green bgColor white offset 0,0,0 |
| 9126 | | |
| 9127 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 9128 | | > bgColor white offset 0,0.7,0 |
| 9129 | | |
| 9130 | | > ~select |
| 9131 | | |
| 9132 | | Nothing selected |
| 9133 | | |
| 9134 | | > save fig2.jpg |
| 9135 | | |
| 9136 | | > sel-ca |
| 9137 | | |
| 9138 | | 13 atoms, 1 model selected |
| 9139 | | 26 atoms, 2 models selected |
| 9140 | | |
| 9141 | | > ~ribbon |
| 9142 | | |
| 9143 | | > size stickRadius 0.05 |
| 9144 | | |
| 9145 | | Changed 4167 bond radii |
| 9146 | | |
| 9147 | | > size #1:138 stickRadius 0.2 |
| 9148 | | |
| 9149 | | Changed 7 bond radii |
| 9150 | | |
| 9151 | | > size #2:176 stickRadius 0.2 |
| 9152 | | |
| 9153 | | Changed 7 bond radii |
| 9154 | | |
| 9155 | | > view sel-residues pad -1 |
| 9156 | | |
| 9157 | | > ~select |
| 9158 | | |
| 9159 | | Nothing selected |
| 9160 | | |
| 9161 | | > save fig3.jpg |
| 9162 | | |
| 9163 | | > sel-ca |
| 9164 | | |
| 9165 | | 13 atoms, 1 model selected |
| 9166 | | 26 atoms, 2 models selected |
| 9167 | | |
| 9168 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 9169 | | |
| 9170 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 9171 | | |
| 9172 | | > view sel-residues pad -1 |
| 9173 | | |
| 9174 | | > sel-ca |
| 9175 | | |
| 9176 | | 13 atoms, 1 model selected |
| 9177 | | 26 atoms, 2 models selected |
| 9178 | | |
| 9179 | | > align #2 & sel toAtoms #1 & sel |
| 9180 | | |
| 9181 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 9182 | | |
| 9183 | | > ~select |
| 9184 | | |
| 9185 | | Nothing selected |
| 9186 | | |
| 9187 | | > save fig4.jpg |
| 9188 | | |
| 9189 | | > sel-ca |
| 9190 | | |
| 9191 | | 13 atoms, 1 model selected |
| 9192 | | 26 atoms, 2 models selected |
| 9193 | | |
| 9194 | | > ribbon sel |
| 9195 | | |
| 9196 | | > ~select |
| 9197 | | |
| 9198 | | Nothing selected |
| 9199 | | |
| 9200 | | > save fig5.jpg |
| 9201 | | |
| 9202 | | executed script.view.cxc |
| 9203 | | |
| 9204 | | > open "/Users/admin/Dropbox (Technion |
| 9205 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 9206 | | |
| 9207 | | > close |
| 9208 | | |
| 9209 | | > graphics bgColor white |
| 9210 | | |
| 9211 | | > open 1WMB |
| 9212 | | |
| 9213 | | 1wmb title: |
| 9214 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 9215 | | info...] |
| 9216 | | |
| 9217 | | Chain information for 1wmb #1 |
| 9218 | | --- |
| 9219 | | Chain | Description |
| 9220 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 9221 | | |
| 9222 | | Non-standard residues in 1wmb #1 |
| 9223 | | --- |
| 9224 | | CAC — cacodylate ion (dimethylarsinate) |
| 9225 | | MG — magnesium ion |
| 9226 | | |
| 9227 | | 1wmb mmCIF Assemblies |
| 9228 | | --- |
| 9229 | | 1| author_and_software_defined_assembly |
| 9230 | | |
| 9231 | | |
| 9232 | | > open 3I3O |
| 9233 | | |
| 9234 | | 3i3o title: |
| 9235 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 9236 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 9237 | | info...] |
| 9238 | | |
| 9239 | | Chain information for 3i3o #2 |
| 9240 | | --- |
| 9241 | | Chain | Description |
| 9242 | | A B C D E F G H | Short chain dehydrogenase |
| 9243 | | |
| 9244 | | Non-standard residues in 3i3o #2 |
| 9245 | | --- |
| 9246 | | CAC — cacodylate ion (dimethylarsinate) |
| 9247 | | CL — chloride ion |
| 9248 | | MG — magnesium ion |
| 9249 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 9250 | | |
| 9251 | | 3i3o mmCIF Assemblies |
| 9252 | | --- |
| 9253 | | 1| author_and_software_defined_assembly |
| 9254 | | 2| author_and_software_defined_assembly |
| 9255 | | |
| 9256 | | |
| 9257 | | > delete ~/a |
| 9258 | | |
| 9259 | | > delete solvent |
| 9260 | | |
| 9261 | | > mmaker #2 to #1 |
| 9262 | | |
| 9263 | | Parameters |
| 9264 | | --- |
| 9265 | | Chain pairing | bb |
| 9266 | | Alignment algorithm | Needleman-Wunsch |
| 9267 | | Similarity matrix | BLOSUM-62 |
| 9268 | | SS fraction | 0.3 |
| 9269 | | Gap open (HH/SS/other) | 18/18/6 |
| 9270 | | Gap extend | 1 |
| 9271 | | SS matrix | | | H | S | O |
| 9272 | | ---|---|---|--- |
| 9273 | | H | 6 | -9 | -6 |
| 9274 | | S | | 6 | -6 |
| 9275 | | O | | | 4 |
| 9276 | | Iteration cutoff | 2 |
| 9277 | | |
| 9278 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 9279 | | score = 499.7 |
| 9280 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 9281 | | 3.736) |
| 9282 | | |
| 9283 | | |
| 9284 | | > color #1 green |
| 9285 | | |
| 9286 | | > color #2 tan |
| 9287 | | |
| 9288 | | > color ~C byatom |
| 9289 | | |
| 9290 | | > ~display |
| 9291 | | |
| 9292 | | > display #1:138 #2:176 |
| 9293 | | |
| 9294 | | > style stick |
| 9295 | | |
| 9296 | | Changed 4099 atom styles |
| 9297 | | |
| 9298 | | > ribbon |
| 9299 | | |
| 9300 | | > transparency 60 target r |
| 9301 | | |
| 9302 | | > view |
| 9303 | | |
| 9304 | | > size #1:138 #2:176 stickRadius 0.3 |
| 9305 | | |
| 9306 | | Changed 14 bond radii |
| 9307 | | |
| 9308 | | > save fig1.jpg |
| 9309 | | |
| 9310 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 9311 | | |
| 9312 | | > sel-ca |
| 9313 | | |
| 9314 | | 13 atoms, 1 model selected |
| 9315 | | 26 atoms, 2 models selected |
| 9316 | | |
| 9317 | | > display sel-residues |
| 9318 | | |
| 9319 | | > color ~C byatom |
| 9320 | | |
| 9321 | | > style stick |
| 9322 | | |
| 9323 | | Changed 4099 atom styles |
| 9324 | | |
| 9325 | | > view #1:138 :< 5 pad -1 |
| 9326 | | |
| 9327 | | > hbonds #1:138 & #1 name hb1 color green |
| 9328 | | |
| 9329 | | 3 hydrogen bonds found |
| 9330 | | |
| 9331 | | > hbonds #2:176 & #2 name hb2 color tan |
| 9332 | | |
| 9333 | | 4 hydrogen bonds found |
| 9334 | | |
| 9335 | | > transparency 90 target r |
| 9336 | | |
| 9337 | | > label #1:138 #2:176 offset 1,-1,1 |
| 9338 | | |
| 9339 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 9340 | | |
| 9341 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 9342 | | |
| 9343 | | > label #1:138 residues attribute number text {0.phi:.1f},{0.psi:.1f} height |
| 9344 | | > 0.5 color green bgColor white offset 0,0,0 |
| 9345 | | |
| 9346 | | Cannot specify both 'text' and 'attribute' keywords |
| 9347 | | |
| 9348 | | > open "/Users/admin/Dropbox (Technion |
| 9349 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 9350 | | |
| 9351 | | > close |
| 9352 | | |
| 9353 | | > graphics bgColor white |
| 9354 | | |
| 9355 | | > open 1WMB |
| 9356 | | |
| 9357 | | 1wmb title: |
| 9358 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 9359 | | info...] |
| 9360 | | |
| 9361 | | Chain information for 1wmb #1 |
| 9362 | | --- |
| 9363 | | Chain | Description |
| 9364 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 9365 | | |
| 9366 | | Non-standard residues in 1wmb #1 |
| 9367 | | --- |
| 9368 | | CAC — cacodylate ion (dimethylarsinate) |
| 9369 | | MG — magnesium ion |
| 9370 | | |
| 9371 | | 1wmb mmCIF Assemblies |
| 9372 | | --- |
| 9373 | | 1| author_and_software_defined_assembly |
| 9374 | | |
| 9375 | | |
| 9376 | | > open 3I3O |
| 9377 | | |
| 9378 | | 3i3o title: |
| 9379 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 9380 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 9381 | | info...] |
| 9382 | | |
| 9383 | | Chain information for 3i3o #2 |
| 9384 | | --- |
| 9385 | | Chain | Description |
| 9386 | | A B C D E F G H | Short chain dehydrogenase |
| 9387 | | |
| 9388 | | Non-standard residues in 3i3o #2 |
| 9389 | | --- |
| 9390 | | CAC — cacodylate ion (dimethylarsinate) |
| 9391 | | CL — chloride ion |
| 9392 | | MG — magnesium ion |
| 9393 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 9394 | | |
| 9395 | | 3i3o mmCIF Assemblies |
| 9396 | | --- |
| 9397 | | 1| author_and_software_defined_assembly |
| 9398 | | 2| author_and_software_defined_assembly |
| 9399 | | |
| 9400 | | |
| 9401 | | > delete ~/a |
| 9402 | | |
| 9403 | | > delete solvent |
| 9404 | | |
| 9405 | | > mmaker #2 to #1 |
| 9406 | | |
| 9407 | | Parameters |
| 9408 | | --- |
| 9409 | | Chain pairing | bb |
| 9410 | | Alignment algorithm | Needleman-Wunsch |
| 9411 | | Similarity matrix | BLOSUM-62 |
| 9412 | | SS fraction | 0.3 |
| 9413 | | Gap open (HH/SS/other) | 18/18/6 |
| 9414 | | Gap extend | 1 |
| 9415 | | SS matrix | | | H | S | O |
| 9416 | | ---|---|---|--- |
| 9417 | | H | 6 | -9 | -6 |
| 9418 | | S | | 6 | -6 |
| 9419 | | O | | | 4 |
| 9420 | | Iteration cutoff | 2 |
| 9421 | | |
| 9422 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 9423 | | score = 499.7 |
| 9424 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 9425 | | 3.736) |
| 9426 | | |
| 9427 | | |
| 9428 | | > color #1 green |
| 9429 | | |
| 9430 | | > color #2 tan |
| 9431 | | |
| 9432 | | > color ~C byatom |
| 9433 | | |
| 9434 | | > ~display |
| 9435 | | |
| 9436 | | > display #1:138 #2:176 |
| 9437 | | |
| 9438 | | > style stick |
| 9439 | | |
| 9440 | | Changed 4099 atom styles |
| 9441 | | |
| 9442 | | > ribbon |
| 9443 | | |
| 9444 | | > transparency 60 target r |
| 9445 | | |
| 9446 | | > view |
| 9447 | | |
| 9448 | | > size #1:138 #2:176 stickRadius 0.3 |
| 9449 | | |
| 9450 | | Changed 14 bond radii |
| 9451 | | |
| 9452 | | > save fig1.jpg |
| 9453 | | |
| 9454 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 9455 | | |
| 9456 | | > sel-ca |
| 9457 | | |
| 9458 | | 13 atoms, 1 model selected |
| 9459 | | 26 atoms, 2 models selected |
| 9460 | | |
| 9461 | | > display sel-residues |
| 9462 | | |
| 9463 | | > color ~C byatom |
| 9464 | | |
| 9465 | | > style stick |
| 9466 | | |
| 9467 | | Changed 4099 atom styles |
| 9468 | | |
| 9469 | | > view #1:138 :< 5 pad -1 |
| 9470 | | |
| 9471 | | > hbonds #1:138 & #1 name hb1 color green |
| 9472 | | |
| 9473 | | 3 hydrogen bonds found |
| 9474 | | |
| 9475 | | > hbonds #2:176 & #2 name hb2 color tan |
| 9476 | | |
| 9477 | | 4 hydrogen bonds found |
| 9478 | | |
| 9479 | | > transparency 90 target r |
| 9480 | | |
| 9481 | | > label #1:138 #2:176 offset 1,-1,1 |
| 9482 | | |
| 9483 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 9484 | | |
| 9485 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 9486 | | |
| 9487 | | > label #1:138 residues attribute number phi psi height 0.5 color green |
| 9488 | | > bgColor white offset 0,0,0 |
| 9489 | | |
| 9490 | | Expected a keyword |
| 9491 | | |
| 9492 | | > open "/Users/admin/Dropbox (Technion |
| 9493 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 9494 | | |
| 9495 | | > close |
| 9496 | | |
| 9497 | | > graphics bgColor white |
| 9498 | | |
| 9499 | | > open 1WMB |
| 9500 | | |
| 9501 | | 1wmb title: |
| 9502 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 9503 | | info...] |
| 9504 | | |
| 9505 | | Chain information for 1wmb #1 |
| 9506 | | --- |
| 9507 | | Chain | Description |
| 9508 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 9509 | | |
| 9510 | | Non-standard residues in 1wmb #1 |
| 9511 | | --- |
| 9512 | | CAC — cacodylate ion (dimethylarsinate) |
| 9513 | | MG — magnesium ion |
| 9514 | | |
| 9515 | | 1wmb mmCIF Assemblies |
| 9516 | | --- |
| 9517 | | 1| author_and_software_defined_assembly |
| 9518 | | |
| 9519 | | |
| 9520 | | > open 3I3O |
| 9521 | | |
| 9522 | | 3i3o title: |
| 9523 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 9524 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 9525 | | info...] |
| 9526 | | |
| 9527 | | Chain information for 3i3o #2 |
| 9528 | | --- |
| 9529 | | Chain | Description |
| 9530 | | A B C D E F G H | Short chain dehydrogenase |
| 9531 | | |
| 9532 | | Non-standard residues in 3i3o #2 |
| 9533 | | --- |
| 9534 | | CAC — cacodylate ion (dimethylarsinate) |
| 9535 | | CL — chloride ion |
| 9536 | | MG — magnesium ion |
| 9537 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 9538 | | |
| 9539 | | 3i3o mmCIF Assemblies |
| 9540 | | --- |
| 9541 | | 1| author_and_software_defined_assembly |
| 9542 | | 2| author_and_software_defined_assembly |
| 9543 | | |
| 9544 | | |
| 9545 | | > delete ~/a |
| 9546 | | |
| 9547 | | > delete solvent |
| 9548 | | |
| 9549 | | > mmaker #2 to #1 |
| 9550 | | |
| 9551 | | Parameters |
| 9552 | | --- |
| 9553 | | Chain pairing | bb |
| 9554 | | Alignment algorithm | Needleman-Wunsch |
| 9555 | | Similarity matrix | BLOSUM-62 |
| 9556 | | SS fraction | 0.3 |
| 9557 | | Gap open (HH/SS/other) | 18/18/6 |
| 9558 | | Gap extend | 1 |
| 9559 | | SS matrix | | | H | S | O |
| 9560 | | ---|---|---|--- |
| 9561 | | H | 6 | -9 | -6 |
| 9562 | | S | | 6 | -6 |
| 9563 | | O | | | 4 |
| 9564 | | Iteration cutoff | 2 |
| 9565 | | |
| 9566 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 9567 | | score = 499.7 |
| 9568 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 9569 | | 3.736) |
| 9570 | | |
| 9571 | | |
| 9572 | | > color #1 green |
| 9573 | | |
| 9574 | | > color #2 tan |
| 9575 | | |
| 9576 | | > color ~C byatom |
| 9577 | | |
| 9578 | | > ~display |
| 9579 | | |
| 9580 | | > display #1:138 #2:176 |
| 9581 | | |
| 9582 | | > style stick |
| 9583 | | |
| 9584 | | Changed 4099 atom styles |
| 9585 | | |
| 9586 | | > ribbon |
| 9587 | | |
| 9588 | | > transparency 60 target r |
| 9589 | | |
| 9590 | | > view |
| 9591 | | |
| 9592 | | > size #1:138 #2:176 stickRadius 0.3 |
| 9593 | | |
| 9594 | | Changed 14 bond radii |
| 9595 | | |
| 9596 | | > save fig1.jpg |
| 9597 | | |
| 9598 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 9599 | | |
| 9600 | | > sel-ca |
| 9601 | | |
| 9602 | | 13 atoms, 1 model selected |
| 9603 | | 26 atoms, 2 models selected |
| 9604 | | |
| 9605 | | > display sel-residues |
| 9606 | | |
| 9607 | | > color ~C byatom |
| 9608 | | |
| 9609 | | > style stick |
| 9610 | | |
| 9611 | | Changed 4099 atom styles |
| 9612 | | |
| 9613 | | > view #1:138 :< 5 pad -1 |
| 9614 | | |
| 9615 | | > hbonds #1:138 & #1 name hb1 color green |
| 9616 | | |
| 9617 | | 3 hydrogen bonds found |
| 9618 | | |
| 9619 | | > hbonds #2:176 & #2 name hb2 color tan |
| 9620 | | |
| 9621 | | 4 hydrogen bonds found |
| 9622 | | |
| 9623 | | > transparency 90 target r |
| 9624 | | |
| 9625 | | > label #1:138 #2:176 offset 1,-1,1 |
| 9626 | | |
| 9627 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 9628 | | |
| 9629 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 9630 | | |
| 9631 | | > label #1:138 residues attribute number "{0.phi:.1f},{0.psi:.1f}" height 0.5 |
| 9632 | | > color green bgColor white offset 0,0,0 |
| 9633 | | |
| 9634 | | Expected a keyword |
| 9635 | | |
| 9636 | | > open "/Users/admin/Dropbox (Technion |
| 9637 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 9638 | | |
| 9639 | | > close |
| 9640 | | |
| 9641 | | > graphics bgColor white |
| 9642 | | |
| 9643 | | > open 1WMB |
| 9644 | | |
| 9645 | | 1wmb title: |
| 9646 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 9647 | | info...] |
| 9648 | | |
| 9649 | | Chain information for 1wmb #1 |
| 9650 | | --- |
| 9651 | | Chain | Description |
| 9652 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 9653 | | |
| 9654 | | Non-standard residues in 1wmb #1 |
| 9655 | | --- |
| 9656 | | CAC — cacodylate ion (dimethylarsinate) |
| 9657 | | MG — magnesium ion |
| 9658 | | |
| 9659 | | 1wmb mmCIF Assemblies |
| 9660 | | --- |
| 9661 | | 1| author_and_software_defined_assembly |
| 9662 | | |
| 9663 | | |
| 9664 | | > open 3I3O |
| 9665 | | |
| 9666 | | 3i3o title: |
| 9667 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 9668 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 9669 | | info...] |
| 9670 | | |
| 9671 | | Chain information for 3i3o #2 |
| 9672 | | --- |
| 9673 | | Chain | Description |
| 9674 | | A B C D E F G H | Short chain dehydrogenase |
| 9675 | | |
| 9676 | | Non-standard residues in 3i3o #2 |
| 9677 | | --- |
| 9678 | | CAC — cacodylate ion (dimethylarsinate) |
| 9679 | | CL — chloride ion |
| 9680 | | MG — magnesium ion |
| 9681 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 9682 | | |
| 9683 | | 3i3o mmCIF Assemblies |
| 9684 | | --- |
| 9685 | | 1| author_and_software_defined_assembly |
| 9686 | | 2| author_and_software_defined_assembly |
| 9687 | | |
| 9688 | | |
| 9689 | | > delete ~/a |
| 9690 | | |
| 9691 | | > delete solvent |
| 9692 | | |
| 9693 | | > mmaker #2 to #1 |
| 9694 | | |
| 9695 | | Parameters |
| 9696 | | --- |
| 9697 | | Chain pairing | bb |
| 9698 | | Alignment algorithm | Needleman-Wunsch |
| 9699 | | Similarity matrix | BLOSUM-62 |
| 9700 | | SS fraction | 0.3 |
| 9701 | | Gap open (HH/SS/other) | 18/18/6 |
| 9702 | | Gap extend | 1 |
| 9703 | | SS matrix | | | H | S | O |
| 9704 | | ---|---|---|--- |
| 9705 | | H | 6 | -9 | -6 |
| 9706 | | S | | 6 | -6 |
| 9707 | | O | | | 4 |
| 9708 | | Iteration cutoff | 2 |
| 9709 | | |
| 9710 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 9711 | | score = 499.7 |
| 9712 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 9713 | | 3.736) |
| 9714 | | |
| 9715 | | |
| 9716 | | > color #1 green |
| 9717 | | |
| 9718 | | > color #2 tan |
| 9719 | | |
| 9720 | | > color ~C byatom |
| 9721 | | |
| 9722 | | > ~display |
| 9723 | | |
| 9724 | | > display #1:138 #2:176 |
| 9725 | | |
| 9726 | | > style stick |
| 9727 | | |
| 9728 | | Changed 4099 atom styles |
| 9729 | | |
| 9730 | | > ribbon |
| 9731 | | |
| 9732 | | > transparency 60 target r |
| 9733 | | |
| 9734 | | > view |
| 9735 | | |
| 9736 | | > size #1:138 #2:176 stickRadius 0.3 |
| 9737 | | |
| 9738 | | Changed 14 bond radii |
| 9739 | | |
| 9740 | | > save fig1.jpg |
| 9741 | | |
| 9742 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 9743 | | |
| 9744 | | > sel-ca |
| 9745 | | |
| 9746 | | 13 atoms, 1 model selected |
| 9747 | | 26 atoms, 2 models selected |
| 9748 | | |
| 9749 | | > display sel-residues |
| 9750 | | |
| 9751 | | > color ~C byatom |
| 9752 | | |
| 9753 | | > style stick |
| 9754 | | |
| 9755 | | Changed 4099 atom styles |
| 9756 | | |
| 9757 | | > view #1:138 :< 5 pad -1 |
| 9758 | | |
| 9759 | | > hbonds #1:138 & #1 name hb1 color green |
| 9760 | | |
| 9761 | | 3 hydrogen bonds found |
| 9762 | | |
| 9763 | | > hbonds #2:176 & #2 name hb2 color tan |
| 9764 | | |
| 9765 | | 4 hydrogen bonds found |
| 9766 | | |
| 9767 | | > transparency 90 target r |
| 9768 | | |
| 9769 | | > label #1:138 #2:176 offset 1,-1,1 |
| 9770 | | |
| 9771 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 9772 | | |
| 9773 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 9774 | | |
| 9775 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 9776 | | > bgColor white offset 0,0,0 |
| 9777 | | |
| 9778 | | > label #1:138 residues height 0.5 color green bgColor white offset 3,0,0 |
| 9779 | | |
| 9780 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 9781 | | > bgColor white offset 0,0.7,0 |
| 9782 | | |
| 9783 | | > ~select |
| 9784 | | |
| 9785 | | Nothing selected |
| 9786 | | |
| 9787 | | > save fig2.jpg |
| 9788 | | |
| 9789 | | > sel-ca |
| 9790 | | |
| 9791 | | 13 atoms, 1 model selected |
| 9792 | | 26 atoms, 2 models selected |
| 9793 | | |
| 9794 | | > ~ribbon |
| 9795 | | |
| 9796 | | > size stickRadius 0.05 |
| 9797 | | |
| 9798 | | Changed 4167 bond radii |
| 9799 | | |
| 9800 | | > size #1:138 stickRadius 0.2 |
| 9801 | | |
| 9802 | | Changed 7 bond radii |
| 9803 | | |
| 9804 | | > size #2:176 stickRadius 0.2 |
| 9805 | | |
| 9806 | | Changed 7 bond radii |
| 9807 | | |
| 9808 | | > view sel-residues pad -1 |
| 9809 | | |
| 9810 | | > ~select |
| 9811 | | |
| 9812 | | Nothing selected |
| 9813 | | |
| 9814 | | > save fig3.jpg |
| 9815 | | |
| 9816 | | > sel-ca |
| 9817 | | |
| 9818 | | 13 atoms, 1 model selected |
| 9819 | | 26 atoms, 2 models selected |
| 9820 | | |
| 9821 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 9822 | | |
| 9823 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 9824 | | |
| 9825 | | > view sel-residues pad -1 |
| 9826 | | |
| 9827 | | > sel-ca |
| 9828 | | |
| 9829 | | 13 atoms, 1 model selected |
| 9830 | | 26 atoms, 2 models selected |
| 9831 | | |
| 9832 | | > align #2 & sel toAtoms #1 & sel |
| 9833 | | |
| 9834 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 9835 | | |
| 9836 | | > ~select |
| 9837 | | |
| 9838 | | Nothing selected |
| 9839 | | |
| 9840 | | > save fig4.jpg |
| 9841 | | |
| 9842 | | > sel-ca |
| 9843 | | |
| 9844 | | 13 atoms, 1 model selected |
| 9845 | | 26 atoms, 2 models selected |
| 9846 | | |
| 9847 | | > ribbon sel |
| 9848 | | |
| 9849 | | > ~select |
| 9850 | | |
| 9851 | | Nothing selected |
| 9852 | | |
| 9853 | | > save fig5.jpg |
| 9854 | | |
| 9855 | | executed script.view.cxc |
| 9856 | | |
| 9857 | | > open "/Users/admin/Dropbox (Technion |
| 9858 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 9859 | | |
| 9860 | | > close |
| 9861 | | |
| 9862 | | > graphics bgColor white |
| 9863 | | |
| 9864 | | > open 1WMB |
| 9865 | | |
| 9866 | | 1wmb title: |
| 9867 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 9868 | | info...] |
| 9869 | | |
| 9870 | | Chain information for 1wmb #1 |
| 9871 | | --- |
| 9872 | | Chain | Description |
| 9873 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 9874 | | |
| 9875 | | Non-standard residues in 1wmb #1 |
| 9876 | | --- |
| 9877 | | CAC — cacodylate ion (dimethylarsinate) |
| 9878 | | MG — magnesium ion |
| 9879 | | |
| 9880 | | 1wmb mmCIF Assemblies |
| 9881 | | --- |
| 9882 | | 1| author_and_software_defined_assembly |
| 9883 | | |
| 9884 | | |
| 9885 | | > open 3I3O |
| 9886 | | |
| 9887 | | 3i3o title: |
| 9888 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 9889 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 9890 | | info...] |
| 9891 | | |
| 9892 | | Chain information for 3i3o #2 |
| 9893 | | --- |
| 9894 | | Chain | Description |
| 9895 | | A B C D E F G H | Short chain dehydrogenase |
| 9896 | | |
| 9897 | | Non-standard residues in 3i3o #2 |
| 9898 | | --- |
| 9899 | | CAC — cacodylate ion (dimethylarsinate) |
| 9900 | | CL — chloride ion |
| 9901 | | MG — magnesium ion |
| 9902 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 9903 | | |
| 9904 | | 3i3o mmCIF Assemblies |
| 9905 | | --- |
| 9906 | | 1| author_and_software_defined_assembly |
| 9907 | | 2| author_and_software_defined_assembly |
| 9908 | | |
| 9909 | | |
| 9910 | | > delete ~/a |
| 9911 | | |
| 9912 | | > delete solvent |
| 9913 | | |
| 9914 | | > mmaker #2 to #1 |
| 9915 | | |
| 9916 | | Parameters |
| 9917 | | --- |
| 9918 | | Chain pairing | bb |
| 9919 | | Alignment algorithm | Needleman-Wunsch |
| 9920 | | Similarity matrix | BLOSUM-62 |
| 9921 | | SS fraction | 0.3 |
| 9922 | | Gap open (HH/SS/other) | 18/18/6 |
| 9923 | | Gap extend | 1 |
| 9924 | | SS matrix | | | H | S | O |
| 9925 | | ---|---|---|--- |
| 9926 | | H | 6 | -9 | -6 |
| 9927 | | S | | 6 | -6 |
| 9928 | | O | | | 4 |
| 9929 | | Iteration cutoff | 2 |
| 9930 | | |
| 9931 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 9932 | | score = 499.7 |
| 9933 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 9934 | | 3.736) |
| 9935 | | |
| 9936 | | |
| 9937 | | > color #1 green |
| 9938 | | |
| 9939 | | > color #2 tan |
| 9940 | | |
| 9941 | | > color ~C byatom |
| 9942 | | |
| 9943 | | > ~display |
| 9944 | | |
| 9945 | | > display #1:138 #2:176 |
| 9946 | | |
| 9947 | | > style stick |
| 9948 | | |
| 9949 | | Changed 4099 atom styles |
| 9950 | | |
| 9951 | | > ribbon |
| 9952 | | |
| 9953 | | > transparency 60 target r |
| 9954 | | |
| 9955 | | > view |
| 9956 | | |
| 9957 | | > size #1:138 #2:176 stickRadius 0.3 |
| 9958 | | |
| 9959 | | Changed 14 bond radii |
| 9960 | | |
| 9961 | | > save fig1.jpg |
| 9962 | | |
| 9963 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 9964 | | |
| 9965 | | > sel-ca |
| 9966 | | |
| 9967 | | 13 atoms, 1 model selected |
| 9968 | | 26 atoms, 2 models selected |
| 9969 | | |
| 9970 | | > display sel-residues |
| 9971 | | |
| 9972 | | > color ~C byatom |
| 9973 | | |
| 9974 | | > style stick |
| 9975 | | |
| 9976 | | Changed 4099 atom styles |
| 9977 | | |
| 9978 | | > view #1:138 :< 5 pad -1 |
| 9979 | | |
| 9980 | | > hbonds #1:138 & #1 name hb1 color green |
| 9981 | | |
| 9982 | | 3 hydrogen bonds found |
| 9983 | | |
| 9984 | | > hbonds #2:176 & #2 name hb2 color tan |
| 9985 | | |
| 9986 | | 4 hydrogen bonds found |
| 9987 | | |
| 9988 | | > transparency 90 target r |
| 9989 | | |
| 9990 | | > label #1:138 #2:176 offset 1,-1,1 |
| 9991 | | |
| 9992 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 9993 | | |
| 9994 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 9995 | | |
| 9996 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 9997 | | > bgColor white offset 0,0,0 |
| 9998 | | |
| 9999 | | > label #1:138 height 0.5 color green bgColor white offset 3,0,0 |
| 10000 | | |
| 10001 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 10002 | | > bgColor white offset 0,0.7,0 |
| 10003 | | |
| 10004 | | > ~select |
| 10005 | | |
| 10006 | | Nothing selected |
| 10007 | | |
| 10008 | | > save fig2.jpg |
| 10009 | | |
| 10010 | | > sel-ca |
| 10011 | | |
| 10012 | | 13 atoms, 1 model selected |
| 10013 | | 26 atoms, 2 models selected |
| 10014 | | |
| 10015 | | > ~ribbon |
| 10016 | | |
| 10017 | | > size stickRadius 0.05 |
| 10018 | | |
| 10019 | | Changed 4167 bond radii |
| 10020 | | |
| 10021 | | > size #1:138 stickRadius 0.2 |
| 10022 | | |
| 10023 | | Changed 7 bond radii |
| 10024 | | |
| 10025 | | > size #2:176 stickRadius 0.2 |
| 10026 | | |
| 10027 | | Changed 7 bond radii |
| 10028 | | |
| 10029 | | > view sel-residues pad -1 |
| 10030 | | |
| 10031 | | > ~select |
| 10032 | | |
| 10033 | | Nothing selected |
| 10034 | | |
| 10035 | | > save fig3.jpg |
| 10036 | | |
| 10037 | | > sel-ca |
| 10038 | | |
| 10039 | | 13 atoms, 1 model selected |
| 10040 | | 26 atoms, 2 models selected |
| 10041 | | |
| 10042 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 10043 | | |
| 10044 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 10045 | | |
| 10046 | | > view sel-residues pad -1 |
| 10047 | | |
| 10048 | | > sel-ca |
| 10049 | | |
| 10050 | | 13 atoms, 1 model selected |
| 10051 | | 26 atoms, 2 models selected |
| 10052 | | |
| 10053 | | > align #2 & sel toAtoms #1 & sel |
| 10054 | | |
| 10055 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 10056 | | |
| 10057 | | > ~select |
| 10058 | | |
| 10059 | | Nothing selected |
| 10060 | | |
| 10061 | | > save fig4.jpg |
| 10062 | | |
| 10063 | | > sel-ca |
| 10064 | | |
| 10065 | | 13 atoms, 1 model selected |
| 10066 | | 26 atoms, 2 models selected |
| 10067 | | |
| 10068 | | > ribbon sel |
| 10069 | | |
| 10070 | | > ~select |
| 10071 | | |
| 10072 | | Nothing selected |
| 10073 | | |
| 10074 | | > save fig5.jpg |
| 10075 | | |
| 10076 | | executed script.view.cxc |
| 10077 | | |
| 10078 | | > open "/Users/admin/Dropbox (Technion |
| 10079 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 10080 | | |
| 10081 | | > close |
| 10082 | | |
| 10083 | | > graphics bgColor white |
| 10084 | | |
| 10085 | | > open 1WMB |
| 10086 | | |
| 10087 | | 1wmb title: |
| 10088 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 10089 | | info...] |
| 10090 | | |
| 10091 | | Chain information for 1wmb #1 |
| 10092 | | --- |
| 10093 | | Chain | Description |
| 10094 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 10095 | | |
| 10096 | | Non-standard residues in 1wmb #1 |
| 10097 | | --- |
| 10098 | | CAC — cacodylate ion (dimethylarsinate) |
| 10099 | | MG — magnesium ion |
| 10100 | | |
| 10101 | | 1wmb mmCIF Assemblies |
| 10102 | | --- |
| 10103 | | 1| author_and_software_defined_assembly |
| 10104 | | |
| 10105 | | |
| 10106 | | > open 3I3O |
| 10107 | | |
| 10108 | | 3i3o title: |
| 10109 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 10110 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 10111 | | info...] |
| 10112 | | |
| 10113 | | Chain information for 3i3o #2 |
| 10114 | | --- |
| 10115 | | Chain | Description |
| 10116 | | A B C D E F G H | Short chain dehydrogenase |
| 10117 | | |
| 10118 | | Non-standard residues in 3i3o #2 |
| 10119 | | --- |
| 10120 | | CAC — cacodylate ion (dimethylarsinate) |
| 10121 | | CL — chloride ion |
| 10122 | | MG — magnesium ion |
| 10123 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 10124 | | |
| 10125 | | 3i3o mmCIF Assemblies |
| 10126 | | --- |
| 10127 | | 1| author_and_software_defined_assembly |
| 10128 | | 2| author_and_software_defined_assembly |
| 10129 | | |
| 10130 | | |
| 10131 | | > delete ~/a |
| 10132 | | |
| 10133 | | > delete solvent |
| 10134 | | |
| 10135 | | > mmaker #2 to #1 |
| 10136 | | |
| 10137 | | Parameters |
| 10138 | | --- |
| 10139 | | Chain pairing | bb |
| 10140 | | Alignment algorithm | Needleman-Wunsch |
| 10141 | | Similarity matrix | BLOSUM-62 |
| 10142 | | SS fraction | 0.3 |
| 10143 | | Gap open (HH/SS/other) | 18/18/6 |
| 10144 | | Gap extend | 1 |
| 10145 | | SS matrix | | | H | S | O |
| 10146 | | ---|---|---|--- |
| 10147 | | H | 6 | -9 | -6 |
| 10148 | | S | | 6 | -6 |
| 10149 | | O | | | 4 |
| 10150 | | Iteration cutoff | 2 |
| 10151 | | |
| 10152 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 10153 | | score = 499.7 |
| 10154 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 10155 | | 3.736) |
| 10156 | | |
| 10157 | | |
| 10158 | | > color #1 green |
| 10159 | | |
| 10160 | | > color #2 tan |
| 10161 | | |
| 10162 | | > color ~C byatom |
| 10163 | | |
| 10164 | | > ~display |
| 10165 | | |
| 10166 | | > display #1:138 #2:176 |
| 10167 | | |
| 10168 | | > style stick |
| 10169 | | |
| 10170 | | Changed 4099 atom styles |
| 10171 | | |
| 10172 | | > ribbon |
| 10173 | | |
| 10174 | | > transparency 60 target r |
| 10175 | | |
| 10176 | | > view |
| 10177 | | |
| 10178 | | > size #1:138 #2:176 stickRadius 0.3 |
| 10179 | | |
| 10180 | | Changed 14 bond radii |
| 10181 | | |
| 10182 | | > save fig1.jpg |
| 10183 | | |
| 10184 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 10185 | | |
| 10186 | | > sel-ca |
| 10187 | | |
| 10188 | | 13 atoms, 1 model selected |
| 10189 | | 26 atoms, 2 models selected |
| 10190 | | |
| 10191 | | > display sel-residues |
| 10192 | | |
| 10193 | | > color ~C byatom |
| 10194 | | |
| 10195 | | > style stick |
| 10196 | | |
| 10197 | | Changed 4099 atom styles |
| 10198 | | |
| 10199 | | > view #1:138 :< 5 pad -1 |
| 10200 | | |
| 10201 | | > hbonds #1:138 & #1 name hb1 color green |
| 10202 | | |
| 10203 | | 3 hydrogen bonds found |
| 10204 | | |
| 10205 | | > hbonds #2:176 & #2 name hb2 color tan |
| 10206 | | |
| 10207 | | 4 hydrogen bonds found |
| 10208 | | |
| 10209 | | > transparency 90 target r |
| 10210 | | |
| 10211 | | > label #1:138 #2:176 offset 1,-1,1 |
| 10212 | | |
| 10213 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 10214 | | |
| 10215 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 10216 | | |
| 10217 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 10218 | | > bgColor white offset 0,0,0 |
| 10219 | | |
| 10220 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 10221 | | > bgColor white offset 0,0.7,0 |
| 10222 | | |
| 10223 | | > atoms #1:138@CA attr residue.number |
| 10224 | | |
| 10225 | | Unknown command: atoms #1:138@CA attr residue.number |
| 10226 | | |
| 10227 | | > open "/Users/admin/Dropbox (Technion |
| 10228 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 10229 | | |
| 10230 | | > close |
| 10231 | | |
| 10232 | | > graphics bgColor white |
| 10233 | | |
| 10234 | | > open 1WMB |
| 10235 | | |
| 10236 | | 1wmb title: |
| 10237 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 10238 | | info...] |
| 10239 | | |
| 10240 | | Chain information for 1wmb #1 |
| 10241 | | --- |
| 10242 | | Chain | Description |
| 10243 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 10244 | | |
| 10245 | | Non-standard residues in 1wmb #1 |
| 10246 | | --- |
| 10247 | | CAC — cacodylate ion (dimethylarsinate) |
| 10248 | | MG — magnesium ion |
| 10249 | | |
| 10250 | | 1wmb mmCIF Assemblies |
| 10251 | | --- |
| 10252 | | 1| author_and_software_defined_assembly |
| 10253 | | |
| 10254 | | |
| 10255 | | > open 3I3O |
| 10256 | | |
| 10257 | | 3i3o title: |
| 10258 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 10259 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 10260 | | info...] |
| 10261 | | |
| 10262 | | Chain information for 3i3o #2 |
| 10263 | | --- |
| 10264 | | Chain | Description |
| 10265 | | A B C D E F G H | Short chain dehydrogenase |
| 10266 | | |
| 10267 | | Non-standard residues in 3i3o #2 |
| 10268 | | --- |
| 10269 | | CAC — cacodylate ion (dimethylarsinate) |
| 10270 | | CL — chloride ion |
| 10271 | | MG — magnesium ion |
| 10272 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 10273 | | |
| 10274 | | 3i3o mmCIF Assemblies |
| 10275 | | --- |
| 10276 | | 1| author_and_software_defined_assembly |
| 10277 | | 2| author_and_software_defined_assembly |
| 10278 | | |
| 10279 | | |
| 10280 | | > delete ~/a |
| 10281 | | |
| 10282 | | > delete solvent |
| 10283 | | |
| 10284 | | > mmaker #2 to #1 |
| 10285 | | |
| 10286 | | Parameters |
| 10287 | | --- |
| 10288 | | Chain pairing | bb |
| 10289 | | Alignment algorithm | Needleman-Wunsch |
| 10290 | | Similarity matrix | BLOSUM-62 |
| 10291 | | SS fraction | 0.3 |
| 10292 | | Gap open (HH/SS/other) | 18/18/6 |
| 10293 | | Gap extend | 1 |
| 10294 | | SS matrix | | | H | S | O |
| 10295 | | ---|---|---|--- |
| 10296 | | H | 6 | -9 | -6 |
| 10297 | | S | | 6 | -6 |
| 10298 | | O | | | 4 |
| 10299 | | Iteration cutoff | 2 |
| 10300 | | |
| 10301 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 10302 | | score = 499.7 |
| 10303 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 10304 | | 3.736) |
| 10305 | | |
| 10306 | | |
| 10307 | | > color #1 green |
| 10308 | | |
| 10309 | | > color #2 tan |
| 10310 | | |
| 10311 | | > color ~C byatom |
| 10312 | | |
| 10313 | | > ~display |
| 10314 | | |
| 10315 | | > display #1:138 #2:176 |
| 10316 | | |
| 10317 | | > style stick |
| 10318 | | |
| 10319 | | Changed 4099 atom styles |
| 10320 | | |
| 10321 | | > ribbon |
| 10322 | | |
| 10323 | | > transparency 60 target r |
| 10324 | | |
| 10325 | | > view |
| 10326 | | |
| 10327 | | > size #1:138 #2:176 stickRadius 0.3 |
| 10328 | | |
| 10329 | | Changed 14 bond radii |
| 10330 | | |
| 10331 | | > save fig1.jpg |
| 10332 | | |
| 10333 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 10334 | | |
| 10335 | | > sel-ca |
| 10336 | | |
| 10337 | | 13 atoms, 1 model selected |
| 10338 | | 26 atoms, 2 models selected |
| 10339 | | |
| 10340 | | > display sel-residues |
| 10341 | | |
| 10342 | | > color ~C byatom |
| 10343 | | |
| 10344 | | > style stick |
| 10345 | | |
| 10346 | | Changed 4099 atom styles |
| 10347 | | |
| 10348 | | > view #1:138 :< 5 pad -1 |
| 10349 | | |
| 10350 | | > hbonds #1:138 & #1 name hb1 color green |
| 10351 | | |
| 10352 | | 3 hydrogen bonds found |
| 10353 | | |
| 10354 | | > hbonds #2:176 & #2 name hb2 color tan |
| 10355 | | |
| 10356 | | 4 hydrogen bonds found |
| 10357 | | |
| 10358 | | > transparency 90 target r |
| 10359 | | |
| 10360 | | > label #1:138 #2:176 offset 1,-1,1 |
| 10361 | | |
| 10362 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 10363 | | |
| 10364 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 10365 | | |
| 10366 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 10367 | | > bgColor white offset 0,0,0 |
| 10368 | | |
| 10369 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 10370 | | > bgColor white offset 0,0.7,0 |
| 10371 | | |
| 10372 | | > label atoms #1:138@CA attr residue.number |
| 10373 | | |
| 10374 | | Expected a keyword |
| 10375 | | |
| 10376 | | > open "/Users/admin/Dropbox (Technion |
| 10377 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 10378 | | |
| 10379 | | > close |
| 10380 | | |
| 10381 | | > graphics bgColor white |
| 10382 | | |
| 10383 | | > open 1WMB |
| 10384 | | |
| 10385 | | 1wmb title: |
| 10386 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 10387 | | info...] |
| 10388 | | |
| 10389 | | Chain information for 1wmb #1 |
| 10390 | | --- |
| 10391 | | Chain | Description |
| 10392 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 10393 | | |
| 10394 | | Non-standard residues in 1wmb #1 |
| 10395 | | --- |
| 10396 | | CAC — cacodylate ion (dimethylarsinate) |
| 10397 | | MG — magnesium ion |
| 10398 | | |
| 10399 | | 1wmb mmCIF Assemblies |
| 10400 | | --- |
| 10401 | | 1| author_and_software_defined_assembly |
| 10402 | | |
| 10403 | | |
| 10404 | | > open 3I3O |
| 10405 | | |
| 10406 | | 3i3o title: |
| 10407 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 10408 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 10409 | | info...] |
| 10410 | | |
| 10411 | | Chain information for 3i3o #2 |
| 10412 | | --- |
| 10413 | | Chain | Description |
| 10414 | | A B C D E F G H | Short chain dehydrogenase |
| 10415 | | |
| 10416 | | Non-standard residues in 3i3o #2 |
| 10417 | | --- |
| 10418 | | CAC — cacodylate ion (dimethylarsinate) |
| 10419 | | CL — chloride ion |
| 10420 | | MG — magnesium ion |
| 10421 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 10422 | | |
| 10423 | | 3i3o mmCIF Assemblies |
| 10424 | | --- |
| 10425 | | 1| author_and_software_defined_assembly |
| 10426 | | 2| author_and_software_defined_assembly |
| 10427 | | |
| 10428 | | |
| 10429 | | > delete ~/a |
| 10430 | | |
| 10431 | | > delete solvent |
| 10432 | | |
| 10433 | | > mmaker #2 to #1 |
| 10434 | | |
| 10435 | | Parameters |
| 10436 | | --- |
| 10437 | | Chain pairing | bb |
| 10438 | | Alignment algorithm | Needleman-Wunsch |
| 10439 | | Similarity matrix | BLOSUM-62 |
| 10440 | | SS fraction | 0.3 |
| 10441 | | Gap open (HH/SS/other) | 18/18/6 |
| 10442 | | Gap extend | 1 |
| 10443 | | SS matrix | | | H | S | O |
| 10444 | | ---|---|---|--- |
| 10445 | | H | 6 | -9 | -6 |
| 10446 | | S | | 6 | -6 |
| 10447 | | O | | | 4 |
| 10448 | | Iteration cutoff | 2 |
| 10449 | | |
| 10450 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 10451 | | score = 499.7 |
| 10452 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 10453 | | 3.736) |
| 10454 | | |
| 10455 | | |
| 10456 | | > color #1 green |
| 10457 | | |
| 10458 | | > color #2 tan |
| 10459 | | |
| 10460 | | > color ~C byatom |
| 10461 | | |
| 10462 | | > ~display |
| 10463 | | |
| 10464 | | > display #1:138 #2:176 |
| 10465 | | |
| 10466 | | > style stick |
| 10467 | | |
| 10468 | | Changed 4099 atom styles |
| 10469 | | |
| 10470 | | > ribbon |
| 10471 | | |
| 10472 | | > transparency 60 target r |
| 10473 | | |
| 10474 | | > view |
| 10475 | | |
| 10476 | | > size #1:138 #2:176 stickRadius 0.3 |
| 10477 | | |
| 10478 | | Changed 14 bond radii |
| 10479 | | |
| 10480 | | > save fig1.jpg |
| 10481 | | |
| 10482 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 10483 | | |
| 10484 | | > sel-ca |
| 10485 | | |
| 10486 | | 13 atoms, 1 model selected |
| 10487 | | 26 atoms, 2 models selected |
| 10488 | | |
| 10489 | | > display sel-residues |
| 10490 | | |
| 10491 | | > color ~C byatom |
| 10492 | | |
| 10493 | | > style stick |
| 10494 | | |
| 10495 | | Changed 4099 atom styles |
| 10496 | | |
| 10497 | | > view #1:138 :< 5 pad -1 |
| 10498 | | |
| 10499 | | > hbonds #1:138 & #1 name hb1 color green |
| 10500 | | |
| 10501 | | 3 hydrogen bonds found |
| 10502 | | |
| 10503 | | > hbonds #2:176 & #2 name hb2 color tan |
| 10504 | | |
| 10505 | | 4 hydrogen bonds found |
| 10506 | | |
| 10507 | | > transparency 90 target r |
| 10508 | | |
| 10509 | | > label #1:138 #2:176 offset 1,-1,1 |
| 10510 | | |
| 10511 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 10512 | | |
| 10513 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 10514 | | |
| 10515 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 10516 | | > bgColor white offset 0,0,0 |
| 10517 | | |
| 10518 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 10519 | | > bgColor white offset 0,0.7,0 |
| 10520 | | |
| 10521 | | > label #1:138@CA atoms attribute residue.number |
| 10522 | | |
| 10523 | | > ~select |
| 10524 | | |
| 10525 | | Nothing selected |
| 10526 | | |
| 10527 | | > save fig2.jpg |
| 10528 | | |
| 10529 | | > sel-ca |
| 10530 | | |
| 10531 | | 13 atoms, 1 model selected |
| 10532 | | 26 atoms, 2 models selected |
| 10533 | | |
| 10534 | | > ~ribbon |
| 10535 | | |
| 10536 | | > size stickRadius 0.05 |
| 10537 | | |
| 10538 | | Changed 4167 bond radii |
| 10539 | | |
| 10540 | | > size #1:138 stickRadius 0.2 |
| 10541 | | |
| 10542 | | Changed 7 bond radii |
| 10543 | | |
| 10544 | | > size #2:176 stickRadius 0.2 |
| 10545 | | |
| 10546 | | Changed 7 bond radii |
| 10547 | | |
| 10548 | | > view sel-residues pad -1 |
| 10549 | | |
| 10550 | | > ~select |
| 10551 | | |
| 10552 | | Nothing selected |
| 10553 | | |
| 10554 | | > save fig3.jpg |
| 10555 | | |
| 10556 | | > sel-ca |
| 10557 | | |
| 10558 | | 13 atoms, 1 model selected |
| 10559 | | 26 atoms, 2 models selected |
| 10560 | | |
| 10561 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 10562 | | |
| 10563 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 10564 | | |
| 10565 | | > view sel-residues pad -1 |
| 10566 | | |
| 10567 | | > sel-ca |
| 10568 | | |
| 10569 | | 13 atoms, 1 model selected |
| 10570 | | 26 atoms, 2 models selected |
| 10571 | | |
| 10572 | | > align #2 & sel toAtoms #1 & sel |
| 10573 | | |
| 10574 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 10575 | | |
| 10576 | | > ~select |
| 10577 | | |
| 10578 | | Nothing selected |
| 10579 | | |
| 10580 | | > save fig4.jpg |
| 10581 | | |
| 10582 | | > sel-ca |
| 10583 | | |
| 10584 | | 13 atoms, 1 model selected |
| 10585 | | 26 atoms, 2 models selected |
| 10586 | | |
| 10587 | | > ribbon sel |
| 10588 | | |
| 10589 | | > ~select |
| 10590 | | |
| 10591 | | Nothing selected |
| 10592 | | |
| 10593 | | > save fig5.jpg |
| 10594 | | |
| 10595 | | executed script.view.cxc |
| 10596 | | |
| 10597 | | > open "/Users/admin/Dropbox (Technion |
| 10598 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 10599 | | |
| 10600 | | > close |
| 10601 | | |
| 10602 | | > graphics bgColor white |
| 10603 | | |
| 10604 | | > open 1WMB |
| 10605 | | |
| 10606 | | 1wmb title: |
| 10607 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 10608 | | info...] |
| 10609 | | |
| 10610 | | Chain information for 1wmb #1 |
| 10611 | | --- |
| 10612 | | Chain | Description |
| 10613 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 10614 | | |
| 10615 | | Non-standard residues in 1wmb #1 |
| 10616 | | --- |
| 10617 | | CAC — cacodylate ion (dimethylarsinate) |
| 10618 | | MG — magnesium ion |
| 10619 | | |
| 10620 | | 1wmb mmCIF Assemblies |
| 10621 | | --- |
| 10622 | | 1| author_and_software_defined_assembly |
| 10623 | | |
| 10624 | | |
| 10625 | | > open 3I3O |
| 10626 | | |
| 10627 | | 3i3o title: |
| 10628 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 10629 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 10630 | | info...] |
| 10631 | | |
| 10632 | | Chain information for 3i3o #2 |
| 10633 | | --- |
| 10634 | | Chain | Description |
| 10635 | | A B C D E F G H | Short chain dehydrogenase |
| 10636 | | |
| 10637 | | Non-standard residues in 3i3o #2 |
| 10638 | | --- |
| 10639 | | CAC — cacodylate ion (dimethylarsinate) |
| 10640 | | CL — chloride ion |
| 10641 | | MG — magnesium ion |
| 10642 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 10643 | | |
| 10644 | | 3i3o mmCIF Assemblies |
| 10645 | | --- |
| 10646 | | 1| author_and_software_defined_assembly |
| 10647 | | 2| author_and_software_defined_assembly |
| 10648 | | |
| 10649 | | |
| 10650 | | > delete ~/a |
| 10651 | | |
| 10652 | | > delete solvent |
| 10653 | | |
| 10654 | | > mmaker #2 to #1 |
| 10655 | | |
| 10656 | | Parameters |
| 10657 | | --- |
| 10658 | | Chain pairing | bb |
| 10659 | | Alignment algorithm | Needleman-Wunsch |
| 10660 | | Similarity matrix | BLOSUM-62 |
| 10661 | | SS fraction | 0.3 |
| 10662 | | Gap open (HH/SS/other) | 18/18/6 |
| 10663 | | Gap extend | 1 |
| 10664 | | SS matrix | | | H | S | O |
| 10665 | | ---|---|---|--- |
| 10666 | | H | 6 | -9 | -6 |
| 10667 | | S | | 6 | -6 |
| 10668 | | O | | | 4 |
| 10669 | | Iteration cutoff | 2 |
| 10670 | | |
| 10671 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 10672 | | score = 499.7 |
| 10673 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 10674 | | 3.736) |
| 10675 | | |
| 10676 | | |
| 10677 | | > color #1 green |
| 10678 | | |
| 10679 | | > color #2 tan |
| 10680 | | |
| 10681 | | > color ~C byatom |
| 10682 | | |
| 10683 | | > ~display |
| 10684 | | |
| 10685 | | > display #1:138 #2:176 |
| 10686 | | |
| 10687 | | > style stick |
| 10688 | | |
| 10689 | | Changed 4099 atom styles |
| 10690 | | |
| 10691 | | > ribbon |
| 10692 | | |
| 10693 | | > transparency 60 target r |
| 10694 | | |
| 10695 | | > view |
| 10696 | | |
| 10697 | | > size #1:138 #2:176 stickRadius 0.3 |
| 10698 | | |
| 10699 | | Changed 14 bond radii |
| 10700 | | |
| 10701 | | > save fig1.jpg |
| 10702 | | |
| 10703 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 10704 | | |
| 10705 | | > sel-ca |
| 10706 | | |
| 10707 | | 13 atoms, 1 model selected |
| 10708 | | 26 atoms, 2 models selected |
| 10709 | | |
| 10710 | | > display sel-residues |
| 10711 | | |
| 10712 | | > color ~C byatom |
| 10713 | | |
| 10714 | | > style stick |
| 10715 | | |
| 10716 | | Changed 4099 atom styles |
| 10717 | | |
| 10718 | | > view #1:138 :< 5 pad -1 |
| 10719 | | |
| 10720 | | > hbonds #1:138 & #1 name hb1 color green |
| 10721 | | |
| 10722 | | 3 hydrogen bonds found |
| 10723 | | |
| 10724 | | > hbonds #2:176 & #2 name hb2 color tan |
| 10725 | | |
| 10726 | | 4 hydrogen bonds found |
| 10727 | | |
| 10728 | | > transparency 90 target r |
| 10729 | | |
| 10730 | | > label #1:138 #2:176 offset 1,-1,1 |
| 10731 | | |
| 10732 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 10733 | | |
| 10734 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 10735 | | |
| 10736 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 10737 | | > bgColor white offset 0,0,0 |
| 10738 | | |
| 10739 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 10740 | | > bgColor white offset 0,0.7,0 |
| 10741 | | |
| 10742 | | > label #1:138@CA atoms attribute residue.number offset 3,3,3 |
| 10743 | | |
| 10744 | | > ~select |
| 10745 | | |
| 10746 | | Nothing selected |
| 10747 | | |
| 10748 | | > save fig2.jpg |
| 10749 | | |
| 10750 | | > sel-ca |
| 10751 | | |
| 10752 | | 13 atoms, 1 model selected |
| 10753 | | 26 atoms, 2 models selected |
| 10754 | | |
| 10755 | | > ~ribbon |
| 10756 | | |
| 10757 | | > size stickRadius 0.05 |
| 10758 | | |
| 10759 | | Changed 4167 bond radii |
| 10760 | | |
| 10761 | | > size #1:138 stickRadius 0.2 |
| 10762 | | |
| 10763 | | Changed 7 bond radii |
| 10764 | | |
| 10765 | | > size #2:176 stickRadius 0.2 |
| 10766 | | |
| 10767 | | Changed 7 bond radii |
| 10768 | | |
| 10769 | | > view sel-residues pad -1 |
| 10770 | | |
| 10771 | | > ~select |
| 10772 | | |
| 10773 | | Nothing selected |
| 10774 | | |
| 10775 | | > save fig3.jpg |
| 10776 | | |
| 10777 | | > sel-ca |
| 10778 | | |
| 10779 | | 13 atoms, 1 model selected |
| 10780 | | 26 atoms, 2 models selected |
| 10781 | | |
| 10782 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 10783 | | |
| 10784 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 10785 | | |
| 10786 | | > view sel-residues pad -1 |
| 10787 | | |
| 10788 | | > sel-ca |
| 10789 | | |
| 10790 | | 13 atoms, 1 model selected |
| 10791 | | 26 atoms, 2 models selected |
| 10792 | | |
| 10793 | | > align #2 & sel toAtoms #1 & sel |
| 10794 | | |
| 10795 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 10796 | | |
| 10797 | | > ~select |
| 10798 | | |
| 10799 | | Nothing selected |
| 10800 | | |
| 10801 | | > save fig4.jpg |
| 10802 | | |
| 10803 | | > sel-ca |
| 10804 | | |
| 10805 | | 13 atoms, 1 model selected |
| 10806 | | 26 atoms, 2 models selected |
| 10807 | | |
| 10808 | | > ribbon sel |
| 10809 | | |
| 10810 | | > ~select |
| 10811 | | |
| 10812 | | Nothing selected |
| 10813 | | |
| 10814 | | > save fig5.jpg |
| 10815 | | |
| 10816 | | executed script.view.cxc |
| 10817 | | |
| 10818 | | > open "/Users/admin/Dropbox (Technion |
| 10819 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 10820 | | |
| 10821 | | > close |
| 10822 | | |
| 10823 | | > graphics bgColor white |
| 10824 | | |
| 10825 | | > open 1WMB |
| 10826 | | |
| 10827 | | 1wmb title: |
| 10828 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 10829 | | info...] |
| 10830 | | |
| 10831 | | Chain information for 1wmb #1 |
| 10832 | | --- |
| 10833 | | Chain | Description |
| 10834 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 10835 | | |
| 10836 | | Non-standard residues in 1wmb #1 |
| 10837 | | --- |
| 10838 | | CAC — cacodylate ion (dimethylarsinate) |
| 10839 | | MG — magnesium ion |
| 10840 | | |
| 10841 | | 1wmb mmCIF Assemblies |
| 10842 | | --- |
| 10843 | | 1| author_and_software_defined_assembly |
| 10844 | | |
| 10845 | | |
| 10846 | | > open 3I3O |
| 10847 | | |
| 10848 | | 3i3o title: |
| 10849 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 10850 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 10851 | | info...] |
| 10852 | | |
| 10853 | | Chain information for 3i3o #2 |
| 10854 | | --- |
| 10855 | | Chain | Description |
| 10856 | | A B C D E F G H | Short chain dehydrogenase |
| 10857 | | |
| 10858 | | Non-standard residues in 3i3o #2 |
| 10859 | | --- |
| 10860 | | CAC — cacodylate ion (dimethylarsinate) |
| 10861 | | CL — chloride ion |
| 10862 | | MG — magnesium ion |
| 10863 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 10864 | | |
| 10865 | | 3i3o mmCIF Assemblies |
| 10866 | | --- |
| 10867 | | 1| author_and_software_defined_assembly |
| 10868 | | 2| author_and_software_defined_assembly |
| 10869 | | |
| 10870 | | |
| 10871 | | > delete ~/a |
| 10872 | | |
| 10873 | | > delete solvent |
| 10874 | | |
| 10875 | | > mmaker #2 to #1 |
| 10876 | | |
| 10877 | | Parameters |
| 10878 | | --- |
| 10879 | | Chain pairing | bb |
| 10880 | | Alignment algorithm | Needleman-Wunsch |
| 10881 | | Similarity matrix | BLOSUM-62 |
| 10882 | | SS fraction | 0.3 |
| 10883 | | Gap open (HH/SS/other) | 18/18/6 |
| 10884 | | Gap extend | 1 |
| 10885 | | SS matrix | | | H | S | O |
| 10886 | | ---|---|---|--- |
| 10887 | | H | 6 | -9 | -6 |
| 10888 | | S | | 6 | -6 |
| 10889 | | O | | | 4 |
| 10890 | | Iteration cutoff | 2 |
| 10891 | | |
| 10892 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 10893 | | score = 499.7 |
| 10894 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 10895 | | 3.736) |
| 10896 | | |
| 10897 | | |
| 10898 | | > color #1 green |
| 10899 | | |
| 10900 | | > color #2 tan |
| 10901 | | |
| 10902 | | > color ~C byatom |
| 10903 | | |
| 10904 | | > ~display |
| 10905 | | |
| 10906 | | > display #1:138 #2:176 |
| 10907 | | |
| 10908 | | > style stick |
| 10909 | | |
| 10910 | | Changed 4099 atom styles |
| 10911 | | |
| 10912 | | > ribbon |
| 10913 | | |
| 10914 | | > transparency 60 target r |
| 10915 | | |
| 10916 | | > view |
| 10917 | | |
| 10918 | | > size #1:138 #2:176 stickRadius 0.3 |
| 10919 | | |
| 10920 | | Changed 14 bond radii |
| 10921 | | |
| 10922 | | > save fig1.jpg |
| 10923 | | |
| 10924 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 10925 | | |
| 10926 | | > sel-ca |
| 10927 | | |
| 10928 | | 13 atoms, 1 model selected |
| 10929 | | 26 atoms, 2 models selected |
| 10930 | | |
| 10931 | | > display sel-residues |
| 10932 | | |
| 10933 | | > color ~C byatom |
| 10934 | | |
| 10935 | | > style stick |
| 10936 | | |
| 10937 | | Changed 4099 atom styles |
| 10938 | | |
| 10939 | | > view #1:138 :< 5 pad -1 |
| 10940 | | |
| 10941 | | > hbonds #1:138 & #1 name hb1 color green |
| 10942 | | |
| 10943 | | 3 hydrogen bonds found |
| 10944 | | |
| 10945 | | > hbonds #2:176 & #2 name hb2 color tan |
| 10946 | | |
| 10947 | | 4 hydrogen bonds found |
| 10948 | | |
| 10949 | | > transparency 90 target r |
| 10950 | | |
| 10951 | | > label #1:138 #2:176 offset 1,-1,1 |
| 10952 | | |
| 10953 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 10954 | | |
| 10955 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 10956 | | |
| 10957 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 10958 | | > bgColor white offset 0,0,0 |
| 10959 | | |
| 10960 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 10961 | | > bgColor white offset 0,0.7,0 |
| 10962 | | |
| 10963 | | > label #1:138@CA atoms attribute residue.number offset 0,0,0 |
| 10964 | | |
| 10965 | | > ~select |
| 10966 | | |
| 10967 | | Nothing selected |
| 10968 | | |
| 10969 | | > save fig2.jpg |
| 10970 | | |
| 10971 | | > sel-ca |
| 10972 | | |
| 10973 | | 13 atoms, 1 model selected |
| 10974 | | 26 atoms, 2 models selected |
| 10975 | | |
| 10976 | | > ~ribbon |
| 10977 | | |
| 10978 | | > size stickRadius 0.05 |
| 10979 | | |
| 10980 | | Changed 4167 bond radii |
| 10981 | | |
| 10982 | | > size #1:138 stickRadius 0.2 |
| 10983 | | |
| 10984 | | Changed 7 bond radii |
| 10985 | | |
| 10986 | | > size #2:176 stickRadius 0.2 |
| 10987 | | |
| 10988 | | Changed 7 bond radii |
| 10989 | | |
| 10990 | | > view sel-residues pad -1 |
| 10991 | | |
| 10992 | | > ~select |
| 10993 | | |
| 10994 | | Nothing selected |
| 10995 | | |
| 10996 | | > save fig3.jpg |
| 10997 | | |
| 10998 | | > sel-ca |
| 10999 | | |
| 11000 | | 13 atoms, 1 model selected |
| 11001 | | 26 atoms, 2 models selected |
| 11002 | | |
| 11003 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 11004 | | |
| 11005 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 11006 | | |
| 11007 | | > view sel-residues pad -1 |
| 11008 | | |
| 11009 | | > sel-ca |
| 11010 | | |
| 11011 | | 13 atoms, 1 model selected |
| 11012 | | 26 atoms, 2 models selected |
| 11013 | | |
| 11014 | | > align #2 & sel toAtoms #1 & sel |
| 11015 | | |
| 11016 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 11017 | | |
| 11018 | | > ~select |
| 11019 | | |
| 11020 | | Nothing selected |
| 11021 | | |
| 11022 | | > save fig4.jpg |
| 11023 | | |
| 11024 | | > sel-ca |
| 11025 | | |
| 11026 | | 13 atoms, 1 model selected |
| 11027 | | 26 atoms, 2 models selected |
| 11028 | | |
| 11029 | | > ribbon sel |
| 11030 | | |
| 11031 | | > ~select |
| 11032 | | |
| 11033 | | Nothing selected |
| 11034 | | |
| 11035 | | > save fig5.jpg |
| 11036 | | |
| 11037 | | executed script.view.cxc |
| 11038 | | |
| 11039 | | > open "/Users/admin/Dropbox (Technion |
| 11040 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 11041 | | |
| 11042 | | > close |
| 11043 | | |
| 11044 | | > graphics bgColor white |
| 11045 | | |
| 11046 | | > open 1WMB |
| 11047 | | |
| 11048 | | 1wmb title: |
| 11049 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 11050 | | info...] |
| 11051 | | |
| 11052 | | Chain information for 1wmb #1 |
| 11053 | | --- |
| 11054 | | Chain | Description |
| 11055 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 11056 | | |
| 11057 | | Non-standard residues in 1wmb #1 |
| 11058 | | --- |
| 11059 | | CAC — cacodylate ion (dimethylarsinate) |
| 11060 | | MG — magnesium ion |
| 11061 | | |
| 11062 | | 1wmb mmCIF Assemblies |
| 11063 | | --- |
| 11064 | | 1| author_and_software_defined_assembly |
| 11065 | | |
| 11066 | | |
| 11067 | | > open 3I3O |
| 11068 | | |
| 11069 | | 3i3o title: |
| 11070 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 11071 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 11072 | | info...] |
| 11073 | | |
| 11074 | | Chain information for 3i3o #2 |
| 11075 | | --- |
| 11076 | | Chain | Description |
| 11077 | | A B C D E F G H | Short chain dehydrogenase |
| 11078 | | |
| 11079 | | Non-standard residues in 3i3o #2 |
| 11080 | | --- |
| 11081 | | CAC — cacodylate ion (dimethylarsinate) |
| 11082 | | CL — chloride ion |
| 11083 | | MG — magnesium ion |
| 11084 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 11085 | | |
| 11086 | | 3i3o mmCIF Assemblies |
| 11087 | | --- |
| 11088 | | 1| author_and_software_defined_assembly |
| 11089 | | 2| author_and_software_defined_assembly |
| 11090 | | |
| 11091 | | |
| 11092 | | > delete ~/a |
| 11093 | | |
| 11094 | | > delete solvent |
| 11095 | | |
| 11096 | | > mmaker #2 to #1 |
| 11097 | | |
| 11098 | | Parameters |
| 11099 | | --- |
| 11100 | | Chain pairing | bb |
| 11101 | | Alignment algorithm | Needleman-Wunsch |
| 11102 | | Similarity matrix | BLOSUM-62 |
| 11103 | | SS fraction | 0.3 |
| 11104 | | Gap open (HH/SS/other) | 18/18/6 |
| 11105 | | Gap extend | 1 |
| 11106 | | SS matrix | | | H | S | O |
| 11107 | | ---|---|---|--- |
| 11108 | | H | 6 | -9 | -6 |
| 11109 | | S | | 6 | -6 |
| 11110 | | O | | | 4 |
| 11111 | | Iteration cutoff | 2 |
| 11112 | | |
| 11113 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 11114 | | score = 499.7 |
| 11115 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 11116 | | 3.736) |
| 11117 | | |
| 11118 | | |
| 11119 | | > color #1 green |
| 11120 | | |
| 11121 | | > color #2 tan |
| 11122 | | |
| 11123 | | > color ~C byatom |
| 11124 | | |
| 11125 | | > ~display |
| 11126 | | |
| 11127 | | > display #1:138 #2:176 |
| 11128 | | |
| 11129 | | > style stick |
| 11130 | | |
| 11131 | | Changed 4099 atom styles |
| 11132 | | |
| 11133 | | > ribbon |
| 11134 | | |
| 11135 | | > transparency 60 target r |
| 11136 | | |
| 11137 | | > view |
| 11138 | | |
| 11139 | | > size #1:138 #2:176 stickRadius 0.3 |
| 11140 | | |
| 11141 | | Changed 14 bond radii |
| 11142 | | |
| 11143 | | > save fig1.jpg |
| 11144 | | |
| 11145 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 11146 | | |
| 11147 | | > sel-ca |
| 11148 | | |
| 11149 | | 13 atoms, 1 model selected |
| 11150 | | 26 atoms, 2 models selected |
| 11151 | | |
| 11152 | | > display sel-residues |
| 11153 | | |
| 11154 | | > color ~C byatom |
| 11155 | | |
| 11156 | | > style stick |
| 11157 | | |
| 11158 | | Changed 4099 atom styles |
| 11159 | | |
| 11160 | | > view #1:138 :< 5 pad -1 |
| 11161 | | |
| 11162 | | > hbonds #1:138 & #1 name hb1 color green |
| 11163 | | |
| 11164 | | 3 hydrogen bonds found |
| 11165 | | |
| 11166 | | > hbonds #2:176 & #2 name hb2 color tan |
| 11167 | | |
| 11168 | | 4 hydrogen bonds found |
| 11169 | | |
| 11170 | | > transparency 90 target r |
| 11171 | | |
| 11172 | | > label #1:138 #2:176 offset 1,-1,1 |
| 11173 | | |
| 11174 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 11175 | | |
| 11176 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 11177 | | |
| 11178 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 11179 | | > bgColor white offset 0,0,0 |
| 11180 | | |
| 11181 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 11182 | | > bgColor white offset 0,0.7,0 |
| 11183 | | |
| 11184 | | > label #1:138@CA atoms attribute residue.number offset 0,1,0 color green |
| 11185 | | > bgColor black |
| 11186 | | |
| 11187 | | > ~select |
| 11188 | | |
| 11189 | | Nothing selected |
| 11190 | | |
| 11191 | | > save fig2.jpg |
| 11192 | | |
| 11193 | | > sel-ca |
| 11194 | | |
| 11195 | | 13 atoms, 1 model selected |
| 11196 | | 26 atoms, 2 models selected |
| 11197 | | |
| 11198 | | > ~ribbon |
| 11199 | | |
| 11200 | | > size stickRadius 0.05 |
| 11201 | | |
| 11202 | | Changed 4167 bond radii |
| 11203 | | |
| 11204 | | > size #1:138 stickRadius 0.2 |
| 11205 | | |
| 11206 | | Changed 7 bond radii |
| 11207 | | |
| 11208 | | > size #2:176 stickRadius 0.2 |
| 11209 | | |
| 11210 | | Changed 7 bond radii |
| 11211 | | |
| 11212 | | > view sel-residues pad -1 |
| 11213 | | |
| 11214 | | > ~select |
| 11215 | | |
| 11216 | | Nothing selected |
| 11217 | | |
| 11218 | | > save fig3.jpg |
| 11219 | | |
| 11220 | | > sel-ca |
| 11221 | | |
| 11222 | | 13 atoms, 1 model selected |
| 11223 | | 26 atoms, 2 models selected |
| 11224 | | |
| 11225 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 11226 | | |
| 11227 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 11228 | | |
| 11229 | | > view sel-residues pad -1 |
| 11230 | | |
| 11231 | | > sel-ca |
| 11232 | | |
| 11233 | | 13 atoms, 1 model selected |
| 11234 | | 26 atoms, 2 models selected |
| 11235 | | |
| 11236 | | > align #2 & sel toAtoms #1 & sel |
| 11237 | | |
| 11238 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 11239 | | |
| 11240 | | > ~select |
| 11241 | | |
| 11242 | | Nothing selected |
| 11243 | | |
| 11244 | | > save fig4.jpg |
| 11245 | | |
| 11246 | | > sel-ca |
| 11247 | | |
| 11248 | | 13 atoms, 1 model selected |
| 11249 | | 26 atoms, 2 models selected |
| 11250 | | |
| 11251 | | > ribbon sel |
| 11252 | | |
| 11253 | | > ~select |
| 11254 | | |
| 11255 | | Nothing selected |
| 11256 | | |
| 11257 | | > save fig5.jpg |
| 11258 | | |
| 11259 | | executed script.view.cxc |
| 11260 | | |
| 11261 | | > open "/Users/admin/Dropbox (Technion |
| 11262 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 11263 | | |
| 11264 | | > close |
| 11265 | | |
| 11266 | | > graphics bgColor white |
| 11267 | | |
| 11268 | | > open 1WMB |
| 11269 | | |
| 11270 | | 1wmb title: |
| 11271 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 11272 | | info...] |
| 11273 | | |
| 11274 | | Chain information for 1wmb #1 |
| 11275 | | --- |
| 11276 | | Chain | Description |
| 11277 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 11278 | | |
| 11279 | | Non-standard residues in 1wmb #1 |
| 11280 | | --- |
| 11281 | | CAC — cacodylate ion (dimethylarsinate) |
| 11282 | | MG — magnesium ion |
| 11283 | | |
| 11284 | | 1wmb mmCIF Assemblies |
| 11285 | | --- |
| 11286 | | 1| author_and_software_defined_assembly |
| 11287 | | |
| 11288 | | |
| 11289 | | > open 3I3O |
| 11290 | | |
| 11291 | | 3i3o title: |
| 11292 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 11293 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 11294 | | info...] |
| 11295 | | |
| 11296 | | Chain information for 3i3o #2 |
| 11297 | | --- |
| 11298 | | Chain | Description |
| 11299 | | A B C D E F G H | Short chain dehydrogenase |
| 11300 | | |
| 11301 | | Non-standard residues in 3i3o #2 |
| 11302 | | --- |
| 11303 | | CAC — cacodylate ion (dimethylarsinate) |
| 11304 | | CL — chloride ion |
| 11305 | | MG — magnesium ion |
| 11306 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 11307 | | |
| 11308 | | 3i3o mmCIF Assemblies |
| 11309 | | --- |
| 11310 | | 1| author_and_software_defined_assembly |
| 11311 | | 2| author_and_software_defined_assembly |
| 11312 | | |
| 11313 | | |
| 11314 | | > delete ~/a |
| 11315 | | |
| 11316 | | > delete solvent |
| 11317 | | |
| 11318 | | > mmaker #2 to #1 |
| 11319 | | |
| 11320 | | Parameters |
| 11321 | | --- |
| 11322 | | Chain pairing | bb |
| 11323 | | Alignment algorithm | Needleman-Wunsch |
| 11324 | | Similarity matrix | BLOSUM-62 |
| 11325 | | SS fraction | 0.3 |
| 11326 | | Gap open (HH/SS/other) | 18/18/6 |
| 11327 | | Gap extend | 1 |
| 11328 | | SS matrix | | | H | S | O |
| 11329 | | ---|---|---|--- |
| 11330 | | H | 6 | -9 | -6 |
| 11331 | | S | | 6 | -6 |
| 11332 | | O | | | 4 |
| 11333 | | Iteration cutoff | 2 |
| 11334 | | |
| 11335 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 11336 | | score = 499.7 |
| 11337 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 11338 | | 3.736) |
| 11339 | | |
| 11340 | | |
| 11341 | | > color #1 green |
| 11342 | | |
| 11343 | | > color #2 tan |
| 11344 | | |
| 11345 | | > color ~C byatom |
| 11346 | | |
| 11347 | | > ~display |
| 11348 | | |
| 11349 | | > display #1:138 #2:176 |
| 11350 | | |
| 11351 | | > style stick |
| 11352 | | |
| 11353 | | Changed 4099 atom styles |
| 11354 | | |
| 11355 | | > ribbon |
| 11356 | | |
| 11357 | | > transparency 60 target r |
| 11358 | | |
| 11359 | | > view |
| 11360 | | |
| 11361 | | > size #1:138 #2:176 stickRadius 0.3 |
| 11362 | | |
| 11363 | | Changed 14 bond radii |
| 11364 | | |
| 11365 | | > save fig1.jpg |
| 11366 | | |
| 11367 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 11368 | | |
| 11369 | | > sel-ca |
| 11370 | | |
| 11371 | | 13 atoms, 1 model selected |
| 11372 | | 26 atoms, 2 models selected |
| 11373 | | |
| 11374 | | > display sel-residues |
| 11375 | | |
| 11376 | | > color ~C byatom |
| 11377 | | |
| 11378 | | > style stick |
| 11379 | | |
| 11380 | | Changed 4099 atom styles |
| 11381 | | |
| 11382 | | > view #1:138 :< 5 pad -1 |
| 11383 | | |
| 11384 | | > hbonds #1:138 & #1 name hb1 color green |
| 11385 | | |
| 11386 | | 3 hydrogen bonds found |
| 11387 | | |
| 11388 | | > hbonds #2:176 & #2 name hb2 color tan |
| 11389 | | |
| 11390 | | 4 hydrogen bonds found |
| 11391 | | |
| 11392 | | > transparency 90 target r |
| 11393 | | |
| 11394 | | > label #1:138 #2:176 offset 1,-1,1 |
| 11395 | | |
| 11396 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 11397 | | |
| 11398 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 11399 | | |
| 11400 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 11401 | | > bgColor white offset 0,0,0 |
| 11402 | | |
| 11403 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 11404 | | > bgColor white offset 0,0.7,0 |
| 11405 | | |
| 11406 | | > label #1:138@CA atoms attribute residue.number residue.name offset 0,1,0 |
| 11407 | | > color green bgColor white |
| 11408 | | |
| 11409 | | Expected a keyword |
| 11410 | | |
| 11411 | | > open "/Users/admin/Dropbox (Technion |
| 11412 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 11413 | | |
| 11414 | | > close |
| 11415 | | |
| 11416 | | > graphics bgColor white |
| 11417 | | |
| 11418 | | > open 1WMB |
| 11419 | | |
| 11420 | | 1wmb title: |
| 11421 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 11422 | | info...] |
| 11423 | | |
| 11424 | | Chain information for 1wmb #1 |
| 11425 | | --- |
| 11426 | | Chain | Description |
| 11427 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 11428 | | |
| 11429 | | Non-standard residues in 1wmb #1 |
| 11430 | | --- |
| 11431 | | CAC — cacodylate ion (dimethylarsinate) |
| 11432 | | MG — magnesium ion |
| 11433 | | |
| 11434 | | 1wmb mmCIF Assemblies |
| 11435 | | --- |
| 11436 | | 1| author_and_software_defined_assembly |
| 11437 | | |
| 11438 | | |
| 11439 | | > open 3I3O |
| 11440 | | |
| 11441 | | 3i3o title: |
| 11442 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 11443 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 11444 | | info...] |
| 11445 | | |
| 11446 | | Chain information for 3i3o #2 |
| 11447 | | --- |
| 11448 | | Chain | Description |
| 11449 | | A B C D E F G H | Short chain dehydrogenase |
| 11450 | | |
| 11451 | | Non-standard residues in 3i3o #2 |
| 11452 | | --- |
| 11453 | | CAC — cacodylate ion (dimethylarsinate) |
| 11454 | | CL — chloride ion |
| 11455 | | MG — magnesium ion |
| 11456 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 11457 | | |
| 11458 | | 3i3o mmCIF Assemblies |
| 11459 | | --- |
| 11460 | | 1| author_and_software_defined_assembly |
| 11461 | | 2| author_and_software_defined_assembly |
| 11462 | | |
| 11463 | | |
| 11464 | | > delete ~/a |
| 11465 | | |
| 11466 | | > delete solvent |
| 11467 | | |
| 11468 | | > mmaker #2 to #1 |
| 11469 | | |
| 11470 | | Parameters |
| 11471 | | --- |
| 11472 | | Chain pairing | bb |
| 11473 | | Alignment algorithm | Needleman-Wunsch |
| 11474 | | Similarity matrix | BLOSUM-62 |
| 11475 | | SS fraction | 0.3 |
| 11476 | | Gap open (HH/SS/other) | 18/18/6 |
| 11477 | | Gap extend | 1 |
| 11478 | | SS matrix | | | H | S | O |
| 11479 | | ---|---|---|--- |
| 11480 | | H | 6 | -9 | -6 |
| 11481 | | S | | 6 | -6 |
| 11482 | | O | | | 4 |
| 11483 | | Iteration cutoff | 2 |
| 11484 | | |
| 11485 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 11486 | | score = 499.7 |
| 11487 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 11488 | | 3.736) |
| 11489 | | |
| 11490 | | |
| 11491 | | > color #1 green |
| 11492 | | |
| 11493 | | > color #2 tan |
| 11494 | | |
| 11495 | | > color ~C byatom |
| 11496 | | |
| 11497 | | > ~display |
| 11498 | | |
| 11499 | | > display #1:138 #2:176 |
| 11500 | | |
| 11501 | | > style stick |
| 11502 | | |
| 11503 | | Changed 4099 atom styles |
| 11504 | | |
| 11505 | | > ribbon |
| 11506 | | |
| 11507 | | > transparency 60 target r |
| 11508 | | |
| 11509 | | > view |
| 11510 | | |
| 11511 | | > size #1:138 #2:176 stickRadius 0.3 |
| 11512 | | |
| 11513 | | Changed 14 bond radii |
| 11514 | | |
| 11515 | | > save fig1.jpg |
| 11516 | | |
| 11517 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 11518 | | |
| 11519 | | > sel-ca |
| 11520 | | |
| 11521 | | 13 atoms, 1 model selected |
| 11522 | | 26 atoms, 2 models selected |
| 11523 | | |
| 11524 | | > display sel-residues |
| 11525 | | |
| 11526 | | > color ~C byatom |
| 11527 | | |
| 11528 | | > style stick |
| 11529 | | |
| 11530 | | Changed 4099 atom styles |
| 11531 | | |
| 11532 | | > view #1:138 :< 5 pad -1 |
| 11533 | | |
| 11534 | | > hbonds #1:138 & #1 name hb1 color green |
| 11535 | | |
| 11536 | | 3 hydrogen bonds found |
| 11537 | | |
| 11538 | | > hbonds #2:176 & #2 name hb2 color tan |
| 11539 | | |
| 11540 | | 4 hydrogen bonds found |
| 11541 | | |
| 11542 | | > transparency 90 target r |
| 11543 | | |
| 11544 | | > label #1:138 #2:176 offset 1,-1,1 |
| 11545 | | |
| 11546 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 11547 | | |
| 11548 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 11549 | | |
| 11550 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 11551 | | > bgColor white offset 0,0,0 |
| 11552 | | |
| 11553 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 11554 | | > bgColor white offset 0,0.7,0 |
| 11555 | | |
| 11556 | | > label #1:138@CA atoms attribute residue.number attribute residue.name offset |
| 11557 | | > 0,1,0 color green bgColor white |
| 11558 | | |
| 11559 | | Repeated keyword argument "attribute" |
| 11560 | | |
| 11561 | | > open "/Users/admin/Dropbox (Technion |
| 11562 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 11563 | | |
| 11564 | | > close |
| 11565 | | |
| 11566 | | > graphics bgColor white |
| 11567 | | |
| 11568 | | > open 1WMB |
| 11569 | | |
| 11570 | | 1wmb title: |
| 11571 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 11572 | | info...] |
| 11573 | | |
| 11574 | | Chain information for 1wmb #1 |
| 11575 | | --- |
| 11576 | | Chain | Description |
| 11577 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 11578 | | |
| 11579 | | Non-standard residues in 1wmb #1 |
| 11580 | | --- |
| 11581 | | CAC — cacodylate ion (dimethylarsinate) |
| 11582 | | MG — magnesium ion |
| 11583 | | |
| 11584 | | 1wmb mmCIF Assemblies |
| 11585 | | --- |
| 11586 | | 1| author_and_software_defined_assembly |
| 11587 | | |
| 11588 | | |
| 11589 | | > open 3I3O |
| 11590 | | |
| 11591 | | 3i3o title: |
| 11592 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 11593 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 11594 | | info...] |
| 11595 | | |
| 11596 | | Chain information for 3i3o #2 |
| 11597 | | --- |
| 11598 | | Chain | Description |
| 11599 | | A B C D E F G H | Short chain dehydrogenase |
| 11600 | | |
| 11601 | | Non-standard residues in 3i3o #2 |
| 11602 | | --- |
| 11603 | | CAC — cacodylate ion (dimethylarsinate) |
| 11604 | | CL — chloride ion |
| 11605 | | MG — magnesium ion |
| 11606 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 11607 | | |
| 11608 | | 3i3o mmCIF Assemblies |
| 11609 | | --- |
| 11610 | | 1| author_and_software_defined_assembly |
| 11611 | | 2| author_and_software_defined_assembly |
| 11612 | | |
| 11613 | | |
| 11614 | | > delete ~/a |
| 11615 | | |
| 11616 | | > delete solvent |
| 11617 | | |
| 11618 | | > mmaker #2 to #1 |
| 11619 | | |
| 11620 | | Parameters |
| 11621 | | --- |
| 11622 | | Chain pairing | bb |
| 11623 | | Alignment algorithm | Needleman-Wunsch |
| 11624 | | Similarity matrix | BLOSUM-62 |
| 11625 | | SS fraction | 0.3 |
| 11626 | | Gap open (HH/SS/other) | 18/18/6 |
| 11627 | | Gap extend | 1 |
| 11628 | | SS matrix | | | H | S | O |
| 11629 | | ---|---|---|--- |
| 11630 | | H | 6 | -9 | -6 |
| 11631 | | S | | 6 | -6 |
| 11632 | | O | | | 4 |
| 11633 | | Iteration cutoff | 2 |
| 11634 | | |
| 11635 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 11636 | | score = 499.7 |
| 11637 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 11638 | | 3.736) |
| 11639 | | |
| 11640 | | |
| 11641 | | > color #1 green |
| 11642 | | |
| 11643 | | > color #2 tan |
| 11644 | | |
| 11645 | | > color ~C byatom |
| 11646 | | |
| 11647 | | > ~display |
| 11648 | | |
| 11649 | | > display #1:138 #2:176 |
| 11650 | | |
| 11651 | | > style stick |
| 11652 | | |
| 11653 | | Changed 4099 atom styles |
| 11654 | | |
| 11655 | | > ribbon |
| 11656 | | |
| 11657 | | > transparency 60 target r |
| 11658 | | |
| 11659 | | > view |
| 11660 | | |
| 11661 | | > size #1:138 #2:176 stickRadius 0.3 |
| 11662 | | |
| 11663 | | Changed 14 bond radii |
| 11664 | | |
| 11665 | | > save fig1.jpg |
| 11666 | | |
| 11667 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 11668 | | |
| 11669 | | > sel-ca |
| 11670 | | |
| 11671 | | 13 atoms, 1 model selected |
| 11672 | | 26 atoms, 2 models selected |
| 11673 | | |
| 11674 | | > display sel-residues |
| 11675 | | |
| 11676 | | > color ~C byatom |
| 11677 | | |
| 11678 | | > style stick |
| 11679 | | |
| 11680 | | Changed 4099 atom styles |
| 11681 | | |
| 11682 | | > view #1:138 :< 5 pad -1 |
| 11683 | | |
| 11684 | | > hbonds #1:138 & #1 name hb1 color green |
| 11685 | | |
| 11686 | | 3 hydrogen bonds found |
| 11687 | | |
| 11688 | | > hbonds #2:176 & #2 name hb2 color tan |
| 11689 | | |
| 11690 | | 4 hydrogen bonds found |
| 11691 | | |
| 11692 | | > transparency 90 target r |
| 11693 | | |
| 11694 | | > label #1:138 #2:176 offset 1,-1,1 |
| 11695 | | |
| 11696 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 11697 | | |
| 11698 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 11699 | | |
| 11700 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 11701 | | > bgColor white offset 0,0,0 |
| 11702 | | |
| 11703 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 11704 | | > bgColor white offset 0,0.7,0 |
| 11705 | | |
| 11706 | | > label #1:138 offset 0,1,0 color green bgColor white |
| 11707 | | |
| 11708 | | > ~select |
| 11709 | | |
| 11710 | | Nothing selected |
| 11711 | | |
| 11712 | | > save fig2.jpg |
| 11713 | | |
| 11714 | | > sel-ca |
| 11715 | | |
| 11716 | | 13 atoms, 1 model selected |
| 11717 | | 26 atoms, 2 models selected |
| 11718 | | |
| 11719 | | > ~ribbon |
| 11720 | | |
| 11721 | | > size stickRadius 0.05 |
| 11722 | | |
| 11723 | | Changed 4167 bond radii |
| 11724 | | |
| 11725 | | > size #1:138 stickRadius 0.2 |
| 11726 | | |
| 11727 | | Changed 7 bond radii |
| 11728 | | |
| 11729 | | > size #2:176 stickRadius 0.2 |
| 11730 | | |
| 11731 | | Changed 7 bond radii |
| 11732 | | |
| 11733 | | > view sel-residues pad -1 |
| 11734 | | |
| 11735 | | > ~select |
| 11736 | | |
| 11737 | | Nothing selected |
| 11738 | | |
| 11739 | | > save fig3.jpg |
| 11740 | | |
| 11741 | | > sel-ca |
| 11742 | | |
| 11743 | | 13 atoms, 1 model selected |
| 11744 | | 26 atoms, 2 models selected |
| 11745 | | |
| 11746 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 11747 | | |
| 11748 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 11749 | | |
| 11750 | | > view sel-residues pad -1 |
| 11751 | | |
| 11752 | | > sel-ca |
| 11753 | | |
| 11754 | | 13 atoms, 1 model selected |
| 11755 | | 26 atoms, 2 models selected |
| 11756 | | |
| 11757 | | > align #2 & sel toAtoms #1 & sel |
| 11758 | | |
| 11759 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 11760 | | |
| 11761 | | > ~select |
| 11762 | | |
| 11763 | | Nothing selected |
| 11764 | | |
| 11765 | | > save fig4.jpg |
| 11766 | | |
| 11767 | | > sel-ca |
| 11768 | | |
| 11769 | | 13 atoms, 1 model selected |
| 11770 | | 26 atoms, 2 models selected |
| 11771 | | |
| 11772 | | > ribbon sel |
| 11773 | | |
| 11774 | | > ~select |
| 11775 | | |
| 11776 | | Nothing selected |
| 11777 | | |
| 11778 | | > save fig5.jpg |
| 11779 | | |
| 11780 | | executed script.view.cxc |
| 11781 | | |
| 11782 | | > open "/Users/admin/Dropbox (Technion |
| 11783 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 11784 | | |
| 11785 | | > close |
| 11786 | | |
| 11787 | | > graphics bgColor white |
| 11788 | | |
| 11789 | | > open 1WMB |
| 11790 | | |
| 11791 | | 1wmb title: |
| 11792 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 11793 | | info...] |
| 11794 | | |
| 11795 | | Chain information for 1wmb #1 |
| 11796 | | --- |
| 11797 | | Chain | Description |
| 11798 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 11799 | | |
| 11800 | | Non-standard residues in 1wmb #1 |
| 11801 | | --- |
| 11802 | | CAC — cacodylate ion (dimethylarsinate) |
| 11803 | | MG — magnesium ion |
| 11804 | | |
| 11805 | | 1wmb mmCIF Assemblies |
| 11806 | | --- |
| 11807 | | 1| author_and_software_defined_assembly |
| 11808 | | |
| 11809 | | |
| 11810 | | > open 3I3O |
| 11811 | | |
| 11812 | | 3i3o title: |
| 11813 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 11814 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 11815 | | info...] |
| 11816 | | |
| 11817 | | Chain information for 3i3o #2 |
| 11818 | | --- |
| 11819 | | Chain | Description |
| 11820 | | A B C D E F G H | Short chain dehydrogenase |
| 11821 | | |
| 11822 | | Non-standard residues in 3i3o #2 |
| 11823 | | --- |
| 11824 | | CAC — cacodylate ion (dimethylarsinate) |
| 11825 | | CL — chloride ion |
| 11826 | | MG — magnesium ion |
| 11827 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 11828 | | |
| 11829 | | 3i3o mmCIF Assemblies |
| 11830 | | --- |
| 11831 | | 1| author_and_software_defined_assembly |
| 11832 | | 2| author_and_software_defined_assembly |
| 11833 | | |
| 11834 | | |
| 11835 | | > delete ~/a |
| 11836 | | |
| 11837 | | > delete solvent |
| 11838 | | |
| 11839 | | > mmaker #2 to #1 |
| 11840 | | |
| 11841 | | Parameters |
| 11842 | | --- |
| 11843 | | Chain pairing | bb |
| 11844 | | Alignment algorithm | Needleman-Wunsch |
| 11845 | | Similarity matrix | BLOSUM-62 |
| 11846 | | SS fraction | 0.3 |
| 11847 | | Gap open (HH/SS/other) | 18/18/6 |
| 11848 | | Gap extend | 1 |
| 11849 | | SS matrix | | | H | S | O |
| 11850 | | ---|---|---|--- |
| 11851 | | H | 6 | -9 | -6 |
| 11852 | | S | | 6 | -6 |
| 11853 | | O | | | 4 |
| 11854 | | Iteration cutoff | 2 |
| 11855 | | |
| 11856 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 11857 | | score = 499.7 |
| 11858 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 11859 | | 3.736) |
| 11860 | | |
| 11861 | | |
| 11862 | | > color #1 green |
| 11863 | | |
| 11864 | | > color #2 tan |
| 11865 | | |
| 11866 | | > color ~C byatom |
| 11867 | | |
| 11868 | | > ~display |
| 11869 | | |
| 11870 | | > display #1:138 #2:176 |
| 11871 | | |
| 11872 | | > style stick |
| 11873 | | |
| 11874 | | Changed 4099 atom styles |
| 11875 | | |
| 11876 | | > ribbon |
| 11877 | | |
| 11878 | | > transparency 60 target r |
| 11879 | | |
| 11880 | | > view |
| 11881 | | |
| 11882 | | > size #1:138 #2:176 stickRadius 0.3 |
| 11883 | | |
| 11884 | | Changed 14 bond radii |
| 11885 | | |
| 11886 | | > save fig1.jpg |
| 11887 | | |
| 11888 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 11889 | | |
| 11890 | | > sel-ca |
| 11891 | | |
| 11892 | | 13 atoms, 1 model selected |
| 11893 | | 26 atoms, 2 models selected |
| 11894 | | |
| 11895 | | > display sel-residues |
| 11896 | | |
| 11897 | | > color ~C byatom |
| 11898 | | |
| 11899 | | > style stick |
| 11900 | | |
| 11901 | | Changed 4099 atom styles |
| 11902 | | |
| 11903 | | > view #1:138 :< 5 pad -1 |
| 11904 | | |
| 11905 | | > hbonds #1:138 & #1 name hb1 color green |
| 11906 | | |
| 11907 | | 3 hydrogen bonds found |
| 11908 | | |
| 11909 | | > hbonds #2:176 & #2 name hb2 color tan |
| 11910 | | |
| 11911 | | 4 hydrogen bonds found |
| 11912 | | |
| 11913 | | > transparency 90 target r |
| 11914 | | |
| 11915 | | > label #1:138 #2:176 offset 1,-1,1 |
| 11916 | | |
| 11917 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 11918 | | |
| 11919 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 11920 | | |
| 11921 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f},{residue.name} height 0.5 |
| 11922 | | > color green bgColor white offset 0,0,0 |
| 11923 | | |
| 11924 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 11925 | | > bgColor white offset 0,0.7,0 |
| 11926 | | |
| 11927 | | > label #1:138 offset 0,1,0 color green bgColor white |
| 11928 | | |
| 11929 | | > ~select |
| 11930 | | |
| 11931 | | Nothing selected |
| 11932 | | |
| 11933 | | > save fig2.jpg |
| 11934 | | |
| 11935 | | > sel-ca |
| 11936 | | |
| 11937 | | 13 atoms, 1 model selected |
| 11938 | | 26 atoms, 2 models selected |
| 11939 | | |
| 11940 | | > ~ribbon |
| 11941 | | |
| 11942 | | > size stickRadius 0.05 |
| 11943 | | |
| 11944 | | Changed 4167 bond radii |
| 11945 | | |
| 11946 | | > size #1:138 stickRadius 0.2 |
| 11947 | | |
| 11948 | | Changed 7 bond radii |
| 11949 | | |
| 11950 | | > size #2:176 stickRadius 0.2 |
| 11951 | | |
| 11952 | | Changed 7 bond radii |
| 11953 | | |
| 11954 | | > view sel-residues pad -1 |
| 11955 | | |
| 11956 | | > ~select |
| 11957 | | |
| 11958 | | Nothing selected |
| 11959 | | |
| 11960 | | > save fig3.jpg |
| 11961 | | |
| 11962 | | > sel-ca |
| 11963 | | |
| 11964 | | 13 atoms, 1 model selected |
| 11965 | | 26 atoms, 2 models selected |
| 11966 | | |
| 11967 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 11968 | | |
| 11969 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 11970 | | |
| 11971 | | > view sel-residues pad -1 |
| 11972 | | |
| 11973 | | > sel-ca |
| 11974 | | |
| 11975 | | 13 atoms, 1 model selected |
| 11976 | | 26 atoms, 2 models selected |
| 11977 | | |
| 11978 | | > align #2 & sel toAtoms #1 & sel |
| 11979 | | |
| 11980 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 11981 | | |
| 11982 | | > ~select |
| 11983 | | |
| 11984 | | Nothing selected |
| 11985 | | |
| 11986 | | > save fig4.jpg |
| 11987 | | |
| 11988 | | > sel-ca |
| 11989 | | |
| 11990 | | 13 atoms, 1 model selected |
| 11991 | | 26 atoms, 2 models selected |
| 11992 | | |
| 11993 | | > ribbon sel |
| 11994 | | |
| 11995 | | > ~select |
| 11996 | | |
| 11997 | | Nothing selected |
| 11998 | | |
| 11999 | | > save fig5.jpg |
| 12000 | | |
| 12001 | | executed script.view.cxc |
| 12002 | | |
| 12003 | | > open "/Users/admin/Dropbox (Technion |
| 12004 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 12005 | | |
| 12006 | | > close |
| 12007 | | |
| 12008 | | > graphics bgColor white |
| 12009 | | |
| 12010 | | > open 1WMB |
| 12011 | | |
| 12012 | | 1wmb title: |
| 12013 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 12014 | | info...] |
| 12015 | | |
| 12016 | | Chain information for 1wmb #1 |
| 12017 | | --- |
| 12018 | | Chain | Description |
| 12019 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 12020 | | |
| 12021 | | Non-standard residues in 1wmb #1 |
| 12022 | | --- |
| 12023 | | CAC — cacodylate ion (dimethylarsinate) |
| 12024 | | MG — magnesium ion |
| 12025 | | |
| 12026 | | 1wmb mmCIF Assemblies |
| 12027 | | --- |
| 12028 | | 1| author_and_software_defined_assembly |
| 12029 | | |
| 12030 | | |
| 12031 | | > open 3I3O |
| 12032 | | |
| 12033 | | 3i3o title: |
| 12034 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 12035 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 12036 | | info...] |
| 12037 | | |
| 12038 | | Chain information for 3i3o #2 |
| 12039 | | --- |
| 12040 | | Chain | Description |
| 12041 | | A B C D E F G H | Short chain dehydrogenase |
| 12042 | | |
| 12043 | | Non-standard residues in 3i3o #2 |
| 12044 | | --- |
| 12045 | | CAC — cacodylate ion (dimethylarsinate) |
| 12046 | | CL — chloride ion |
| 12047 | | MG — magnesium ion |
| 12048 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 12049 | | |
| 12050 | | 3i3o mmCIF Assemblies |
| 12051 | | --- |
| 12052 | | 1| author_and_software_defined_assembly |
| 12053 | | 2| author_and_software_defined_assembly |
| 12054 | | |
| 12055 | | |
| 12056 | | > delete ~/a |
| 12057 | | |
| 12058 | | > delete solvent |
| 12059 | | |
| 12060 | | > mmaker #2 to #1 |
| 12061 | | |
| 12062 | | Parameters |
| 12063 | | --- |
| 12064 | | Chain pairing | bb |
| 12065 | | Alignment algorithm | Needleman-Wunsch |
| 12066 | | Similarity matrix | BLOSUM-62 |
| 12067 | | SS fraction | 0.3 |
| 12068 | | Gap open (HH/SS/other) | 18/18/6 |
| 12069 | | Gap extend | 1 |
| 12070 | | SS matrix | | | H | S | O |
| 12071 | | ---|---|---|--- |
| 12072 | | H | 6 | -9 | -6 |
| 12073 | | S | | 6 | -6 |
| 12074 | | O | | | 4 |
| 12075 | | Iteration cutoff | 2 |
| 12076 | | |
| 12077 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 12078 | | score = 499.7 |
| 12079 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 12080 | | 3.736) |
| 12081 | | |
| 12082 | | |
| 12083 | | > color #1 green |
| 12084 | | |
| 12085 | | > color #2 tan |
| 12086 | | |
| 12087 | | > color ~C byatom |
| 12088 | | |
| 12089 | | > ~display |
| 12090 | | |
| 12091 | | > display #1:138 #2:176 |
| 12092 | | |
| 12093 | | > style stick |
| 12094 | | |
| 12095 | | Changed 4099 atom styles |
| 12096 | | |
| 12097 | | > ribbon |
| 12098 | | |
| 12099 | | > transparency 60 target r |
| 12100 | | |
| 12101 | | > view |
| 12102 | | |
| 12103 | | > size #1:138 #2:176 stickRadius 0.3 |
| 12104 | | |
| 12105 | | Changed 14 bond radii |
| 12106 | | |
| 12107 | | > save fig1.jpg |
| 12108 | | |
| 12109 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 12110 | | |
| 12111 | | > sel-ca |
| 12112 | | |
| 12113 | | 13 atoms, 1 model selected |
| 12114 | | 26 atoms, 2 models selected |
| 12115 | | |
| 12116 | | > display sel-residues |
| 12117 | | |
| 12118 | | > color ~C byatom |
| 12119 | | |
| 12120 | | > style stick |
| 12121 | | |
| 12122 | | Changed 4099 atom styles |
| 12123 | | |
| 12124 | | > view #1:138 :< 5 pad -1 |
| 12125 | | |
| 12126 | | > hbonds #1:138 & #1 name hb1 color green |
| 12127 | | |
| 12128 | | 3 hydrogen bonds found |
| 12129 | | |
| 12130 | | > hbonds #2:176 & #2 name hb2 color tan |
| 12131 | | |
| 12132 | | 4 hydrogen bonds found |
| 12133 | | |
| 12134 | | > transparency 90 target r |
| 12135 | | |
| 12136 | | > label #1:138 #2:176 offset 1,-1,1 |
| 12137 | | |
| 12138 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 12139 | | |
| 12140 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 12141 | | |
| 12142 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f},{0.residue.name} height |
| 12143 | | > 0.5 color green bgColor white offset 0,0,0 |
| 12144 | | |
| 12145 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 12146 | | > bgColor white offset 0,0.7,0 |
| 12147 | | |
| 12148 | | > label #1:138 offset 0,1,0 color green bgColor white |
| 12149 | | |
| 12150 | | > ~select |
| 12151 | | |
| 12152 | | Nothing selected |
| 12153 | | |
| 12154 | | > save fig2.jpg |
| 12155 | | |
| 12156 | | > sel-ca |
| 12157 | | |
| 12158 | | 13 atoms, 1 model selected |
| 12159 | | 26 atoms, 2 models selected |
| 12160 | | |
| 12161 | | > ~ribbon |
| 12162 | | |
| 12163 | | > size stickRadius 0.05 |
| 12164 | | |
| 12165 | | Changed 4167 bond radii |
| 12166 | | |
| 12167 | | > size #1:138 stickRadius 0.2 |
| 12168 | | |
| 12169 | | Changed 7 bond radii |
| 12170 | | |
| 12171 | | > size #2:176 stickRadius 0.2 |
| 12172 | | |
| 12173 | | Changed 7 bond radii |
| 12174 | | |
| 12175 | | > view sel-residues pad -1 |
| 12176 | | |
| 12177 | | > ~select |
| 12178 | | |
| 12179 | | Nothing selected |
| 12180 | | |
| 12181 | | > save fig3.jpg |
| 12182 | | |
| 12183 | | > sel-ca |
| 12184 | | |
| 12185 | | 13 atoms, 1 model selected |
| 12186 | | 26 atoms, 2 models selected |
| 12187 | | |
| 12188 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 12189 | | |
| 12190 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 12191 | | |
| 12192 | | > view sel-residues pad -1 |
| 12193 | | |
| 12194 | | > sel-ca |
| 12195 | | |
| 12196 | | 13 atoms, 1 model selected |
| 12197 | | 26 atoms, 2 models selected |
| 12198 | | |
| 12199 | | > align #2 & sel toAtoms #1 & sel |
| 12200 | | |
| 12201 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 12202 | | |
| 12203 | | > ~select |
| 12204 | | |
| 12205 | | Nothing selected |
| 12206 | | |
| 12207 | | > save fig4.jpg |
| 12208 | | |
| 12209 | | > sel-ca |
| 12210 | | |
| 12211 | | 13 atoms, 1 model selected |
| 12212 | | 26 atoms, 2 models selected |
| 12213 | | |
| 12214 | | > ribbon sel |
| 12215 | | |
| 12216 | | > ~select |
| 12217 | | |
| 12218 | | Nothing selected |
| 12219 | | |
| 12220 | | > save fig5.jpg |
| 12221 | | |
| 12222 | | executed script.view.cxc |
| 12223 | | |
| 12224 | | > open "/Users/admin/Dropbox (Technion |
| 12225 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 12226 | | |
| 12227 | | > close |
| 12228 | | |
| 12229 | | > graphics bgColor white |
| 12230 | | |
| 12231 | | > open 1WMB |
| 12232 | | |
| 12233 | | 1wmb title: |
| 12234 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 12235 | | info...] |
| 12236 | | |
| 12237 | | Chain information for 1wmb #1 |
| 12238 | | --- |
| 12239 | | Chain | Description |
| 12240 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 12241 | | |
| 12242 | | Non-standard residues in 1wmb #1 |
| 12243 | | --- |
| 12244 | | CAC — cacodylate ion (dimethylarsinate) |
| 12245 | | MG — magnesium ion |
| 12246 | | |
| 12247 | | 1wmb mmCIF Assemblies |
| 12248 | | --- |
| 12249 | | 1| author_and_software_defined_assembly |
| 12250 | | |
| 12251 | | |
| 12252 | | > open 3I3O |
| 12253 | | |
| 12254 | | 3i3o title: |
| 12255 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 12256 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 12257 | | info...] |
| 12258 | | |
| 12259 | | Chain information for 3i3o #2 |
| 12260 | | --- |
| 12261 | | Chain | Description |
| 12262 | | A B C D E F G H | Short chain dehydrogenase |
| 12263 | | |
| 12264 | | Non-standard residues in 3i3o #2 |
| 12265 | | --- |
| 12266 | | CAC — cacodylate ion (dimethylarsinate) |
| 12267 | | CL — chloride ion |
| 12268 | | MG — magnesium ion |
| 12269 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 12270 | | |
| 12271 | | 3i3o mmCIF Assemblies |
| 12272 | | --- |
| 12273 | | 1| author_and_software_defined_assembly |
| 12274 | | 2| author_and_software_defined_assembly |
| 12275 | | |
| 12276 | | |
| 12277 | | > delete ~/a |
| 12278 | | |
| 12279 | | > delete solvent |
| 12280 | | |
| 12281 | | > mmaker #2 to #1 |
| 12282 | | |
| 12283 | | Parameters |
| 12284 | | --- |
| 12285 | | Chain pairing | bb |
| 12286 | | Alignment algorithm | Needleman-Wunsch |
| 12287 | | Similarity matrix | BLOSUM-62 |
| 12288 | | SS fraction | 0.3 |
| 12289 | | Gap open (HH/SS/other) | 18/18/6 |
| 12290 | | Gap extend | 1 |
| 12291 | | SS matrix | | | H | S | O |
| 12292 | | ---|---|---|--- |
| 12293 | | H | 6 | -9 | -6 |
| 12294 | | S | | 6 | -6 |
| 12295 | | O | | | 4 |
| 12296 | | Iteration cutoff | 2 |
| 12297 | | |
| 12298 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 12299 | | score = 499.7 |
| 12300 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 12301 | | 3.736) |
| 12302 | | |
| 12303 | | |
| 12304 | | > color #1 green |
| 12305 | | |
| 12306 | | > color #2 tan |
| 12307 | | |
| 12308 | | > color ~C byatom |
| 12309 | | |
| 12310 | | > ~display |
| 12311 | | |
| 12312 | | > display #1:138 #2:176 |
| 12313 | | |
| 12314 | | > style stick |
| 12315 | | |
| 12316 | | Changed 4099 atom styles |
| 12317 | | |
| 12318 | | > ribbon |
| 12319 | | |
| 12320 | | > transparency 60 target r |
| 12321 | | |
| 12322 | | > view |
| 12323 | | |
| 12324 | | > size #1:138 #2:176 stickRadius 0.3 |
| 12325 | | |
| 12326 | | Changed 14 bond radii |
| 12327 | | |
| 12328 | | > save fig1.jpg |
| 12329 | | |
| 12330 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 12331 | | |
| 12332 | | > sel-ca |
| 12333 | | |
| 12334 | | 13 atoms, 1 model selected |
| 12335 | | 26 atoms, 2 models selected |
| 12336 | | |
| 12337 | | > display sel-residues |
| 12338 | | |
| 12339 | | > color ~C byatom |
| 12340 | | |
| 12341 | | > style stick |
| 12342 | | |
| 12343 | | Changed 4099 atom styles |
| 12344 | | |
| 12345 | | > view #1:138 :< 5 pad -1 |
| 12346 | | |
| 12347 | | > hbonds #1:138 & #1 name hb1 color green |
| 12348 | | |
| 12349 | | 3 hydrogen bonds found |
| 12350 | | |
| 12351 | | > hbonds #2:176 & #2 name hb2 color tan |
| 12352 | | |
| 12353 | | 4 hydrogen bonds found |
| 12354 | | |
| 12355 | | > transparency 90 target r |
| 12356 | | |
| 12357 | | > label #1:138 #2:176 offset 1,-1,1 |
| 12358 | | |
| 12359 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 12360 | | |
| 12361 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 12362 | | |
| 12363 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f},{0.residue.name} height |
| 12364 | | > 0.5 color green bgColor white offset 0,0,0 |
| 12365 | | |
| 12366 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 12367 | | > bgColor white offset 0,0.7,0 |
| 12368 | | |
| 12369 | | > ~select |
| 12370 | | |
| 12371 | | Nothing selected |
| 12372 | | |
| 12373 | | > save fig2.jpg |
| 12374 | | |
| 12375 | | > sel-ca |
| 12376 | | |
| 12377 | | 13 atoms, 1 model selected |
| 12378 | | 26 atoms, 2 models selected |
| 12379 | | |
| 12380 | | > ~ribbon |
| 12381 | | |
| 12382 | | > size stickRadius 0.05 |
| 12383 | | |
| 12384 | | Changed 4167 bond radii |
| 12385 | | |
| 12386 | | > size #1:138 stickRadius 0.2 |
| 12387 | | |
| 12388 | | Changed 7 bond radii |
| 12389 | | |
| 12390 | | > size #2:176 stickRadius 0.2 |
| 12391 | | |
| 12392 | | Changed 7 bond radii |
| 12393 | | |
| 12394 | | > view sel-residues pad -1 |
| 12395 | | |
| 12396 | | > ~select |
| 12397 | | |
| 12398 | | Nothing selected |
| 12399 | | |
| 12400 | | > save fig3.jpg |
| 12401 | | |
| 12402 | | > sel-ca |
| 12403 | | |
| 12404 | | 13 atoms, 1 model selected |
| 12405 | | 26 atoms, 2 models selected |
| 12406 | | |
| 12407 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 12408 | | |
| 12409 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 12410 | | |
| 12411 | | > view sel-residues pad -1 |
| 12412 | | |
| 12413 | | > sel-ca |
| 12414 | | |
| 12415 | | 13 atoms, 1 model selected |
| 12416 | | 26 atoms, 2 models selected |
| 12417 | | |
| 12418 | | > align #2 & sel toAtoms #1 & sel |
| 12419 | | |
| 12420 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 12421 | | |
| 12422 | | > ~select |
| 12423 | | |
| 12424 | | Nothing selected |
| 12425 | | |
| 12426 | | > save fig4.jpg |
| 12427 | | |
| 12428 | | > sel-ca |
| 12429 | | |
| 12430 | | 13 atoms, 1 model selected |
| 12431 | | 26 atoms, 2 models selected |
| 12432 | | |
| 12433 | | > ribbon sel |
| 12434 | | |
| 12435 | | > ~select |
| 12436 | | |
| 12437 | | Nothing selected |
| 12438 | | |
| 12439 | | > save fig5.jpg |
| 12440 | | |
| 12441 | | executed script.view.cxc |
| 12442 | | |
| 12443 | | > open "/Users/admin/Dropbox (Technion |
| 12444 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 12445 | | |
| 12446 | | > close |
| 12447 | | |
| 12448 | | > graphics bgColor white |
| 12449 | | |
| 12450 | | > open 1WMB |
| 12451 | | |
| 12452 | | 1wmb title: |
| 12453 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 12454 | | info...] |
| 12455 | | |
| 12456 | | Chain information for 1wmb #1 |
| 12457 | | --- |
| 12458 | | Chain | Description |
| 12459 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 12460 | | |
| 12461 | | Non-standard residues in 1wmb #1 |
| 12462 | | --- |
| 12463 | | CAC — cacodylate ion (dimethylarsinate) |
| 12464 | | MG — magnesium ion |
| 12465 | | |
| 12466 | | 1wmb mmCIF Assemblies |
| 12467 | | --- |
| 12468 | | 1| author_and_software_defined_assembly |
| 12469 | | |
| 12470 | | |
| 12471 | | > open 3I3O |
| 12472 | | |
| 12473 | | 3i3o title: |
| 12474 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 12475 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 12476 | | info...] |
| 12477 | | |
| 12478 | | Chain information for 3i3o #2 |
| 12479 | | --- |
| 12480 | | Chain | Description |
| 12481 | | A B C D E F G H | Short chain dehydrogenase |
| 12482 | | |
| 12483 | | Non-standard residues in 3i3o #2 |
| 12484 | | --- |
| 12485 | | CAC — cacodylate ion (dimethylarsinate) |
| 12486 | | CL — chloride ion |
| 12487 | | MG — magnesium ion |
| 12488 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 12489 | | |
| 12490 | | 3i3o mmCIF Assemblies |
| 12491 | | --- |
| 12492 | | 1| author_and_software_defined_assembly |
| 12493 | | 2| author_and_software_defined_assembly |
| 12494 | | |
| 12495 | | |
| 12496 | | > delete ~/a |
| 12497 | | |
| 12498 | | > delete solvent |
| 12499 | | |
| 12500 | | > mmaker #2 to #1 |
| 12501 | | |
| 12502 | | Parameters |
| 12503 | | --- |
| 12504 | | Chain pairing | bb |
| 12505 | | Alignment algorithm | Needleman-Wunsch |
| 12506 | | Similarity matrix | BLOSUM-62 |
| 12507 | | SS fraction | 0.3 |
| 12508 | | Gap open (HH/SS/other) | 18/18/6 |
| 12509 | | Gap extend | 1 |
| 12510 | | SS matrix | | | H | S | O |
| 12511 | | ---|---|---|--- |
| 12512 | | H | 6 | -9 | -6 |
| 12513 | | S | | 6 | -6 |
| 12514 | | O | | | 4 |
| 12515 | | Iteration cutoff | 2 |
| 12516 | | |
| 12517 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 12518 | | score = 499.7 |
| 12519 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 12520 | | 3.736) |
| 12521 | | |
| 12522 | | |
| 12523 | | > color #1 green |
| 12524 | | |
| 12525 | | > color #2 tan |
| 12526 | | |
| 12527 | | > color ~C byatom |
| 12528 | | |
| 12529 | | > ~display |
| 12530 | | |
| 12531 | | > display #1:138 #2:176 |
| 12532 | | |
| 12533 | | > style stick |
| 12534 | | |
| 12535 | | Changed 4099 atom styles |
| 12536 | | |
| 12537 | | > ribbon |
| 12538 | | |
| 12539 | | > transparency 60 target r |
| 12540 | | |
| 12541 | | > view |
| 12542 | | |
| 12543 | | > size #1:138 #2:176 stickRadius 0.3 |
| 12544 | | |
| 12545 | | Changed 14 bond radii |
| 12546 | | |
| 12547 | | > save fig1.jpg |
| 12548 | | |
| 12549 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 12550 | | |
| 12551 | | > sel-ca |
| 12552 | | |
| 12553 | | 13 atoms, 1 model selected |
| 12554 | | 26 atoms, 2 models selected |
| 12555 | | |
| 12556 | | > display sel-residues |
| 12557 | | |
| 12558 | | > color ~C byatom |
| 12559 | | |
| 12560 | | > style stick |
| 12561 | | |
| 12562 | | Changed 4099 atom styles |
| 12563 | | |
| 12564 | | > view #1:138 :< 5 pad -1 |
| 12565 | | |
| 12566 | | > hbonds #1:138 & #1 name hb1 color green |
| 12567 | | |
| 12568 | | 3 hydrogen bonds found |
| 12569 | | |
| 12570 | | > hbonds #2:176 & #2 name hb2 color tan |
| 12571 | | |
| 12572 | | 4 hydrogen bonds found |
| 12573 | | |
| 12574 | | > transparency 90 target r |
| 12575 | | |
| 12576 | | > label #1:138 #2:176 offset 1,-1,1 |
| 12577 | | |
| 12578 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 12579 | | |
| 12580 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 12581 | | |
| 12582 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f},{0.residue.number} height |
| 12583 | | > 0.5 color green bgColor white offset 0,0,0 |
| 12584 | | |
| 12585 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 12586 | | > bgColor white offset 0,0.7,0 |
| 12587 | | |
| 12588 | | > ~select |
| 12589 | | |
| 12590 | | Nothing selected |
| 12591 | | |
| 12592 | | > save fig2.jpg |
| 12593 | | |
| 12594 | | > sel-ca |
| 12595 | | |
| 12596 | | 13 atoms, 1 model selected |
| 12597 | | 26 atoms, 2 models selected |
| 12598 | | |
| 12599 | | > ~ribbon |
| 12600 | | |
| 12601 | | > size stickRadius 0.05 |
| 12602 | | |
| 12603 | | Changed 4167 bond radii |
| 12604 | | |
| 12605 | | > size #1:138 stickRadius 0.2 |
| 12606 | | |
| 12607 | | Changed 7 bond radii |
| 12608 | | |
| 12609 | | > size #2:176 stickRadius 0.2 |
| 12610 | | |
| 12611 | | Changed 7 bond radii |
| 12612 | | |
| 12613 | | > view sel-residues pad -1 |
| 12614 | | |
| 12615 | | > ~select |
| 12616 | | |
| 12617 | | Nothing selected |
| 12618 | | |
| 12619 | | > save fig3.jpg |
| 12620 | | |
| 12621 | | > sel-ca |
| 12622 | | |
| 12623 | | 13 atoms, 1 model selected |
| 12624 | | 26 atoms, 2 models selected |
| 12625 | | |
| 12626 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 12627 | | |
| 12628 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 12629 | | |
| 12630 | | > view sel-residues pad -1 |
| 12631 | | |
| 12632 | | > sel-ca |
| 12633 | | |
| 12634 | | 13 atoms, 1 model selected |
| 12635 | | 26 atoms, 2 models selected |
| 12636 | | |
| 12637 | | > align #2 & sel toAtoms #1 & sel |
| 12638 | | |
| 12639 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 12640 | | |
| 12641 | | > ~select |
| 12642 | | |
| 12643 | | Nothing selected |
| 12644 | | |
| 12645 | | > save fig4.jpg |
| 12646 | | |
| 12647 | | > sel-ca |
| 12648 | | |
| 12649 | | 13 atoms, 1 model selected |
| 12650 | | 26 atoms, 2 models selected |
| 12651 | | |
| 12652 | | > ribbon sel |
| 12653 | | |
| 12654 | | > ~select |
| 12655 | | |
| 12656 | | Nothing selected |
| 12657 | | |
| 12658 | | > save fig5.jpg |
| 12659 | | |
| 12660 | | executed script.view.cxc |
| 12661 | | |
| 12662 | | > open "/Users/admin/Dropbox (Technion |
| 12663 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 12664 | | |
| 12665 | | > close |
| 12666 | | |
| 12667 | | > graphics bgColor white |
| 12668 | | |
| 12669 | | > open 1WMB |
| 12670 | | |
| 12671 | | 1wmb title: |
| 12672 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 12673 | | info...] |
| 12674 | | |
| 12675 | | Chain information for 1wmb #1 |
| 12676 | | --- |
| 12677 | | Chain | Description |
| 12678 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 12679 | | |
| 12680 | | Non-standard residues in 1wmb #1 |
| 12681 | | --- |
| 12682 | | CAC — cacodylate ion (dimethylarsinate) |
| 12683 | | MG — magnesium ion |
| 12684 | | |
| 12685 | | 1wmb mmCIF Assemblies |
| 12686 | | --- |
| 12687 | | 1| author_and_software_defined_assembly |
| 12688 | | |
| 12689 | | |
| 12690 | | > open 3I3O |
| 12691 | | |
| 12692 | | 3i3o title: |
| 12693 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 12694 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 12695 | | info...] |
| 12696 | | |
| 12697 | | Chain information for 3i3o #2 |
| 12698 | | --- |
| 12699 | | Chain | Description |
| 12700 | | A B C D E F G H | Short chain dehydrogenase |
| 12701 | | |
| 12702 | | Non-standard residues in 3i3o #2 |
| 12703 | | --- |
| 12704 | | CAC — cacodylate ion (dimethylarsinate) |
| 12705 | | CL — chloride ion |
| 12706 | | MG — magnesium ion |
| 12707 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 12708 | | |
| 12709 | | 3i3o mmCIF Assemblies |
| 12710 | | --- |
| 12711 | | 1| author_and_software_defined_assembly |
| 12712 | | 2| author_and_software_defined_assembly |
| 12713 | | |
| 12714 | | |
| 12715 | | > delete ~/a |
| 12716 | | |
| 12717 | | > delete solvent |
| 12718 | | |
| 12719 | | > mmaker #2 to #1 |
| 12720 | | |
| 12721 | | Parameters |
| 12722 | | --- |
| 12723 | | Chain pairing | bb |
| 12724 | | Alignment algorithm | Needleman-Wunsch |
| 12725 | | Similarity matrix | BLOSUM-62 |
| 12726 | | SS fraction | 0.3 |
| 12727 | | Gap open (HH/SS/other) | 18/18/6 |
| 12728 | | Gap extend | 1 |
| 12729 | | SS matrix | | | H | S | O |
| 12730 | | ---|---|---|--- |
| 12731 | | H | 6 | -9 | -6 |
| 12732 | | S | | 6 | -6 |
| 12733 | | O | | | 4 |
| 12734 | | Iteration cutoff | 2 |
| 12735 | | |
| 12736 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 12737 | | score = 499.7 |
| 12738 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 12739 | | 3.736) |
| 12740 | | |
| 12741 | | |
| 12742 | | > color #1 green |
| 12743 | | |
| 12744 | | > color #2 tan |
| 12745 | | |
| 12746 | | > color ~C byatom |
| 12747 | | |
| 12748 | | > ~display |
| 12749 | | |
| 12750 | | > display #1:138 #2:176 |
| 12751 | | |
| 12752 | | > style stick |
| 12753 | | |
| 12754 | | Changed 4099 atom styles |
| 12755 | | |
| 12756 | | > ribbon |
| 12757 | | |
| 12758 | | > transparency 60 target r |
| 12759 | | |
| 12760 | | > view |
| 12761 | | |
| 12762 | | > size #1:138 #2:176 stickRadius 0.3 |
| 12763 | | |
| 12764 | | Changed 14 bond radii |
| 12765 | | |
| 12766 | | > save fig1.jpg |
| 12767 | | |
| 12768 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 12769 | | |
| 12770 | | > sel-ca |
| 12771 | | |
| 12772 | | 13 atoms, 1 model selected |
| 12773 | | 26 atoms, 2 models selected |
| 12774 | | |
| 12775 | | > display sel-residues |
| 12776 | | |
| 12777 | | > color ~C byatom |
| 12778 | | |
| 12779 | | > style stick |
| 12780 | | |
| 12781 | | Changed 4099 atom styles |
| 12782 | | |
| 12783 | | > view #1:138 :< 5 pad -1 |
| 12784 | | |
| 12785 | | > hbonds #1:138 & #1 name hb1 color green |
| 12786 | | |
| 12787 | | 3 hydrogen bonds found |
| 12788 | | |
| 12789 | | > hbonds #2:176 & #2 name hb2 color tan |
| 12790 | | |
| 12791 | | 4 hydrogen bonds found |
| 12792 | | |
| 12793 | | > transparency 90 target r |
| 12794 | | |
| 12795 | | > label #1:138 #2:176 offset 1,-1,1 |
| 12796 | | |
| 12797 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 12798 | | |
| 12799 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 12800 | | |
| 12801 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f},{0.residue.number} height |
| 12802 | | > 0.5 color green bgColor white offset 0,0,0 |
| 12803 | | |
| 12804 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 12805 | | > bgColor white offset 0,0.7,0 |
| 12806 | | |
| 12807 | | > ~select |
| 12808 | | |
| 12809 | | Nothing selected |
| 12810 | | |
| 12811 | | > save fig2.jpg |
| 12812 | | |
| 12813 | | > sel-ca |
| 12814 | | |
| 12815 | | 13 atoms, 1 model selected |
| 12816 | | 26 atoms, 2 models selected |
| 12817 | | |
| 12818 | | > ~ribbon |
| 12819 | | |
| 12820 | | > size stickRadius 0.05 |
| 12821 | | |
| 12822 | | Changed 4167 bond radii |
| 12823 | | |
| 12824 | | > size #1:138 stickRadius 0.2 |
| 12825 | | |
| 12826 | | Changed 7 bond radii |
| 12827 | | |
| 12828 | | > size #2:176 stickRadius 0.2 |
| 12829 | | |
| 12830 | | Changed 7 bond radii |
| 12831 | | |
| 12832 | | > view sel-residues pad -1 |
| 12833 | | |
| 12834 | | > ~select |
| 12835 | | |
| 12836 | | Nothing selected |
| 12837 | | |
| 12838 | | > save fig3.jpg |
| 12839 | | |
| 12840 | | > sel-ca |
| 12841 | | |
| 12842 | | 13 atoms, 1 model selected |
| 12843 | | 26 atoms, 2 models selected |
| 12844 | | |
| 12845 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 12846 | | |
| 12847 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 12848 | | |
| 12849 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f},{0.residue.number} height |
| 12850 | | > 0.5 color green bgColor white offset 0,0,0 |
| 12851 | | |
| 12852 | | > view sel-residues pad -1 |
| 12853 | | |
| 12854 | | > sel-ca |
| 12855 | | |
| 12856 | | 13 atoms, 1 model selected |
| 12857 | | 26 atoms, 2 models selected |
| 12858 | | |
| 12859 | | > align #2 & sel toAtoms #1 & sel |
| 12860 | | |
| 12861 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 12862 | | |
| 12863 | | > ~select |
| 12864 | | |
| 12865 | | Nothing selected |
| 12866 | | |
| 12867 | | > save fig4.jpg |
| 12868 | | |
| 12869 | | > sel-ca |
| 12870 | | |
| 12871 | | 13 atoms, 1 model selected |
| 12872 | | 26 atoms, 2 models selected |
| 12873 | | |
| 12874 | | > ribbon sel |
| 12875 | | |
| 12876 | | > ~select |
| 12877 | | |
| 12878 | | Nothing selected |
| 12879 | | |
| 12880 | | > save fig5.jpg |
| 12881 | | |
| 12882 | | executed script.view.cxc |
| 12883 | | |
| 12884 | | > open "/Users/admin/Dropbox (Technion |
| 12885 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 12886 | | |
| 12887 | | > close |
| 12888 | | |
| 12889 | | > graphics bgColor white |
| 12890 | | |
| 12891 | | > open 1WMB |
| 12892 | | |
| 12893 | | 1wmb title: |
| 12894 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 12895 | | info...] |
| 12896 | | |
| 12897 | | Chain information for 1wmb #1 |
| 12898 | | --- |
| 12899 | | Chain | Description |
| 12900 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 12901 | | |
| 12902 | | Non-standard residues in 1wmb #1 |
| 12903 | | --- |
| 12904 | | CAC — cacodylate ion (dimethylarsinate) |
| 12905 | | MG — magnesium ion |
| 12906 | | |
| 12907 | | 1wmb mmCIF Assemblies |
| 12908 | | --- |
| 12909 | | 1| author_and_software_defined_assembly |
| 12910 | | |
| 12911 | | |
| 12912 | | > open 3I3O |
| 12913 | | |
| 12914 | | 3i3o title: |
| 12915 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 12916 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 12917 | | info...] |
| 12918 | | |
| 12919 | | Chain information for 3i3o #2 |
| 12920 | | --- |
| 12921 | | Chain | Description |
| 12922 | | A B C D E F G H | Short chain dehydrogenase |
| 12923 | | |
| 12924 | | Non-standard residues in 3i3o #2 |
| 12925 | | --- |
| 12926 | | CAC — cacodylate ion (dimethylarsinate) |
| 12927 | | CL — chloride ion |
| 12928 | | MG — magnesium ion |
| 12929 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 12930 | | |
| 12931 | | 3i3o mmCIF Assemblies |
| 12932 | | --- |
| 12933 | | 1| author_and_software_defined_assembly |
| 12934 | | 2| author_and_software_defined_assembly |
| 12935 | | |
| 12936 | | |
| 12937 | | > delete ~/a |
| 12938 | | |
| 12939 | | > delete solvent |
| 12940 | | |
| 12941 | | > mmaker #2 to #1 |
| 12942 | | |
| 12943 | | Parameters |
| 12944 | | --- |
| 12945 | | Chain pairing | bb |
| 12946 | | Alignment algorithm | Needleman-Wunsch |
| 12947 | | Similarity matrix | BLOSUM-62 |
| 12948 | | SS fraction | 0.3 |
| 12949 | | Gap open (HH/SS/other) | 18/18/6 |
| 12950 | | Gap extend | 1 |
| 12951 | | SS matrix | | | H | S | O |
| 12952 | | ---|---|---|--- |
| 12953 | | H | 6 | -9 | -6 |
| 12954 | | S | | 6 | -6 |
| 12955 | | O | | | 4 |
| 12956 | | Iteration cutoff | 2 |
| 12957 | | |
| 12958 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 12959 | | score = 499.7 |
| 12960 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 12961 | | 3.736) |
| 12962 | | |
| 12963 | | |
| 12964 | | > color #1 green |
| 12965 | | |
| 12966 | | > color #2 tan |
| 12967 | | |
| 12968 | | > color ~C byatom |
| 12969 | | |
| 12970 | | > ~display |
| 12971 | | |
| 12972 | | > display #1:138 #2:176 |
| 12973 | | |
| 12974 | | > style stick |
| 12975 | | |
| 12976 | | Changed 4099 atom styles |
| 12977 | | |
| 12978 | | > ribbon |
| 12979 | | |
| 12980 | | > transparency 60 target r |
| 12981 | | |
| 12982 | | > view |
| 12983 | | |
| 12984 | | > size #1:138 #2:176 stickRadius 0.3 |
| 12985 | | |
| 12986 | | Changed 14 bond radii |
| 12987 | | |
| 12988 | | > save fig1.jpg |
| 12989 | | |
| 12990 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 12991 | | |
| 12992 | | > sel-ca |
| 12993 | | |
| 12994 | | 13 atoms, 1 model selected |
| 12995 | | 26 atoms, 2 models selected |
| 12996 | | |
| 12997 | | > display sel-residues |
| 12998 | | |
| 12999 | | > color ~C byatom |
| 13000 | | |
| 13001 | | > style stick |
| 13002 | | |
| 13003 | | Changed 4099 atom styles |
| 13004 | | |
| 13005 | | > view #1:138 :< 5 pad -1 |
| 13006 | | |
| 13007 | | > hbonds #1:138 & #1 name hb1 color green |
| 13008 | | |
| 13009 | | 3 hydrogen bonds found |
| 13010 | | |
| 13011 | | > hbonds #2:176 & #2 name hb2 color tan |
| 13012 | | |
| 13013 | | 4 hydrogen bonds found |
| 13014 | | |
| 13015 | | > transparency 90 target r |
| 13016 | | |
| 13017 | | > label #1:138 #2:176 offset 1,-1,1 |
| 13018 | | |
| 13019 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 13020 | | |
| 13021 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 13022 | | |
| 13023 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 13024 | | > bgColor white offset 0,0.7,0 |
| 13025 | | |
| 13026 | | > ~select |
| 13027 | | |
| 13028 | | Nothing selected |
| 13029 | | |
| 13030 | | > save fig2.jpg |
| 13031 | | |
| 13032 | | > sel-ca |
| 13033 | | |
| 13034 | | 13 atoms, 1 model selected |
| 13035 | | 26 atoms, 2 models selected |
| 13036 | | |
| 13037 | | > ~ribbon |
| 13038 | | |
| 13039 | | > size stickRadius 0.05 |
| 13040 | | |
| 13041 | | Changed 4167 bond radii |
| 13042 | | |
| 13043 | | > size #1:138 stickRadius 0.2 |
| 13044 | | |
| 13045 | | Changed 7 bond radii |
| 13046 | | |
| 13047 | | > size #2:176 stickRadius 0.2 |
| 13048 | | |
| 13049 | | Changed 7 bond radii |
| 13050 | | |
| 13051 | | > view sel-residues pad -1 |
| 13052 | | |
| 13053 | | > ~select |
| 13054 | | |
| 13055 | | Nothing selected |
| 13056 | | |
| 13057 | | > save fig3.jpg |
| 13058 | | |
| 13059 | | > sel-ca |
| 13060 | | |
| 13061 | | 13 atoms, 1 model selected |
| 13062 | | 26 atoms, 2 models selected |
| 13063 | | |
| 13064 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 13065 | | |
| 13066 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 13067 | | |
| 13068 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f},{0.residue.number} height |
| 13069 | | > 0.5 color green bgColor white offset 0,0,0 |
| 13070 | | |
| 13071 | | > view sel-residues pad -1 |
| 13072 | | |
| 13073 | | > sel-ca |
| 13074 | | |
| 13075 | | 13 atoms, 1 model selected |
| 13076 | | 26 atoms, 2 models selected |
| 13077 | | |
| 13078 | | > align #2 & sel toAtoms #1 & sel |
| 13079 | | |
| 13080 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 13081 | | |
| 13082 | | > ~select |
| 13083 | | |
| 13084 | | Nothing selected |
| 13085 | | |
| 13086 | | > save fig4.jpg |
| 13087 | | |
| 13088 | | > sel-ca |
| 13089 | | |
| 13090 | | 13 atoms, 1 model selected |
| 13091 | | 26 atoms, 2 models selected |
| 13092 | | |
| 13093 | | > ribbon sel |
| 13094 | | |
| 13095 | | > ~select |
| 13096 | | |
| 13097 | | Nothing selected |
| 13098 | | |
| 13099 | | > save fig5.jpg |
| 13100 | | |
| 13101 | | executed script.view.cxc |
| 13102 | | |
| 13103 | | > open "/Users/admin/Dropbox (Technion |
| 13104 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 13105 | | |
| 13106 | | > close |
| 13107 | | |
| 13108 | | > graphics bgColor white |
| 13109 | | |
| 13110 | | > open 1WMB |
| 13111 | | |
| 13112 | | 1wmb title: |
| 13113 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 13114 | | info...] |
| 13115 | | |
| 13116 | | Chain information for 1wmb #1 |
| 13117 | | --- |
| 13118 | | Chain | Description |
| 13119 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 13120 | | |
| 13121 | | Non-standard residues in 1wmb #1 |
| 13122 | | --- |
| 13123 | | CAC — cacodylate ion (dimethylarsinate) |
| 13124 | | MG — magnesium ion |
| 13125 | | |
| 13126 | | 1wmb mmCIF Assemblies |
| 13127 | | --- |
| 13128 | | 1| author_and_software_defined_assembly |
| 13129 | | |
| 13130 | | |
| 13131 | | > open 3I3O |
| 13132 | | |
| 13133 | | 3i3o title: |
| 13134 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 13135 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 13136 | | info...] |
| 13137 | | |
| 13138 | | Chain information for 3i3o #2 |
| 13139 | | --- |
| 13140 | | Chain | Description |
| 13141 | | A B C D E F G H | Short chain dehydrogenase |
| 13142 | | |
| 13143 | | Non-standard residues in 3i3o #2 |
| 13144 | | --- |
| 13145 | | CAC — cacodylate ion (dimethylarsinate) |
| 13146 | | CL — chloride ion |
| 13147 | | MG — magnesium ion |
| 13148 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 13149 | | |
| 13150 | | 3i3o mmCIF Assemblies |
| 13151 | | --- |
| 13152 | | 1| author_and_software_defined_assembly |
| 13153 | | 2| author_and_software_defined_assembly |
| 13154 | | |
| 13155 | | |
| 13156 | | > delete ~/a |
| 13157 | | |
| 13158 | | > delete solvent |
| 13159 | | |
| 13160 | | > mmaker #2 to #1 |
| 13161 | | |
| 13162 | | Parameters |
| 13163 | | --- |
| 13164 | | Chain pairing | bb |
| 13165 | | Alignment algorithm | Needleman-Wunsch |
| 13166 | | Similarity matrix | BLOSUM-62 |
| 13167 | | SS fraction | 0.3 |
| 13168 | | Gap open (HH/SS/other) | 18/18/6 |
| 13169 | | Gap extend | 1 |
| 13170 | | SS matrix | | | H | S | O |
| 13171 | | ---|---|---|--- |
| 13172 | | H | 6 | -9 | -6 |
| 13173 | | S | | 6 | -6 |
| 13174 | | O | | | 4 |
| 13175 | | Iteration cutoff | 2 |
| 13176 | | |
| 13177 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 13178 | | score = 499.7 |
| 13179 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 13180 | | 3.736) |
| 13181 | | |
| 13182 | | |
| 13183 | | > color #1 green |
| 13184 | | |
| 13185 | | > color #2 tan |
| 13186 | | |
| 13187 | | > color ~C byatom |
| 13188 | | |
| 13189 | | > ~display |
| 13190 | | |
| 13191 | | > display #1:138 #2:176 |
| 13192 | | |
| 13193 | | > style stick |
| 13194 | | |
| 13195 | | Changed 4099 atom styles |
| 13196 | | |
| 13197 | | > ribbon |
| 13198 | | |
| 13199 | | > transparency 60 target r |
| 13200 | | |
| 13201 | | > view |
| 13202 | | |
| 13203 | | > size #1:138 #2:176 stickRadius 0.3 |
| 13204 | | |
| 13205 | | Changed 14 bond radii |
| 13206 | | |
| 13207 | | > save fig1.jpg |
| 13208 | | |
| 13209 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 13210 | | |
| 13211 | | > sel-ca |
| 13212 | | |
| 13213 | | 13 atoms, 1 model selected |
| 13214 | | 26 atoms, 2 models selected |
| 13215 | | |
| 13216 | | > display sel-residues |
| 13217 | | |
| 13218 | | > color ~C byatom |
| 13219 | | |
| 13220 | | > style stick |
| 13221 | | |
| 13222 | | Changed 4099 atom styles |
| 13223 | | |
| 13224 | | > view #1:138 :< 5 pad -1 |
| 13225 | | |
| 13226 | | > hbonds #1:138 & #1 name hb1 color green |
| 13227 | | |
| 13228 | | 3 hydrogen bonds found |
| 13229 | | |
| 13230 | | > hbonds #2:176 & #2 name hb2 color tan |
| 13231 | | |
| 13232 | | 4 hydrogen bonds found |
| 13233 | | |
| 13234 | | > transparency 90 target r |
| 13235 | | |
| 13236 | | > label #1:138 #2:176 offset 1,-1,1 |
| 13237 | | |
| 13238 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 13239 | | |
| 13240 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 13241 | | |
| 13242 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 13243 | | > bgColor white offset 0,0.7,0 |
| 13244 | | |
| 13245 | | > ~select |
| 13246 | | |
| 13247 | | Nothing selected |
| 13248 | | |
| 13249 | | > save fig2.jpg |
| 13250 | | |
| 13251 | | > sel-ca |
| 13252 | | |
| 13253 | | 13 atoms, 1 model selected |
| 13254 | | 26 atoms, 2 models selected |
| 13255 | | |
| 13256 | | > ~ribbon |
| 13257 | | |
| 13258 | | > size stickRadius 0.05 |
| 13259 | | |
| 13260 | | Changed 4167 bond radii |
| 13261 | | |
| 13262 | | > size #1:138 stickRadius 0.2 |
| 13263 | | |
| 13264 | | Changed 7 bond radii |
| 13265 | | |
| 13266 | | > size #2:176 stickRadius 0.2 |
| 13267 | | |
| 13268 | | Changed 7 bond radii |
| 13269 | | |
| 13270 | | > view sel-residues pad -1 |
| 13271 | | |
| 13272 | | > ~select |
| 13273 | | |
| 13274 | | Nothing selected |
| 13275 | | |
| 13276 | | > save fig3.jpg |
| 13277 | | |
| 13278 | | > sel-ca |
| 13279 | | |
| 13280 | | 13 atoms, 1 model selected |
| 13281 | | 26 atoms, 2 models selected |
| 13282 | | |
| 13283 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 13284 | | |
| 13285 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 13286 | | |
| 13287 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f},{0.residue.number} height |
| 13288 | | > 0.5 color green bgColor white offset 0,2,0 |
| 13289 | | |
| 13290 | | > view sel-residues pad -1 |
| 13291 | | |
| 13292 | | > sel-ca |
| 13293 | | |
| 13294 | | 13 atoms, 1 model selected |
| 13295 | | 26 atoms, 2 models selected |
| 13296 | | |
| 13297 | | > align #2 & sel toAtoms #1 & sel |
| 13298 | | |
| 13299 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 13300 | | |
| 13301 | | > ~select |
| 13302 | | |
| 13303 | | Nothing selected |
| 13304 | | |
| 13305 | | > save fig4.jpg |
| 13306 | | |
| 13307 | | > sel-ca |
| 13308 | | |
| 13309 | | 13 atoms, 1 model selected |
| 13310 | | 26 atoms, 2 models selected |
| 13311 | | |
| 13312 | | > ribbon sel |
| 13313 | | |
| 13314 | | > ~select |
| 13315 | | |
| 13316 | | Nothing selected |
| 13317 | | |
| 13318 | | > save fig5.jpg |
| 13319 | | |
| 13320 | | executed script.view.cxc |
| 13321 | | |
| 13322 | | > open "/Users/admin/Dropbox (Technion |
| 13323 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 13324 | | |
| 13325 | | > close |
| 13326 | | |
| 13327 | | > graphics bgColor white |
| 13328 | | |
| 13329 | | > open 1WMB |
| 13330 | | |
| 13331 | | 1wmb title: |
| 13332 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 13333 | | info...] |
| 13334 | | |
| 13335 | | Chain information for 1wmb #1 |
| 13336 | | --- |
| 13337 | | Chain | Description |
| 13338 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 13339 | | |
| 13340 | | Non-standard residues in 1wmb #1 |
| 13341 | | --- |
| 13342 | | CAC — cacodylate ion (dimethylarsinate) |
| 13343 | | MG — magnesium ion |
| 13344 | | |
| 13345 | | 1wmb mmCIF Assemblies |
| 13346 | | --- |
| 13347 | | 1| author_and_software_defined_assembly |
| 13348 | | |
| 13349 | | |
| 13350 | | > open 3I3O |
| 13351 | | |
| 13352 | | 3i3o title: |
| 13353 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 13354 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 13355 | | info...] |
| 13356 | | |
| 13357 | | Chain information for 3i3o #2 |
| 13358 | | --- |
| 13359 | | Chain | Description |
| 13360 | | A B C D E F G H | Short chain dehydrogenase |
| 13361 | | |
| 13362 | | Non-standard residues in 3i3o #2 |
| 13363 | | --- |
| 13364 | | CAC — cacodylate ion (dimethylarsinate) |
| 13365 | | CL — chloride ion |
| 13366 | | MG — magnesium ion |
| 13367 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 13368 | | |
| 13369 | | 3i3o mmCIF Assemblies |
| 13370 | | --- |
| 13371 | | 1| author_and_software_defined_assembly |
| 13372 | | 2| author_and_software_defined_assembly |
| 13373 | | |
| 13374 | | |
| 13375 | | > delete ~/a |
| 13376 | | |
| 13377 | | > delete solvent |
| 13378 | | |
| 13379 | | > mmaker #2 to #1 |
| 13380 | | |
| 13381 | | Parameters |
| 13382 | | --- |
| 13383 | | Chain pairing | bb |
| 13384 | | Alignment algorithm | Needleman-Wunsch |
| 13385 | | Similarity matrix | BLOSUM-62 |
| 13386 | | SS fraction | 0.3 |
| 13387 | | Gap open (HH/SS/other) | 18/18/6 |
| 13388 | | Gap extend | 1 |
| 13389 | | SS matrix | | | H | S | O |
| 13390 | | ---|---|---|--- |
| 13391 | | H | 6 | -9 | -6 |
| 13392 | | S | | 6 | -6 |
| 13393 | | O | | | 4 |
| 13394 | | Iteration cutoff | 2 |
| 13395 | | |
| 13396 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 13397 | | score = 499.7 |
| 13398 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 13399 | | 3.736) |
| 13400 | | |
| 13401 | | |
| 13402 | | > color #1 green |
| 13403 | | |
| 13404 | | > color #2 tan |
| 13405 | | |
| 13406 | | > color ~C byatom |
| 13407 | | |
| 13408 | | > ~display |
| 13409 | | |
| 13410 | | > display #1:138 #2:176 |
| 13411 | | |
| 13412 | | > style stick |
| 13413 | | |
| 13414 | | Changed 4099 atom styles |
| 13415 | | |
| 13416 | | > ribbon |
| 13417 | | |
| 13418 | | > transparency 60 target r |
| 13419 | | |
| 13420 | | > view |
| 13421 | | |
| 13422 | | > size #1:138 #2:176 stickRadius 0.3 |
| 13423 | | |
| 13424 | | Changed 14 bond radii |
| 13425 | | |
| 13426 | | > save fig1.jpg |
| 13427 | | |
| 13428 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 13429 | | |
| 13430 | | > sel-ca |
| 13431 | | |
| 13432 | | 13 atoms, 1 model selected |
| 13433 | | 26 atoms, 2 models selected |
| 13434 | | |
| 13435 | | > display sel-residues |
| 13436 | | |
| 13437 | | > color ~C byatom |
| 13438 | | |
| 13439 | | > style stick |
| 13440 | | |
| 13441 | | Changed 4099 atom styles |
| 13442 | | |
| 13443 | | > view #1:138 :< 5 pad -1 |
| 13444 | | |
| 13445 | | > hbonds #1:138 & #1 name hb1 color green |
| 13446 | | |
| 13447 | | 3 hydrogen bonds found |
| 13448 | | |
| 13449 | | > hbonds #2:176 & #2 name hb2 color tan |
| 13450 | | |
| 13451 | | 4 hydrogen bonds found |
| 13452 | | |
| 13453 | | > transparency 90 target r |
| 13454 | | |
| 13455 | | > label #1:138 #2:176 offset 1,-1,1 |
| 13456 | | |
| 13457 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 13458 | | |
| 13459 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 13460 | | |
| 13461 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 13462 | | > bgColor white offset 0,0.7,0 |
| 13463 | | |
| 13464 | | > ~select |
| 13465 | | |
| 13466 | | Nothing selected |
| 13467 | | |
| 13468 | | > save fig2.jpg |
| 13469 | | |
| 13470 | | > sel-ca |
| 13471 | | |
| 13472 | | 13 atoms, 1 model selected |
| 13473 | | 26 atoms, 2 models selected |
| 13474 | | |
| 13475 | | > ~ribbon |
| 13476 | | |
| 13477 | | > size stickRadius 0.05 |
| 13478 | | |
| 13479 | | Changed 4167 bond radii |
| 13480 | | |
| 13481 | | > size #1:138 stickRadius 0.2 |
| 13482 | | |
| 13483 | | Changed 7 bond radii |
| 13484 | | |
| 13485 | | > size #2:176 stickRadius 0.2 |
| 13486 | | |
| 13487 | | Changed 7 bond radii |
| 13488 | | |
| 13489 | | > view sel-residues pad -1 |
| 13490 | | |
| 13491 | | > ~select |
| 13492 | | |
| 13493 | | Nothing selected |
| 13494 | | |
| 13495 | | > save fig3.jpg |
| 13496 | | |
| 13497 | | > sel-ca |
| 13498 | | |
| 13499 | | 13 atoms, 1 model selected |
| 13500 | | 26 atoms, 2 models selected |
| 13501 | | |
| 13502 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 13503 | | |
| 13504 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 13505 | | |
| 13506 | | > label #1:138 residues text {0.residue.number} height 0.5 color green bgColor |
| 13507 | | > white offset 0,2,0 |
| 13508 | | |
| 13509 | | > view sel-residues pad -1 |
| 13510 | | |
| 13511 | | > sel-ca |
| 13512 | | |
| 13513 | | 13 atoms, 1 model selected |
| 13514 | | 26 atoms, 2 models selected |
| 13515 | | |
| 13516 | | > align #2 & sel toAtoms #1 & sel |
| 13517 | | |
| 13518 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 13519 | | |
| 13520 | | > ~select |
| 13521 | | |
| 13522 | | Nothing selected |
| 13523 | | |
| 13524 | | > save fig4.jpg |
| 13525 | | |
| 13526 | | > sel-ca |
| 13527 | | |
| 13528 | | 13 atoms, 1 model selected |
| 13529 | | 26 atoms, 2 models selected |
| 13530 | | |
| 13531 | | > ribbon sel |
| 13532 | | |
| 13533 | | > ~select |
| 13534 | | |
| 13535 | | Nothing selected |
| 13536 | | |
| 13537 | | > save fig5.jpg |
| 13538 | | |
| 13539 | | executed script.view.cxc |
| 13540 | | |
| 13541 | | > open "/Users/admin/Dropbox (Technion |
| 13542 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 13543 | | |
| 13544 | | > close |
| 13545 | | |
| 13546 | | > graphics bgColor white |
| 13547 | | |
| 13548 | | > open 1WMB |
| 13549 | | |
| 13550 | | 1wmb title: |
| 13551 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 13552 | | info...] |
| 13553 | | |
| 13554 | | Chain information for 1wmb #1 |
| 13555 | | --- |
| 13556 | | Chain | Description |
| 13557 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 13558 | | |
| 13559 | | Non-standard residues in 1wmb #1 |
| 13560 | | --- |
| 13561 | | CAC — cacodylate ion (dimethylarsinate) |
| 13562 | | MG — magnesium ion |
| 13563 | | |
| 13564 | | 1wmb mmCIF Assemblies |
| 13565 | | --- |
| 13566 | | 1| author_and_software_defined_assembly |
| 13567 | | |
| 13568 | | |
| 13569 | | > open 3I3O |
| 13570 | | |
| 13571 | | 3i3o title: |
| 13572 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 13573 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 13574 | | info...] |
| 13575 | | |
| 13576 | | Chain information for 3i3o #2 |
| 13577 | | --- |
| 13578 | | Chain | Description |
| 13579 | | A B C D E F G H | Short chain dehydrogenase |
| 13580 | | |
| 13581 | | Non-standard residues in 3i3o #2 |
| 13582 | | --- |
| 13583 | | CAC — cacodylate ion (dimethylarsinate) |
| 13584 | | CL — chloride ion |
| 13585 | | MG — magnesium ion |
| 13586 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 13587 | | |
| 13588 | | 3i3o mmCIF Assemblies |
| 13589 | | --- |
| 13590 | | 1| author_and_software_defined_assembly |
| 13591 | | 2| author_and_software_defined_assembly |
| 13592 | | |
| 13593 | | |
| 13594 | | > delete ~/a |
| 13595 | | |
| 13596 | | > delete solvent |
| 13597 | | |
| 13598 | | > mmaker #2 to #1 |
| 13599 | | |
| 13600 | | Parameters |
| 13601 | | --- |
| 13602 | | Chain pairing | bb |
| 13603 | | Alignment algorithm | Needleman-Wunsch |
| 13604 | | Similarity matrix | BLOSUM-62 |
| 13605 | | SS fraction | 0.3 |
| 13606 | | Gap open (HH/SS/other) | 18/18/6 |
| 13607 | | Gap extend | 1 |
| 13608 | | SS matrix | | | H | S | O |
| 13609 | | ---|---|---|--- |
| 13610 | | H | 6 | -9 | -6 |
| 13611 | | S | | 6 | -6 |
| 13612 | | O | | | 4 |
| 13613 | | Iteration cutoff | 2 |
| 13614 | | |
| 13615 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 13616 | | score = 499.7 |
| 13617 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 13618 | | 3.736) |
| 13619 | | |
| 13620 | | |
| 13621 | | > color #1 green |
| 13622 | | |
| 13623 | | > color #2 tan |
| 13624 | | |
| 13625 | | > color ~C byatom |
| 13626 | | |
| 13627 | | > ~display |
| 13628 | | |
| 13629 | | > display #1:138 #2:176 |
| 13630 | | |
| 13631 | | > style stick |
| 13632 | | |
| 13633 | | Changed 4099 atom styles |
| 13634 | | |
| 13635 | | > ribbon |
| 13636 | | |
| 13637 | | > transparency 60 target r |
| 13638 | | |
| 13639 | | > view |
| 13640 | | |
| 13641 | | > size #1:138 #2:176 stickRadius 0.3 |
| 13642 | | |
| 13643 | | Changed 14 bond radii |
| 13644 | | |
| 13645 | | > save fig1.jpg |
| 13646 | | |
| 13647 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 13648 | | |
| 13649 | | > sel-ca |
| 13650 | | |
| 13651 | | 13 atoms, 1 model selected |
| 13652 | | 26 atoms, 2 models selected |
| 13653 | | |
| 13654 | | > display sel-residues |
| 13655 | | |
| 13656 | | > color ~C byatom |
| 13657 | | |
| 13658 | | > style stick |
| 13659 | | |
| 13660 | | Changed 4099 atom styles |
| 13661 | | |
| 13662 | | > view #1:138 :< 5 pad -1 |
| 13663 | | |
| 13664 | | > hbonds #1:138 & #1 name hb1 color green |
| 13665 | | |
| 13666 | | 3 hydrogen bonds found |
| 13667 | | |
| 13668 | | > hbonds #2:176 & #2 name hb2 color tan |
| 13669 | | |
| 13670 | | 4 hydrogen bonds found |
| 13671 | | |
| 13672 | | > transparency 90 target r |
| 13673 | | |
| 13674 | | > label #1:138 #2:176 offset 1,-1,1 |
| 13675 | | |
| 13676 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 13677 | | |
| 13678 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 13679 | | |
| 13680 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 13681 | | > bgColor white offset 0,0.7,0 |
| 13682 | | |
| 13683 | | > ~select |
| 13684 | | |
| 13685 | | Nothing selected |
| 13686 | | |
| 13687 | | > save fig2.jpg |
| 13688 | | |
| 13689 | | > sel-ca |
| 13690 | | |
| 13691 | | 13 atoms, 1 model selected |
| 13692 | | 26 atoms, 2 models selected |
| 13693 | | |
| 13694 | | > ~ribbon |
| 13695 | | |
| 13696 | | > size stickRadius 0.05 |
| 13697 | | |
| 13698 | | Changed 4167 bond radii |
| 13699 | | |
| 13700 | | > size #1:138 stickRadius 0.2 |
| 13701 | | |
| 13702 | | Changed 7 bond radii |
| 13703 | | |
| 13704 | | > size #2:176 stickRadius 0.2 |
| 13705 | | |
| 13706 | | Changed 7 bond radii |
| 13707 | | |
| 13708 | | > view sel-residues pad -1 |
| 13709 | | |
| 13710 | | > ~select |
| 13711 | | |
| 13712 | | Nothing selected |
| 13713 | | |
| 13714 | | > save fig3.jpg |
| 13715 | | |
| 13716 | | > sel-ca |
| 13717 | | |
| 13718 | | 13 atoms, 1 model selected |
| 13719 | | 26 atoms, 2 models selected |
| 13720 | | |
| 13721 | | > label sel-residues & #1 & ~#1:138 height 0.4 offset 0,0,0 color green |
| 13722 | | > bgColor white |
| 13723 | | |
| 13724 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 13725 | | |
| 13726 | | > label #1:138 residues text {0.residue.number} height 0.5 color green bgColor |
| 13727 | | > white offset 0,2,0 |
| 13728 | | |
| 13729 | | > view sel-residues pad -1 |
| 13730 | | |
| 13731 | | > sel-ca |
| 13732 | | |
| 13733 | | 13 atoms, 1 model selected |
| 13734 | | 26 atoms, 2 models selected |
| 13735 | | |
| 13736 | | > align #2 & sel toAtoms #1 & sel |
| 13737 | | |
| 13738 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 13739 | | |
| 13740 | | > ~select |
| 13741 | | |
| 13742 | | Nothing selected |
| 13743 | | |
| 13744 | | > save fig4.jpg |
| 13745 | | |
| 13746 | | > sel-ca |
| 13747 | | |
| 13748 | | 13 atoms, 1 model selected |
| 13749 | | 26 atoms, 2 models selected |
| 13750 | | |
| 13751 | | > ribbon sel |
| 13752 | | |
| 13753 | | > ~select |
| 13754 | | |
| 13755 | | Nothing selected |
| 13756 | | |
| 13757 | | > save fig5.jpg |
| 13758 | | |
| 13759 | | executed script.view.cxc |
| 13760 | | |
| 13761 | | > open "/Users/admin/Dropbox (Technion |
| 13762 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 13763 | | |
| 13764 | | > close |
| 13765 | | |
| 13766 | | > graphics bgColor white |
| 13767 | | |
| 13768 | | > open 1WMB |
| 13769 | | |
| 13770 | | 1wmb title: |
| 13771 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 13772 | | info...] |
| 13773 | | |
| 13774 | | Chain information for 1wmb #1 |
| 13775 | | --- |
| 13776 | | Chain | Description |
| 13777 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 13778 | | |
| 13779 | | Non-standard residues in 1wmb #1 |
| 13780 | | --- |
| 13781 | | CAC — cacodylate ion (dimethylarsinate) |
| 13782 | | MG — magnesium ion |
| 13783 | | |
| 13784 | | 1wmb mmCIF Assemblies |
| 13785 | | --- |
| 13786 | | 1| author_and_software_defined_assembly |
| 13787 | | |
| 13788 | | |
| 13789 | | > open 3I3O |
| 13790 | | |
| 13791 | | 3i3o title: |
| 13792 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 13793 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 13794 | | info...] |
| 13795 | | |
| 13796 | | Chain information for 3i3o #2 |
| 13797 | | --- |
| 13798 | | Chain | Description |
| 13799 | | A B C D E F G H | Short chain dehydrogenase |
| 13800 | | |
| 13801 | | Non-standard residues in 3i3o #2 |
| 13802 | | --- |
| 13803 | | CAC — cacodylate ion (dimethylarsinate) |
| 13804 | | CL — chloride ion |
| 13805 | | MG — magnesium ion |
| 13806 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 13807 | | |
| 13808 | | 3i3o mmCIF Assemblies |
| 13809 | | --- |
| 13810 | | 1| author_and_software_defined_assembly |
| 13811 | | 2| author_and_software_defined_assembly |
| 13812 | | |
| 13813 | | |
| 13814 | | > delete ~/a |
| 13815 | | |
| 13816 | | > delete solvent |
| 13817 | | |
| 13818 | | > mmaker #2 to #1 |
| 13819 | | |
| 13820 | | Parameters |
| 13821 | | --- |
| 13822 | | Chain pairing | bb |
| 13823 | | Alignment algorithm | Needleman-Wunsch |
| 13824 | | Similarity matrix | BLOSUM-62 |
| 13825 | | SS fraction | 0.3 |
| 13826 | | Gap open (HH/SS/other) | 18/18/6 |
| 13827 | | Gap extend | 1 |
| 13828 | | SS matrix | | | H | S | O |
| 13829 | | ---|---|---|--- |
| 13830 | | H | 6 | -9 | -6 |
| 13831 | | S | | 6 | -6 |
| 13832 | | O | | | 4 |
| 13833 | | Iteration cutoff | 2 |
| 13834 | | |
| 13835 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 13836 | | score = 499.7 |
| 13837 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 13838 | | 3.736) |
| 13839 | | |
| 13840 | | |
| 13841 | | > color #1 green |
| 13842 | | |
| 13843 | | > color #2 tan |
| 13844 | | |
| 13845 | | > color ~C byatom |
| 13846 | | |
| 13847 | | > ~display |
| 13848 | | |
| 13849 | | > display #1:138 #2:176 |
| 13850 | | |
| 13851 | | > style stick |
| 13852 | | |
| 13853 | | Changed 4099 atom styles |
| 13854 | | |
| 13855 | | > ribbon |
| 13856 | | |
| 13857 | | > transparency 60 target r |
| 13858 | | |
| 13859 | | > view |
| 13860 | | |
| 13861 | | > size #1:138 #2:176 stickRadius 0.3 |
| 13862 | | |
| 13863 | | Changed 14 bond radii |
| 13864 | | |
| 13865 | | > save fig1.jpg |
| 13866 | | |
| 13867 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 13868 | | |
| 13869 | | > sel-ca |
| 13870 | | |
| 13871 | | 13 atoms, 1 model selected |
| 13872 | | 26 atoms, 2 models selected |
| 13873 | | |
| 13874 | | > display sel-residues |
| 13875 | | |
| 13876 | | > color ~C byatom |
| 13877 | | |
| 13878 | | > style stick |
| 13879 | | |
| 13880 | | Changed 4099 atom styles |
| 13881 | | |
| 13882 | | > view #1:138 :< 5 pad -1 |
| 13883 | | |
| 13884 | | > hbonds #1:138 & #1 name hb1 color green |
| 13885 | | |
| 13886 | | 3 hydrogen bonds found |
| 13887 | | |
| 13888 | | > hbonds #2:176 & #2 name hb2 color tan |
| 13889 | | |
| 13890 | | 4 hydrogen bonds found |
| 13891 | | |
| 13892 | | > transparency 90 target r |
| 13893 | | |
| 13894 | | > label #1:138 #2:176 offset 1,-1,1 |
| 13895 | | |
| 13896 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 13897 | | |
| 13898 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 13899 | | |
| 13900 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 13901 | | > bgColor white offset 0,0.7,0 |
| 13902 | | |
| 13903 | | > ~select |
| 13904 | | |
| 13905 | | Nothing selected |
| 13906 | | |
| 13907 | | > save fig2.jpg |
| 13908 | | |
| 13909 | | > sel-ca |
| 13910 | | |
| 13911 | | 13 atoms, 1 model selected |
| 13912 | | 26 atoms, 2 models selected |
| 13913 | | |
| 13914 | | > ~ribbon |
| 13915 | | |
| 13916 | | > size stickRadius 0.05 |
| 13917 | | |
| 13918 | | Changed 4167 bond radii |
| 13919 | | |
| 13920 | | > size #1:138 stickRadius 0.2 |
| 13921 | | |
| 13922 | | Changed 7 bond radii |
| 13923 | | |
| 13924 | | > size #2:176 stickRadius 0.2 |
| 13925 | | |
| 13926 | | Changed 7 bond radii |
| 13927 | | |
| 13928 | | > view sel-residues pad -1 |
| 13929 | | |
| 13930 | | > ~select |
| 13931 | | |
| 13932 | | Nothing selected |
| 13933 | | |
| 13934 | | > save fig3.jpg |
| 13935 | | |
| 13936 | | > sel-ca |
| 13937 | | |
| 13938 | | 13 atoms, 1 model selected |
| 13939 | | 26 atoms, 2 models selected |
| 13940 | | |
| 13941 | | > label sel-residues & #1 & ~#1:138 height 0.4 offset 0,0,0 color green |
| 13942 | | > bgColor white |
| 13943 | | |
| 13944 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 13945 | | |
| 13946 | | > label #1:138 height 0.5 color green bgColor white offset 0,2,0 |
| 13947 | | |
| 13948 | | > view sel-residues pad -1 |
| 13949 | | |
| 13950 | | > sel-ca |
| 13951 | | |
| 13952 | | 13 atoms, 1 model selected |
| 13953 | | 26 atoms, 2 models selected |
| 13954 | | |
| 13955 | | > align #2 & sel toAtoms #1 & sel |
| 13956 | | |
| 13957 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 13958 | | |
| 13959 | | > ~select |
| 13960 | | |
| 13961 | | Nothing selected |
| 13962 | | |
| 13963 | | > save fig4.jpg |
| 13964 | | |
| 13965 | | > sel-ca |
| 13966 | | |
| 13967 | | 13 atoms, 1 model selected |
| 13968 | | 26 atoms, 2 models selected |
| 13969 | | |
| 13970 | | > ribbon sel |
| 13971 | | |
| 13972 | | > ~select |
| 13973 | | |
| 13974 | | Nothing selected |
| 13975 | | |
| 13976 | | > save fig5.jpg |
| 13977 | | |
| 13978 | | executed script.view.cxc |
| 13979 | | |
| 13980 | | > open "/Users/admin/Dropbox (Technion |
| 13981 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 13982 | | |
| 13983 | | > close |
| 13984 | | |
| 13985 | | > graphics bgColor white |
| 13986 | | |
| 13987 | | > open 1WMB |
| 13988 | | |
| 13989 | | 1wmb title: |
| 13990 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 13991 | | info...] |
| 13992 | | |
| 13993 | | Chain information for 1wmb #1 |
| 13994 | | --- |
| 13995 | | Chain | Description |
| 13996 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 13997 | | |
| 13998 | | Non-standard residues in 1wmb #1 |
| 13999 | | --- |
| 14000 | | CAC — cacodylate ion (dimethylarsinate) |
| 14001 | | MG — magnesium ion |
| 14002 | | |
| 14003 | | 1wmb mmCIF Assemblies |
| 14004 | | --- |
| 14005 | | 1| author_and_software_defined_assembly |
| 14006 | | |
| 14007 | | |
| 14008 | | > open 3I3O |
| 14009 | | |
| 14010 | | 3i3o title: |
| 14011 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 14012 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 14013 | | info...] |
| 14014 | | |
| 14015 | | Chain information for 3i3o #2 |
| 14016 | | --- |
| 14017 | | Chain | Description |
| 14018 | | A B C D E F G H | Short chain dehydrogenase |
| 14019 | | |
| 14020 | | Non-standard residues in 3i3o #2 |
| 14021 | | --- |
| 14022 | | CAC — cacodylate ion (dimethylarsinate) |
| 14023 | | CL — chloride ion |
| 14024 | | MG — magnesium ion |
| 14025 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 14026 | | |
| 14027 | | 3i3o mmCIF Assemblies |
| 14028 | | --- |
| 14029 | | 1| author_and_software_defined_assembly |
| 14030 | | 2| author_and_software_defined_assembly |
| 14031 | | |
| 14032 | | |
| 14033 | | > delete ~/a |
| 14034 | | |
| 14035 | | > delete solvent |
| 14036 | | |
| 14037 | | > mmaker #2 to #1 |
| 14038 | | |
| 14039 | | Parameters |
| 14040 | | --- |
| 14041 | | Chain pairing | bb |
| 14042 | | Alignment algorithm | Needleman-Wunsch |
| 14043 | | Similarity matrix | BLOSUM-62 |
| 14044 | | SS fraction | 0.3 |
| 14045 | | Gap open (HH/SS/other) | 18/18/6 |
| 14046 | | Gap extend | 1 |
| 14047 | | SS matrix | | | H | S | O |
| 14048 | | ---|---|---|--- |
| 14049 | | H | 6 | -9 | -6 |
| 14050 | | S | | 6 | -6 |
| 14051 | | O | | | 4 |
| 14052 | | Iteration cutoff | 2 |
| 14053 | | |
| 14054 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 14055 | | score = 499.7 |
| 14056 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 14057 | | 3.736) |
| 14058 | | |
| 14059 | | |
| 14060 | | > color #1 green |
| 14061 | | |
| 14062 | | > color #2 tan |
| 14063 | | |
| 14064 | | > color ~C byatom |
| 14065 | | |
| 14066 | | > ~display |
| 14067 | | |
| 14068 | | > display #1:138 #2:176 |
| 14069 | | |
| 14070 | | > style stick |
| 14071 | | |
| 14072 | | Changed 4099 atom styles |
| 14073 | | |
| 14074 | | > ribbon |
| 14075 | | |
| 14076 | | > transparency 60 target r |
| 14077 | | |
| 14078 | | > view |
| 14079 | | |
| 14080 | | > size #1:138 #2:176 stickRadius 0.3 |
| 14081 | | |
| 14082 | | Changed 14 bond radii |
| 14083 | | |
| 14084 | | > save fig1.jpg |
| 14085 | | |
| 14086 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 14087 | | |
| 14088 | | > sel-ca |
| 14089 | | |
| 14090 | | 13 atoms, 1 model selected |
| 14091 | | 26 atoms, 2 models selected |
| 14092 | | |
| 14093 | | > display sel-residues |
| 14094 | | |
| 14095 | | > color ~C byatom |
| 14096 | | |
| 14097 | | > style stick |
| 14098 | | |
| 14099 | | Changed 4099 atom styles |
| 14100 | | |
| 14101 | | > view #1:138 :< 5 pad -1 |
| 14102 | | |
| 14103 | | > hbonds #1:138 & #1 name hb1 color green |
| 14104 | | |
| 14105 | | 3 hydrogen bonds found |
| 14106 | | |
| 14107 | | > hbonds #2:176 & #2 name hb2 color tan |
| 14108 | | |
| 14109 | | 4 hydrogen bonds found |
| 14110 | | |
| 14111 | | > transparency 90 target r |
| 14112 | | |
| 14113 | | > label #1:138 #2:176 offset 1,-1,1 |
| 14114 | | |
| 14115 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 14116 | | |
| 14117 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 14118 | | |
| 14119 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 14120 | | > bgColor white offset 0,0.7,0 |
| 14121 | | |
| 14122 | | > ~select |
| 14123 | | |
| 14124 | | Nothing selected |
| 14125 | | |
| 14126 | | > save fig2.jpg |
| 14127 | | |
| 14128 | | > sel-ca |
| 14129 | | |
| 14130 | | 13 atoms, 1 model selected |
| 14131 | | 26 atoms, 2 models selected |
| 14132 | | |
| 14133 | | > ~ribbon |
| 14134 | | |
| 14135 | | > size stickRadius 0.05 |
| 14136 | | |
| 14137 | | Changed 4167 bond radii |
| 14138 | | |
| 14139 | | > size #1:138 stickRadius 0.2 |
| 14140 | | |
| 14141 | | Changed 7 bond radii |
| 14142 | | |
| 14143 | | > size #2:176 stickRadius 0.2 |
| 14144 | | |
| 14145 | | Changed 7 bond radii |
| 14146 | | |
| 14147 | | > view sel-residues pad -1 |
| 14148 | | |
| 14149 | | > ~select |
| 14150 | | |
| 14151 | | Nothing selected |
| 14152 | | |
| 14153 | | > save fig3.jpg |
| 14154 | | |
| 14155 | | > sel-ca |
| 14156 | | |
| 14157 | | 13 atoms, 1 model selected |
| 14158 | | 26 atoms, 2 models selected |
| 14159 | | |
| 14160 | | > label sel-residues & #1 & ~#1:138 height 0.4 offset 0,0,0 color green |
| 14161 | | > bgColor white |
| 14162 | | |
| 14163 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 14164 | | |
| 14165 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 14166 | | > bgColor white offset 0,2,0 |
| 14167 | | |
| 14168 | | > view sel-residues pad -1 |
| 14169 | | |
| 14170 | | > sel-ca |
| 14171 | | |
| 14172 | | 13 atoms, 1 model selected |
| 14173 | | 26 atoms, 2 models selected |
| 14174 | | |
| 14175 | | > align #2 & sel toAtoms #1 & sel |
| 14176 | | |
| 14177 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 14178 | | |
| 14179 | | > ~select |
| 14180 | | |
| 14181 | | Nothing selected |
| 14182 | | |
| 14183 | | > save fig4.jpg |
| 14184 | | |
| 14185 | | > sel-ca |
| 14186 | | |
| 14187 | | 13 atoms, 1 model selected |
| 14188 | | 26 atoms, 2 models selected |
| 14189 | | |
| 14190 | | > ribbon sel |
| 14191 | | |
| 14192 | | > ~select |
| 14193 | | |
| 14194 | | Nothing selected |
| 14195 | | |
| 14196 | | > save fig5.jpg |
| 14197 | | |
| 14198 | | executed script.view.cxc |
| 14199 | | |
| 14200 | | > open "/Users/admin/Dropbox (Technion |
| 14201 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 14202 | | |
| 14203 | | > close |
| 14204 | | |
| 14205 | | > graphics bgColor white |
| 14206 | | |
| 14207 | | > open 1WMB |
| 14208 | | |
| 14209 | | 1wmb title: |
| 14210 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 14211 | | info...] |
| 14212 | | |
| 14213 | | Chain information for 1wmb #1 |
| 14214 | | --- |
| 14215 | | Chain | Description |
| 14216 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 14217 | | |
| 14218 | | Non-standard residues in 1wmb #1 |
| 14219 | | --- |
| 14220 | | CAC — cacodylate ion (dimethylarsinate) |
| 14221 | | MG — magnesium ion |
| 14222 | | |
| 14223 | | 1wmb mmCIF Assemblies |
| 14224 | | --- |
| 14225 | | 1| author_and_software_defined_assembly |
| 14226 | | |
| 14227 | | |
| 14228 | | > open 3I3O |
| 14229 | | |
| 14230 | | 3i3o title: |
| 14231 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 14232 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 14233 | | info...] |
| 14234 | | |
| 14235 | | Chain information for 3i3o #2 |
| 14236 | | --- |
| 14237 | | Chain | Description |
| 14238 | | A B C D E F G H | Short chain dehydrogenase |
| 14239 | | |
| 14240 | | Non-standard residues in 3i3o #2 |
| 14241 | | --- |
| 14242 | | CAC — cacodylate ion (dimethylarsinate) |
| 14243 | | CL — chloride ion |
| 14244 | | MG — magnesium ion |
| 14245 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 14246 | | |
| 14247 | | 3i3o mmCIF Assemblies |
| 14248 | | --- |
| 14249 | | 1| author_and_software_defined_assembly |
| 14250 | | 2| author_and_software_defined_assembly |
| 14251 | | |
| 14252 | | |
| 14253 | | > delete ~/a |
| 14254 | | |
| 14255 | | > delete solvent |
| 14256 | | |
| 14257 | | > mmaker #2 to #1 |
| 14258 | | |
| 14259 | | Parameters |
| 14260 | | --- |
| 14261 | | Chain pairing | bb |
| 14262 | | Alignment algorithm | Needleman-Wunsch |
| 14263 | | Similarity matrix | BLOSUM-62 |
| 14264 | | SS fraction | 0.3 |
| 14265 | | Gap open (HH/SS/other) | 18/18/6 |
| 14266 | | Gap extend | 1 |
| 14267 | | SS matrix | | | H | S | O |
| 14268 | | ---|---|---|--- |
| 14269 | | H | 6 | -9 | -6 |
| 14270 | | S | | 6 | -6 |
| 14271 | | O | | | 4 |
| 14272 | | Iteration cutoff | 2 |
| 14273 | | |
| 14274 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 14275 | | score = 499.7 |
| 14276 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 14277 | | 3.736) |
| 14278 | | |
| 14279 | | |
| 14280 | | > color #1 green |
| 14281 | | |
| 14282 | | > color #2 tan |
| 14283 | | |
| 14284 | | > color ~C byatom |
| 14285 | | |
| 14286 | | > ~display |
| 14287 | | |
| 14288 | | > display #1:138 #2:176 |
| 14289 | | |
| 14290 | | > style stick |
| 14291 | | |
| 14292 | | Changed 4099 atom styles |
| 14293 | | |
| 14294 | | > ribbon |
| 14295 | | |
| 14296 | | > transparency 60 target r |
| 14297 | | |
| 14298 | | > view |
| 14299 | | |
| 14300 | | > size #1:138 #2:176 stickRadius 0.3 |
| 14301 | | |
| 14302 | | Changed 14 bond radii |
| 14303 | | |
| 14304 | | > save fig1.jpg |
| 14305 | | |
| 14306 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 14307 | | |
| 14308 | | > sel-ca |
| 14309 | | |
| 14310 | | 13 atoms, 1 model selected |
| 14311 | | 26 atoms, 2 models selected |
| 14312 | | |
| 14313 | | > display sel-residues |
| 14314 | | |
| 14315 | | > color ~C byatom |
| 14316 | | |
| 14317 | | > style stick |
| 14318 | | |
| 14319 | | Changed 4099 atom styles |
| 14320 | | |
| 14321 | | > view #1:138 :< 5 pad -1 |
| 14322 | | |
| 14323 | | > hbonds #1:138 & #1 name hb1 color green |
| 14324 | | |
| 14325 | | 3 hydrogen bonds found |
| 14326 | | |
| 14327 | | > hbonds #2:176 & #2 name hb2 color tan |
| 14328 | | |
| 14329 | | 4 hydrogen bonds found |
| 14330 | | |
| 14331 | | > transparency 90 target r |
| 14332 | | |
| 14333 | | > label #1:138 #2:176 offset 1,-1,1 |
| 14334 | | |
| 14335 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 14336 | | |
| 14337 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 14338 | | |
| 14339 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 14340 | | > bgColor white offset 0,0.7,0 |
| 14341 | | |
| 14342 | | > ~select |
| 14343 | | |
| 14344 | | Nothing selected |
| 14345 | | |
| 14346 | | > save fig2.jpg |
| 14347 | | |
| 14348 | | > sel-ca |
| 14349 | | |
| 14350 | | 13 atoms, 1 model selected |
| 14351 | | 26 atoms, 2 models selected |
| 14352 | | |
| 14353 | | > ~ribbon |
| 14354 | | |
| 14355 | | > size stickRadius 0.05 |
| 14356 | | |
| 14357 | | Changed 4167 bond radii |
| 14358 | | |
| 14359 | | > size #1:138 stickRadius 0.2 |
| 14360 | | |
| 14361 | | Changed 7 bond radii |
| 14362 | | |
| 14363 | | > size #2:176 stickRadius 0.2 |
| 14364 | | |
| 14365 | | Changed 7 bond radii |
| 14366 | | |
| 14367 | | > view sel-residues pad -1 |
| 14368 | | |
| 14369 | | > ~select |
| 14370 | | |
| 14371 | | Nothing selected |
| 14372 | | |
| 14373 | | > save fig3.jpg |
| 14374 | | |
| 14375 | | > sel-ca |
| 14376 | | |
| 14377 | | 13 atoms, 1 model selected |
| 14378 | | 26 atoms, 2 models selected |
| 14379 | | |
| 14380 | | > label sel-residues & #1 & ~#1:138 height 0.4 offset 0,0,0 color green |
| 14381 | | > bgColor white |
| 14382 | | |
| 14383 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 14384 | | |
| 14385 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f},{0.residue.number} height |
| 14386 | | > 0.5 color green bgColor white offset 0,2,0 |
| 14387 | | |
| 14388 | | > view sel-residues pad -1 |
| 14389 | | |
| 14390 | | > sel-ca |
| 14391 | | |
| 14392 | | 13 atoms, 1 model selected |
| 14393 | | 26 atoms, 2 models selected |
| 14394 | | |
| 14395 | | > align #2 & sel toAtoms #1 & sel |
| 14396 | | |
| 14397 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 14398 | | |
| 14399 | | > ~select |
| 14400 | | |
| 14401 | | Nothing selected |
| 14402 | | |
| 14403 | | > save fig4.jpg |
| 14404 | | |
| 14405 | | > sel-ca |
| 14406 | | |
| 14407 | | 13 atoms, 1 model selected |
| 14408 | | 26 atoms, 2 models selected |
| 14409 | | |
| 14410 | | > ribbon sel |
| 14411 | | |
| 14412 | | > ~select |
| 14413 | | |
| 14414 | | Nothing selected |
| 14415 | | |
| 14416 | | > save fig5.jpg |
| 14417 | | |
| 14418 | | executed script.view.cxc |
| 14419 | | |
| 14420 | | > open "/Users/admin/Dropbox (Technion |
| 14421 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 14422 | | |
| 14423 | | > close |
| 14424 | | |
| 14425 | | > graphics bgColor white |
| 14426 | | |
| 14427 | | > open 1WMB |
| 14428 | | |
| 14429 | | 1wmb title: |
| 14430 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 14431 | | info...] |
| 14432 | | |
| 14433 | | Chain information for 1wmb #1 |
| 14434 | | --- |
| 14435 | | Chain | Description |
| 14436 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 14437 | | |
| 14438 | | Non-standard residues in 1wmb #1 |
| 14439 | | --- |
| 14440 | | CAC — cacodylate ion (dimethylarsinate) |
| 14441 | | MG — magnesium ion |
| 14442 | | |
| 14443 | | 1wmb mmCIF Assemblies |
| 14444 | | --- |
| 14445 | | 1| author_and_software_defined_assembly |
| 14446 | | |
| 14447 | | |
| 14448 | | > open 3I3O |
| 14449 | | |
| 14450 | | 3i3o title: |
| 14451 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 14452 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 14453 | | info...] |
| 14454 | | |
| 14455 | | Chain information for 3i3o #2 |
| 14456 | | --- |
| 14457 | | Chain | Description |
| 14458 | | A B C D E F G H | Short chain dehydrogenase |
| 14459 | | |
| 14460 | | Non-standard residues in 3i3o #2 |
| 14461 | | --- |
| 14462 | | CAC — cacodylate ion (dimethylarsinate) |
| 14463 | | CL — chloride ion |
| 14464 | | MG — magnesium ion |
| 14465 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 14466 | | |
| 14467 | | 3i3o mmCIF Assemblies |
| 14468 | | --- |
| 14469 | | 1| author_and_software_defined_assembly |
| 14470 | | 2| author_and_software_defined_assembly |
| 14471 | | |
| 14472 | | |
| 14473 | | > delete ~/a |
| 14474 | | |
| 14475 | | > delete solvent |
| 14476 | | |
| 14477 | | > mmaker #2 to #1 |
| 14478 | | |
| 14479 | | Parameters |
| 14480 | | --- |
| 14481 | | Chain pairing | bb |
| 14482 | | Alignment algorithm | Needleman-Wunsch |
| 14483 | | Similarity matrix | BLOSUM-62 |
| 14484 | | SS fraction | 0.3 |
| 14485 | | Gap open (HH/SS/other) | 18/18/6 |
| 14486 | | Gap extend | 1 |
| 14487 | | SS matrix | | | H | S | O |
| 14488 | | ---|---|---|--- |
| 14489 | | H | 6 | -9 | -6 |
| 14490 | | S | | 6 | -6 |
| 14491 | | O | | | 4 |
| 14492 | | Iteration cutoff | 2 |
| 14493 | | |
| 14494 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 14495 | | score = 499.7 |
| 14496 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 14497 | | 3.736) |
| 14498 | | |
| 14499 | | |
| 14500 | | > color #1 green |
| 14501 | | |
| 14502 | | > color #2 tan |
| 14503 | | |
| 14504 | | > color ~C byatom |
| 14505 | | |
| 14506 | | > ~display |
| 14507 | | |
| 14508 | | > display #1:138 #2:176 |
| 14509 | | |
| 14510 | | > style stick |
| 14511 | | |
| 14512 | | Changed 4099 atom styles |
| 14513 | | |
| 14514 | | > ribbon |
| 14515 | | |
| 14516 | | > transparency 60 target r |
| 14517 | | |
| 14518 | | > view |
| 14519 | | |
| 14520 | | > size #1:138 #2:176 stickRadius 0.3 |
| 14521 | | |
| 14522 | | Changed 14 bond radii |
| 14523 | | |
| 14524 | | > save fig1.jpg |
| 14525 | | |
| 14526 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 14527 | | |
| 14528 | | > sel-ca |
| 14529 | | |
| 14530 | | 13 atoms, 1 model selected |
| 14531 | | 26 atoms, 2 models selected |
| 14532 | | |
| 14533 | | > display sel-residues |
| 14534 | | |
| 14535 | | > color ~C byatom |
| 14536 | | |
| 14537 | | > style stick |
| 14538 | | |
| 14539 | | Changed 4099 atom styles |
| 14540 | | |
| 14541 | | > view #1:138 :< 5 pad -1 |
| 14542 | | |
| 14543 | | > hbonds #1:138 & #1 name hb1 color green |
| 14544 | | |
| 14545 | | 3 hydrogen bonds found |
| 14546 | | |
| 14547 | | > hbonds #2:176 & #2 name hb2 color tan |
| 14548 | | |
| 14549 | | 4 hydrogen bonds found |
| 14550 | | |
| 14551 | | > transparency 90 target r |
| 14552 | | |
| 14553 | | > label #1:138 #2:176 offset 1,-1,1 |
| 14554 | | |
| 14555 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 14556 | | |
| 14557 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 14558 | | |
| 14559 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f},{0.residue.number} height |
| 14560 | | > 0.5 color green bgColor white offset 0,0,0 |
| 14561 | | |
| 14562 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 14563 | | > bgColor white offset 0,0.7,0 |
| 14564 | | |
| 14565 | | > ~select |
| 14566 | | |
| 14567 | | Nothing selected |
| 14568 | | |
| 14569 | | > save fig2.jpg |
| 14570 | | |
| 14571 | | > sel-ca |
| 14572 | | |
| 14573 | | 13 atoms, 1 model selected |
| 14574 | | 26 atoms, 2 models selected |
| 14575 | | |
| 14576 | | > ~ribbon |
| 14577 | | |
| 14578 | | > size stickRadius 0.05 |
| 14579 | | |
| 14580 | | Changed 4167 bond radii |
| 14581 | | |
| 14582 | | > size #1:138 stickRadius 0.2 |
| 14583 | | |
| 14584 | | Changed 7 bond radii |
| 14585 | | |
| 14586 | | > size #2:176 stickRadius 0.2 |
| 14587 | | |
| 14588 | | Changed 7 bond radii |
| 14589 | | |
| 14590 | | > view sel-residues pad -1 |
| 14591 | | |
| 14592 | | > ~select |
| 14593 | | |
| 14594 | | Nothing selected |
| 14595 | | |
| 14596 | | > save fig3.jpg |
| 14597 | | |
| 14598 | | > sel-ca |
| 14599 | | |
| 14600 | | 13 atoms, 1 model selected |
| 14601 | | 26 atoms, 2 models selected |
| 14602 | | |
| 14603 | | > label sel-residues & #1 height 0.4 offset 0,1,0 color green bgColor white |
| 14604 | | |
| 14605 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 14606 | | |
| 14607 | | > view sel-residues pad -1 |
| 14608 | | |
| 14609 | | > sel-ca |
| 14610 | | |
| 14611 | | 13 atoms, 1 model selected |
| 14612 | | 26 atoms, 2 models selected |
| 14613 | | |
| 14614 | | > align #2 & sel toAtoms #1 & sel |
| 14615 | | |
| 14616 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 14617 | | |
| 14618 | | > ~select |
| 14619 | | |
| 14620 | | Nothing selected |
| 14621 | | |
| 14622 | | > save fig4.jpg |
| 14623 | | |
| 14624 | | > sel-ca |
| 14625 | | |
| 14626 | | 13 atoms, 1 model selected |
| 14627 | | 26 atoms, 2 models selected |
| 14628 | | |
| 14629 | | > ribbon sel |
| 14630 | | |
| 14631 | | > ~select |
| 14632 | | |
| 14633 | | Nothing selected |
| 14634 | | |
| 14635 | | > save fig5.jpg |
| 14636 | | |
| 14637 | | executed script.view.cxc |
| 14638 | | |
| 14639 | | > open "/Users/admin/Dropbox (Technion |
| 14640 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 14641 | | |
| 14642 | | > close |
| 14643 | | |
| 14644 | | > graphics bgColor white |
| 14645 | | |
| 14646 | | > open 1WMB |
| 14647 | | |
| 14648 | | 1wmb title: |
| 14649 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 14650 | | info...] |
| 14651 | | |
| 14652 | | Chain information for 1wmb #1 |
| 14653 | | --- |
| 14654 | | Chain | Description |
| 14655 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 14656 | | |
| 14657 | | Non-standard residues in 1wmb #1 |
| 14658 | | --- |
| 14659 | | CAC — cacodylate ion (dimethylarsinate) |
| 14660 | | MG — magnesium ion |
| 14661 | | |
| 14662 | | 1wmb mmCIF Assemblies |
| 14663 | | --- |
| 14664 | | 1| author_and_software_defined_assembly |
| 14665 | | |
| 14666 | | |
| 14667 | | > open 3I3O |
| 14668 | | |
| 14669 | | 3i3o title: |
| 14670 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 14671 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 14672 | | info...] |
| 14673 | | |
| 14674 | | Chain information for 3i3o #2 |
| 14675 | | --- |
| 14676 | | Chain | Description |
| 14677 | | A B C D E F G H | Short chain dehydrogenase |
| 14678 | | |
| 14679 | | Non-standard residues in 3i3o #2 |
| 14680 | | --- |
| 14681 | | CAC — cacodylate ion (dimethylarsinate) |
| 14682 | | CL — chloride ion |
| 14683 | | MG — magnesium ion |
| 14684 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 14685 | | |
| 14686 | | 3i3o mmCIF Assemblies |
| 14687 | | --- |
| 14688 | | 1| author_and_software_defined_assembly |
| 14689 | | 2| author_and_software_defined_assembly |
| 14690 | | |
| 14691 | | |
| 14692 | | > delete ~/a |
| 14693 | | |
| 14694 | | > delete solvent |
| 14695 | | |
| 14696 | | > mmaker #2 to #1 |
| 14697 | | |
| 14698 | | Parameters |
| 14699 | | --- |
| 14700 | | Chain pairing | bb |
| 14701 | | Alignment algorithm | Needleman-Wunsch |
| 14702 | | Similarity matrix | BLOSUM-62 |
| 14703 | | SS fraction | 0.3 |
| 14704 | | Gap open (HH/SS/other) | 18/18/6 |
| 14705 | | Gap extend | 1 |
| 14706 | | SS matrix | | | H | S | O |
| 14707 | | ---|---|---|--- |
| 14708 | | H | 6 | -9 | -6 |
| 14709 | | S | | 6 | -6 |
| 14710 | | O | | | 4 |
| 14711 | | Iteration cutoff | 2 |
| 14712 | | |
| 14713 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 14714 | | score = 499.7 |
| 14715 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 14716 | | 3.736) |
| 14717 | | |
| 14718 | | |
| 14719 | | > color #1 green |
| 14720 | | |
| 14721 | | > color #2 tan |
| 14722 | | |
| 14723 | | > color ~C byatom |
| 14724 | | |
| 14725 | | > ~display |
| 14726 | | |
| 14727 | | > display #1:138 #2:176 |
| 14728 | | |
| 14729 | | > style stick |
| 14730 | | |
| 14731 | | Changed 4099 atom styles |
| 14732 | | |
| 14733 | | > ribbon |
| 14734 | | |
| 14735 | | > transparency 60 target r |
| 14736 | | |
| 14737 | | > view |
| 14738 | | |
| 14739 | | > size #1:138 #2:176 stickRadius 0.3 |
| 14740 | | |
| 14741 | | Changed 14 bond radii |
| 14742 | | |
| 14743 | | > save fig1.jpg |
| 14744 | | |
| 14745 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 14746 | | |
| 14747 | | > sel-ca |
| 14748 | | |
| 14749 | | 13 atoms, 1 model selected |
| 14750 | | 26 atoms, 2 models selected |
| 14751 | | |
| 14752 | | > display sel-residues |
| 14753 | | |
| 14754 | | > color ~C byatom |
| 14755 | | |
| 14756 | | > style stick |
| 14757 | | |
| 14758 | | Changed 4099 atom styles |
| 14759 | | |
| 14760 | | > view #1:138 :< 5 pad -1 |
| 14761 | | |
| 14762 | | > hbonds #1:138 & #1 name hb1 color green |
| 14763 | | |
| 14764 | | 3 hydrogen bonds found |
| 14765 | | |
| 14766 | | > hbonds #2:176 & #2 name hb2 color tan |
| 14767 | | |
| 14768 | | 4 hydrogen bonds found |
| 14769 | | |
| 14770 | | > transparency 90 target r |
| 14771 | | |
| 14772 | | > label #1:138 #2:176 offset 1,-1,1 |
| 14773 | | |
| 14774 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 14775 | | |
| 14776 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 14777 | | |
| 14778 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 14779 | | > bgColor white offset 0,0,0 |
| 14780 | | |
| 14781 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 14782 | | > bgColor white offset 0,0.7,0 |
| 14783 | | |
| 14784 | | > ~select |
| 14785 | | |
| 14786 | | Nothing selected |
| 14787 | | |
| 14788 | | > save fig2.jpg |
| 14789 | | |
| 14790 | | > sel-ca |
| 14791 | | |
| 14792 | | 13 atoms, 1 model selected |
| 14793 | | 26 atoms, 2 models selected |
| 14794 | | |
| 14795 | | > ~ribbon |
| 14796 | | |
| 14797 | | > size stickRadius 0.05 |
| 14798 | | |
| 14799 | | Changed 4167 bond radii |
| 14800 | | |
| 14801 | | > size #1:138 stickRadius 0.2 |
| 14802 | | |
| 14803 | | Changed 7 bond radii |
| 14804 | | |
| 14805 | | > size #2:176 stickRadius 0.2 |
| 14806 | | |
| 14807 | | Changed 7 bond radii |
| 14808 | | |
| 14809 | | > view sel-residues pad -1 |
| 14810 | | |
| 14811 | | > ~select |
| 14812 | | |
| 14813 | | Nothing selected |
| 14814 | | |
| 14815 | | > save fig3.jpg |
| 14816 | | |
| 14817 | | > sel-ca |
| 14818 | | |
| 14819 | | 13 atoms, 1 model selected |
| 14820 | | 26 atoms, 2 models selected |
| 14821 | | |
| 14822 | | > label sel-residues & #1 residues text |
| 14823 | | > {0.phi:.1f},{0.psi:.1f},{0.residue.number} height 0.4 offset 0,1,0 color |
| 14824 | | > green bgColor white |
| 14825 | | |
| 14826 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 14827 | | |
| 14828 | | > view sel-residues pad -1 |
| 14829 | | |
| 14830 | | > sel-ca |
| 14831 | | |
| 14832 | | 13 atoms, 1 model selected |
| 14833 | | 26 atoms, 2 models selected |
| 14834 | | |
| 14835 | | > align #2 & sel toAtoms #1 & sel |
| 14836 | | |
| 14837 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 14838 | | |
| 14839 | | > ~select |
| 14840 | | |
| 14841 | | Nothing selected |
| 14842 | | |
| 14843 | | > save fig4.jpg |
| 14844 | | |
| 14845 | | > sel-ca |
| 14846 | | |
| 14847 | | 13 atoms, 1 model selected |
| 14848 | | 26 atoms, 2 models selected |
| 14849 | | |
| 14850 | | > ribbon sel |
| 14851 | | |
| 14852 | | > ~select |
| 14853 | | |
| 14854 | | Nothing selected |
| 14855 | | |
| 14856 | | > save fig5.jpg |
| 14857 | | |
| 14858 | | executed script.view.cxc |
| 14859 | | |
| 14860 | | > open "/Users/admin/Dropbox (Technion |
| 14861 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 14862 | | |
| 14863 | | > close |
| 14864 | | |
| 14865 | | > graphics bgColor white |
| 14866 | | |
| 14867 | | > open 1WMB |
| 14868 | | |
| 14869 | | 1wmb title: |
| 14870 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 14871 | | info...] |
| 14872 | | |
| 14873 | | Chain information for 1wmb #1 |
| 14874 | | --- |
| 14875 | | Chain | Description |
| 14876 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 14877 | | |
| 14878 | | Non-standard residues in 1wmb #1 |
| 14879 | | --- |
| 14880 | | CAC — cacodylate ion (dimethylarsinate) |
| 14881 | | MG — magnesium ion |
| 14882 | | |
| 14883 | | 1wmb mmCIF Assemblies |
| 14884 | | --- |
| 14885 | | 1| author_and_software_defined_assembly |
| 14886 | | |
| 14887 | | |
| 14888 | | > open 3I3O |
| 14889 | | |
| 14890 | | 3i3o title: |
| 14891 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 14892 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 14893 | | info...] |
| 14894 | | |
| 14895 | | Chain information for 3i3o #2 |
| 14896 | | --- |
| 14897 | | Chain | Description |
| 14898 | | A B C D E F G H | Short chain dehydrogenase |
| 14899 | | |
| 14900 | | Non-standard residues in 3i3o #2 |
| 14901 | | --- |
| 14902 | | CAC — cacodylate ion (dimethylarsinate) |
| 14903 | | CL — chloride ion |
| 14904 | | MG — magnesium ion |
| 14905 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 14906 | | |
| 14907 | | 3i3o mmCIF Assemblies |
| 14908 | | --- |
| 14909 | | 1| author_and_software_defined_assembly |
| 14910 | | 2| author_and_software_defined_assembly |
| 14911 | | |
| 14912 | | |
| 14913 | | > delete ~/a |
| 14914 | | |
| 14915 | | > delete solvent |
| 14916 | | |
| 14917 | | > mmaker #2 to #1 |
| 14918 | | |
| 14919 | | Parameters |
| 14920 | | --- |
| 14921 | | Chain pairing | bb |
| 14922 | | Alignment algorithm | Needleman-Wunsch |
| 14923 | | Similarity matrix | BLOSUM-62 |
| 14924 | | SS fraction | 0.3 |
| 14925 | | Gap open (HH/SS/other) | 18/18/6 |
| 14926 | | Gap extend | 1 |
| 14927 | | SS matrix | | | H | S | O |
| 14928 | | ---|---|---|--- |
| 14929 | | H | 6 | -9 | -6 |
| 14930 | | S | | 6 | -6 |
| 14931 | | O | | | 4 |
| 14932 | | Iteration cutoff | 2 |
| 14933 | | |
| 14934 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 14935 | | score = 499.7 |
| 14936 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 14937 | | 3.736) |
| 14938 | | |
| 14939 | | |
| 14940 | | > color #1 green |
| 14941 | | |
| 14942 | | > color #2 tan |
| 14943 | | |
| 14944 | | > color ~C byatom |
| 14945 | | |
| 14946 | | > ~display |
| 14947 | | |
| 14948 | | > display #1:138 #2:176 |
| 14949 | | |
| 14950 | | > style stick |
| 14951 | | |
| 14952 | | Changed 4099 atom styles |
| 14953 | | |
| 14954 | | > ribbon |
| 14955 | | |
| 14956 | | > transparency 60 target r |
| 14957 | | |
| 14958 | | > view |
| 14959 | | |
| 14960 | | > size #1:138 #2:176 stickRadius 0.3 |
| 14961 | | |
| 14962 | | Changed 14 bond radii |
| 14963 | | |
| 14964 | | > save fig1.jpg |
| 14965 | | |
| 14966 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 14967 | | |
| 14968 | | > sel-ca |
| 14969 | | |
| 14970 | | 13 atoms, 1 model selected |
| 14971 | | 26 atoms, 2 models selected |
| 14972 | | |
| 14973 | | > display sel-residues |
| 14974 | | |
| 14975 | | > color ~C byatom |
| 14976 | | |
| 14977 | | > style stick |
| 14978 | | |
| 14979 | | Changed 4099 atom styles |
| 14980 | | |
| 14981 | | > view #1:138 :< 5 pad -1 |
| 14982 | | |
| 14983 | | > hbonds #1:138 & #1 name hb1 color green |
| 14984 | | |
| 14985 | | 3 hydrogen bonds found |
| 14986 | | |
| 14987 | | > hbonds #2:176 & #2 name hb2 color tan |
| 14988 | | |
| 14989 | | 4 hydrogen bonds found |
| 14990 | | |
| 14991 | | > transparency 90 target r |
| 14992 | | |
| 14993 | | > label #1:138 #2:176 offset 1,-1,1 |
| 14994 | | |
| 14995 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 14996 | | |
| 14997 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 14998 | | |
| 14999 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 15000 | | > bgColor white offset 0,0,0 |
| 15001 | | |
| 15002 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 15003 | | > bgColor white offset 0,0.7,0 |
| 15004 | | |
| 15005 | | > ~select |
| 15006 | | |
| 15007 | | Nothing selected |
| 15008 | | |
| 15009 | | > save fig2.jpg |
| 15010 | | |
| 15011 | | > sel-ca |
| 15012 | | |
| 15013 | | 13 atoms, 1 model selected |
| 15014 | | 26 atoms, 2 models selected |
| 15015 | | |
| 15016 | | > ~ribbon |
| 15017 | | |
| 15018 | | > size stickRadius 0.05 |
| 15019 | | |
| 15020 | | Changed 4167 bond radii |
| 15021 | | |
| 15022 | | > size #1:138 stickRadius 0.2 |
| 15023 | | |
| 15024 | | Changed 7 bond radii |
| 15025 | | |
| 15026 | | > size #2:176 stickRadius 0.2 |
| 15027 | | |
| 15028 | | Changed 7 bond radii |
| 15029 | | |
| 15030 | | > view sel-residues pad -1 |
| 15031 | | |
| 15032 | | > ~select |
| 15033 | | |
| 15034 | | Nothing selected |
| 15035 | | |
| 15036 | | > save fig3.jpg |
| 15037 | | |
| 15038 | | > sel-ca |
| 15039 | | |
| 15040 | | 13 atoms, 1 model selected |
| 15041 | | 26 atoms, 2 models selected |
| 15042 | | |
| 15043 | | > label sel-residues & #1 height 0.4 offset 0,1,0 color green bgColor white |
| 15044 | | |
| 15045 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 15046 | | |
| 15047 | | > view sel-residues pad -1 |
| 15048 | | |
| 15049 | | > sel-ca |
| 15050 | | |
| 15051 | | 13 atoms, 1 model selected |
| 15052 | | 26 atoms, 2 models selected |
| 15053 | | |
| 15054 | | > align #2 & sel toAtoms #1 & sel |
| 15055 | | |
| 15056 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 15057 | | |
| 15058 | | > ~select |
| 15059 | | |
| 15060 | | Nothing selected |
| 15061 | | |
| 15062 | | > save fig4.jpg |
| 15063 | | |
| 15064 | | > sel-ca |
| 15065 | | |
| 15066 | | 13 atoms, 1 model selected |
| 15067 | | 26 atoms, 2 models selected |
| 15068 | | |
| 15069 | | > ribbon sel |
| 15070 | | |
| 15071 | | > ~select |
| 15072 | | |
| 15073 | | Nothing selected |
| 15074 | | |
| 15075 | | > save fig5.jpg |
| 15076 | | |
| 15077 | | executed script.view.cxc |
| 15078 | | |
| 15079 | | > open "/Users/admin/Dropbox (Technion |
| 15080 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 15081 | | |
| 15082 | | > close |
| 15083 | | |
| 15084 | | > graphics bgColor white |
| 15085 | | |
| 15086 | | > open 1WMB |
| 15087 | | |
| 15088 | | 1wmb title: |
| 15089 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 15090 | | info...] |
| 15091 | | |
| 15092 | | Chain information for 1wmb #1 |
| 15093 | | --- |
| 15094 | | Chain | Description |
| 15095 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 15096 | | |
| 15097 | | Non-standard residues in 1wmb #1 |
| 15098 | | --- |
| 15099 | | CAC — cacodylate ion (dimethylarsinate) |
| 15100 | | MG — magnesium ion |
| 15101 | | |
| 15102 | | 1wmb mmCIF Assemblies |
| 15103 | | --- |
| 15104 | | 1| author_and_software_defined_assembly |
| 15105 | | |
| 15106 | | |
| 15107 | | > open 3I3O |
| 15108 | | |
| 15109 | | 3i3o title: |
| 15110 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 15111 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 15112 | | info...] |
| 15113 | | |
| 15114 | | Chain information for 3i3o #2 |
| 15115 | | --- |
| 15116 | | Chain | Description |
| 15117 | | A B C D E F G H | Short chain dehydrogenase |
| 15118 | | |
| 15119 | | Non-standard residues in 3i3o #2 |
| 15120 | | --- |
| 15121 | | CAC — cacodylate ion (dimethylarsinate) |
| 15122 | | CL — chloride ion |
| 15123 | | MG — magnesium ion |
| 15124 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 15125 | | |
| 15126 | | 3i3o mmCIF Assemblies |
| 15127 | | --- |
| 15128 | | 1| author_and_software_defined_assembly |
| 15129 | | 2| author_and_software_defined_assembly |
| 15130 | | |
| 15131 | | |
| 15132 | | > delete ~/a |
| 15133 | | |
| 15134 | | > delete solvent |
| 15135 | | |
| 15136 | | > mmaker #2 to #1 |
| 15137 | | |
| 15138 | | Parameters |
| 15139 | | --- |
| 15140 | | Chain pairing | bb |
| 15141 | | Alignment algorithm | Needleman-Wunsch |
| 15142 | | Similarity matrix | BLOSUM-62 |
| 15143 | | SS fraction | 0.3 |
| 15144 | | Gap open (HH/SS/other) | 18/18/6 |
| 15145 | | Gap extend | 1 |
| 15146 | | SS matrix | | | H | S | O |
| 15147 | | ---|---|---|--- |
| 15148 | | H | 6 | -9 | -6 |
| 15149 | | S | | 6 | -6 |
| 15150 | | O | | | 4 |
| 15151 | | Iteration cutoff | 2 |
| 15152 | | |
| 15153 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 15154 | | score = 499.7 |
| 15155 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 15156 | | 3.736) |
| 15157 | | |
| 15158 | | |
| 15159 | | > color #1 green |
| 15160 | | |
| 15161 | | > color #2 tan |
| 15162 | | |
| 15163 | | > color ~C byatom |
| 15164 | | |
| 15165 | | > ~display |
| 15166 | | |
| 15167 | | > display #1:138 #2:176 |
| 15168 | | |
| 15169 | | > style stick |
| 15170 | | |
| 15171 | | Changed 4099 atom styles |
| 15172 | | |
| 15173 | | > ribbon |
| 15174 | | |
| 15175 | | > transparency 60 target r |
| 15176 | | |
| 15177 | | > view |
| 15178 | | |
| 15179 | | > size #1:138 #2:176 stickRadius 0.3 |
| 15180 | | |
| 15181 | | Changed 14 bond radii |
| 15182 | | |
| 15183 | | > save fig1.jpg |
| 15184 | | |
| 15185 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 15186 | | |
| 15187 | | > sel-ca |
| 15188 | | |
| 15189 | | 13 atoms, 1 model selected |
| 15190 | | 26 atoms, 2 models selected |
| 15191 | | |
| 15192 | | > display sel-residues |
| 15193 | | |
| 15194 | | > color ~C byatom |
| 15195 | | |
| 15196 | | > style stick |
| 15197 | | |
| 15198 | | Changed 4099 atom styles |
| 15199 | | |
| 15200 | | > view #1:138 :< 5 pad -1 |
| 15201 | | |
| 15202 | | > hbonds #1:138 & #1 name hb1 color green |
| 15203 | | |
| 15204 | | 3 hydrogen bonds found |
| 15205 | | |
| 15206 | | > hbonds #2:176 & #2 name hb2 color tan |
| 15207 | | |
| 15208 | | 4 hydrogen bonds found |
| 15209 | | |
| 15210 | | > transparency 90 target r |
| 15211 | | |
| 15212 | | > label #1:138 #2:176 offset 1,-1,1 |
| 15213 | | |
| 15214 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 15215 | | |
| 15216 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 15217 | | |
| 15218 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 15219 | | > bgColor white offset 0,0,0 |
| 15220 | | |
| 15221 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 15222 | | > bgColor white offset 0,0.7,0 |
| 15223 | | |
| 15224 | | > ~select |
| 15225 | | |
| 15226 | | Nothing selected |
| 15227 | | |
| 15228 | | > save fig2.jpg |
| 15229 | | |
| 15230 | | > sel-ca |
| 15231 | | |
| 15232 | | 13 atoms, 1 model selected |
| 15233 | | 26 atoms, 2 models selected |
| 15234 | | |
| 15235 | | > ~ribbon |
| 15236 | | |
| 15237 | | > size stickRadius 0.05 |
| 15238 | | |
| 15239 | | Changed 4167 bond radii |
| 15240 | | |
| 15241 | | > size #1:138 stickRadius 0.2 |
| 15242 | | |
| 15243 | | Changed 7 bond radii |
| 15244 | | |
| 15245 | | > size #2:176 stickRadius 0.2 |
| 15246 | | |
| 15247 | | Changed 7 bond radii |
| 15248 | | |
| 15249 | | > view sel-residues pad -1 |
| 15250 | | |
| 15251 | | > ~select |
| 15252 | | |
| 15253 | | Nothing selected |
| 15254 | | |
| 15255 | | > save fig3.jpg |
| 15256 | | |
| 15257 | | > sel-ca |
| 15258 | | |
| 15259 | | 13 atoms, 1 model selected |
| 15260 | | 26 atoms, 2 models selected |
| 15261 | | |
| 15262 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 15263 | | |
| 15264 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 15265 | | |
| 15266 | | > view sel-residues pad -1 |
| 15267 | | |
| 15268 | | > sel-ca |
| 15269 | | |
| 15270 | | 13 atoms, 1 model selected |
| 15271 | | 26 atoms, 2 models selected |
| 15272 | | |
| 15273 | | > align #2 & sel toAtoms #1 & sel |
| 15274 | | |
| 15275 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 15276 | | |
| 15277 | | > ~select |
| 15278 | | |
| 15279 | | Nothing selected |
| 15280 | | |
| 15281 | | > save fig4.jpg |
| 15282 | | |
| 15283 | | > sel-ca |
| 15284 | | |
| 15285 | | 13 atoms, 1 model selected |
| 15286 | | 26 atoms, 2 models selected |
| 15287 | | |
| 15288 | | > ribbon sel |
| 15289 | | |
| 15290 | | > ~select |
| 15291 | | |
| 15292 | | Nothing selected |
| 15293 | | |
| 15294 | | > save fig5.jpg |
| 15295 | | |
| 15296 | | executed script.view.cxc |
| 15297 | | |
| 15298 | | > open "/Users/admin/Dropbox (Technion |
| 15299 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 15300 | | |
| 15301 | | > close |
| 15302 | | |
| 15303 | | > graphics bgColor white |
| 15304 | | |
| 15305 | | > open 1WMB |
| 15306 | | |
| 15307 | | 1wmb title: |
| 15308 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 15309 | | info...] |
| 15310 | | |
| 15311 | | Chain information for 1wmb #1 |
| 15312 | | --- |
| 15313 | | Chain | Description |
| 15314 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 15315 | | |
| 15316 | | Non-standard residues in 1wmb #1 |
| 15317 | | --- |
| 15318 | | CAC — cacodylate ion (dimethylarsinate) |
| 15319 | | MG — magnesium ion |
| 15320 | | |
| 15321 | | 1wmb mmCIF Assemblies |
| 15322 | | --- |
| 15323 | | 1| author_and_software_defined_assembly |
| 15324 | | |
| 15325 | | |
| 15326 | | > open 3I3O |
| 15327 | | |
| 15328 | | 3i3o title: |
| 15329 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 15330 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 15331 | | info...] |
| 15332 | | |
| 15333 | | Chain information for 3i3o #2 |
| 15334 | | --- |
| 15335 | | Chain | Description |
| 15336 | | A B C D E F G H | Short chain dehydrogenase |
| 15337 | | |
| 15338 | | Non-standard residues in 3i3o #2 |
| 15339 | | --- |
| 15340 | | CAC — cacodylate ion (dimethylarsinate) |
| 15341 | | CL — chloride ion |
| 15342 | | MG — magnesium ion |
| 15343 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 15344 | | |
| 15345 | | 3i3o mmCIF Assemblies |
| 15346 | | --- |
| 15347 | | 1| author_and_software_defined_assembly |
| 15348 | | 2| author_and_software_defined_assembly |
| 15349 | | |
| 15350 | | |
| 15351 | | > delete ~/a |
| 15352 | | |
| 15353 | | > delete solvent |
| 15354 | | |
| 15355 | | > mmaker #2 to #1 |
| 15356 | | |
| 15357 | | Parameters |
| 15358 | | --- |
| 15359 | | Chain pairing | bb |
| 15360 | | Alignment algorithm | Needleman-Wunsch |
| 15361 | | Similarity matrix | BLOSUM-62 |
| 15362 | | SS fraction | 0.3 |
| 15363 | | Gap open (HH/SS/other) | 18/18/6 |
| 15364 | | Gap extend | 1 |
| 15365 | | SS matrix | | | H | S | O |
| 15366 | | ---|---|---|--- |
| 15367 | | H | 6 | -9 | -6 |
| 15368 | | S | | 6 | -6 |
| 15369 | | O | | | 4 |
| 15370 | | Iteration cutoff | 2 |
| 15371 | | |
| 15372 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 15373 | | score = 499.7 |
| 15374 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 15375 | | 3.736) |
| 15376 | | |
| 15377 | | |
| 15378 | | > color #1 green |
| 15379 | | |
| 15380 | | > color #2 tan |
| 15381 | | |
| 15382 | | > color ~C byatom |
| 15383 | | |
| 15384 | | > ~display |
| 15385 | | |
| 15386 | | > display #1:138 #2:176 |
| 15387 | | |
| 15388 | | > style stick |
| 15389 | | |
| 15390 | | Changed 4099 atom styles |
| 15391 | | |
| 15392 | | > ribbon |
| 15393 | | |
| 15394 | | > transparency 60 target r |
| 15395 | | |
| 15396 | | > view |
| 15397 | | |
| 15398 | | > size #1:138 #2:176 stickRadius 0.3 |
| 15399 | | |
| 15400 | | Changed 14 bond radii |
| 15401 | | |
| 15402 | | > save fig1.jpg |
| 15403 | | |
| 15404 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 15405 | | |
| 15406 | | > sel-ca |
| 15407 | | |
| 15408 | | 13 atoms, 1 model selected |
| 15409 | | 26 atoms, 2 models selected |
| 15410 | | |
| 15411 | | > display sel-residues |
| 15412 | | |
| 15413 | | > color ~C byatom |
| 15414 | | |
| 15415 | | > style stick |
| 15416 | | |
| 15417 | | Changed 4099 atom styles |
| 15418 | | |
| 15419 | | > view #1:138 :< 5 pad -1 |
| 15420 | | |
| 15421 | | > hbonds #1:138 & #1 name hb1 color green |
| 15422 | | |
| 15423 | | 3 hydrogen bonds found |
| 15424 | | |
| 15425 | | > hbonds #2:176 & #2 name hb2 color tan |
| 15426 | | |
| 15427 | | 4 hydrogen bonds found |
| 15428 | | |
| 15429 | | > transparency 90 target r |
| 15430 | | |
| 15431 | | > label #1:138 #2:176 offset 1,-1,1 |
| 15432 | | |
| 15433 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 15434 | | |
| 15435 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 15436 | | |
| 15437 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 15438 | | > bgColor white offset 0,0,0 |
| 15439 | | |
| 15440 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 15441 | | > bgColor white offset 0,0.7,0 |
| 15442 | | |
| 15443 | | > ~select |
| 15444 | | |
| 15445 | | Nothing selected |
| 15446 | | |
| 15447 | | > save fig2.jpg |
| 15448 | | |
| 15449 | | > sel-ca |
| 15450 | | |
| 15451 | | 13 atoms, 1 model selected |
| 15452 | | 26 atoms, 2 models selected |
| 15453 | | |
| 15454 | | > ~ribbon |
| 15455 | | |
| 15456 | | > size stickRadius 0.05 |
| 15457 | | |
| 15458 | | Changed 4167 bond radii |
| 15459 | | |
| 15460 | | > size #1:138 stickRadius 0.2 |
| 15461 | | |
| 15462 | | Changed 7 bond radii |
| 15463 | | |
| 15464 | | > size #2:176 stickRadius 0.2 |
| 15465 | | |
| 15466 | | Changed 7 bond radii |
| 15467 | | |
| 15468 | | > view sel-residues pad -1 |
| 15469 | | |
| 15470 | | > ~select |
| 15471 | | |
| 15472 | | Nothing selected |
| 15473 | | |
| 15474 | | > save fig3.jpg |
| 15475 | | |
| 15476 | | > sel-ca |
| 15477 | | |
| 15478 | | 13 atoms, 1 model selected |
| 15479 | | 26 atoms, 2 models selected |
| 15480 | | |
| 15481 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 15482 | | |
| 15483 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 15484 | | |
| 15485 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 15486 | | > bgColor white offset 0,0,0 |
| 15487 | | |
| 15488 | | > view sel-residues pad -1 |
| 15489 | | |
| 15490 | | > sel-ca |
| 15491 | | |
| 15492 | | 13 atoms, 1 model selected |
| 15493 | | 26 atoms, 2 models selected |
| 15494 | | |
| 15495 | | > align #2 & sel toAtoms #1 & sel |
| 15496 | | |
| 15497 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 15498 | | |
| 15499 | | > ~select |
| 15500 | | |
| 15501 | | Nothing selected |
| 15502 | | |
| 15503 | | > save fig4.jpg |
| 15504 | | |
| 15505 | | > sel-ca |
| 15506 | | |
| 15507 | | 13 atoms, 1 model selected |
| 15508 | | 26 atoms, 2 models selected |
| 15509 | | |
| 15510 | | > ribbon sel |
| 15511 | | |
| 15512 | | > ~select |
| 15513 | | |
| 15514 | | Nothing selected |
| 15515 | | |
| 15516 | | > save fig5.jpg |
| 15517 | | |
| 15518 | | executed script.view.cxc |
| 15519 | | |
| 15520 | | > open "/Users/admin/Dropbox (Technion |
| 15521 | | > Dropbox)/PROJECTS/alexB/chimerax/fig5.jpg" |
| 15522 | | |
| 15523 | | Unrecognized file suffix '.jpg' |
| 15524 | | |
| 15525 | | > open "/Users/admin/Dropbox (Technion |
| 15526 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 15527 | | |
| 15528 | | > close |
| 15529 | | |
| 15530 | | > graphics bgColor white |
| 15531 | | |
| 15532 | | > open 1WMB |
| 15533 | | |
| 15534 | | 1wmb title: |
| 15535 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 15536 | | info...] |
| 15537 | | |
| 15538 | | Chain information for 1wmb #1 |
| 15539 | | --- |
| 15540 | | Chain | Description |
| 15541 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 15542 | | |
| 15543 | | Non-standard residues in 1wmb #1 |
| 15544 | | --- |
| 15545 | | CAC — cacodylate ion (dimethylarsinate) |
| 15546 | | MG — magnesium ion |
| 15547 | | |
| 15548 | | 1wmb mmCIF Assemblies |
| 15549 | | --- |
| 15550 | | 1| author_and_software_defined_assembly |
| 15551 | | |
| 15552 | | |
| 15553 | | > open 3I3O |
| 15554 | | |
| 15555 | | 3i3o title: |
| 15556 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 15557 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 15558 | | info...] |
| 15559 | | |
| 15560 | | Chain information for 3i3o #2 |
| 15561 | | --- |
| 15562 | | Chain | Description |
| 15563 | | A B C D E F G H | Short chain dehydrogenase |
| 15564 | | |
| 15565 | | Non-standard residues in 3i3o #2 |
| 15566 | | --- |
| 15567 | | CAC — cacodylate ion (dimethylarsinate) |
| 15568 | | CL — chloride ion |
| 15569 | | MG — magnesium ion |
| 15570 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 15571 | | |
| 15572 | | 3i3o mmCIF Assemblies |
| 15573 | | --- |
| 15574 | | 1| author_and_software_defined_assembly |
| 15575 | | 2| author_and_software_defined_assembly |
| 15576 | | |
| 15577 | | |
| 15578 | | > delete ~/a |
| 15579 | | |
| 15580 | | > delete solvent |
| 15581 | | |
| 15582 | | > mmaker #2 to #1 |
| 15583 | | |
| 15584 | | Parameters |
| 15585 | | --- |
| 15586 | | Chain pairing | bb |
| 15587 | | Alignment algorithm | Needleman-Wunsch |
| 15588 | | Similarity matrix | BLOSUM-62 |
| 15589 | | SS fraction | 0.3 |
| 15590 | | Gap open (HH/SS/other) | 18/18/6 |
| 15591 | | Gap extend | 1 |
| 15592 | | SS matrix | | | H | S | O |
| 15593 | | ---|---|---|--- |
| 15594 | | H | 6 | -9 | -6 |
| 15595 | | S | | 6 | -6 |
| 15596 | | O | | | 4 |
| 15597 | | Iteration cutoff | 2 |
| 15598 | | |
| 15599 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 15600 | | score = 499.7 |
| 15601 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 15602 | | 3.736) |
| 15603 | | |
| 15604 | | |
| 15605 | | > color #1 green |
| 15606 | | |
| 15607 | | > color #2 tan |
| 15608 | | |
| 15609 | | > color ~C byatom |
| 15610 | | |
| 15611 | | > ~display |
| 15612 | | |
| 15613 | | > display #1:138 #2:176 |
| 15614 | | |
| 15615 | | > style stick |
| 15616 | | |
| 15617 | | Changed 4099 atom styles |
| 15618 | | |
| 15619 | | > ribbon |
| 15620 | | |
| 15621 | | > transparency 60 target r |
| 15622 | | |
| 15623 | | > view |
| 15624 | | |
| 15625 | | > size #1:138 #2:176 stickRadius 0.3 |
| 15626 | | |
| 15627 | | Changed 14 bond radii |
| 15628 | | |
| 15629 | | > save fig1.jpg |
| 15630 | | |
| 15631 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 15632 | | |
| 15633 | | > sel-ca |
| 15634 | | |
| 15635 | | 13 atoms, 1 model selected |
| 15636 | | 26 atoms, 2 models selected |
| 15637 | | |
| 15638 | | > display sel-residues |
| 15639 | | |
| 15640 | | > color ~C byatom |
| 15641 | | |
| 15642 | | > style stick |
| 15643 | | |
| 15644 | | Changed 4099 atom styles |
| 15645 | | |
| 15646 | | > view #1:138 :< 5 pad -1 |
| 15647 | | |
| 15648 | | > hbonds #1:138 & #1 name hb1 color green |
| 15649 | | |
| 15650 | | 3 hydrogen bonds found |
| 15651 | | |
| 15652 | | > hbonds #2:176 & #2 name hb2 color tan |
| 15653 | | |
| 15654 | | 4 hydrogen bonds found |
| 15655 | | |
| 15656 | | > transparency 90 target r |
| 15657 | | |
| 15658 | | > label #1:138 #2:176 offset 1,-1,1 |
| 15659 | | |
| 15660 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 15661 | | |
| 15662 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 15663 | | |
| 15664 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 15665 | | > bgColor white offset 0,0,0 |
| 15666 | | |
| 15667 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 15668 | | > bgColor white offset 0,0.7,0 |
| 15669 | | |
| 15670 | | > ~select |
| 15671 | | |
| 15672 | | Nothing selected |
| 15673 | | |
| 15674 | | > save fig2.jpg |
| 15675 | | |
| 15676 | | > sel-ca |
| 15677 | | |
| 15678 | | 13 atoms, 1 model selected |
| 15679 | | 26 atoms, 2 models selected |
| 15680 | | |
| 15681 | | > ~ribbon |
| 15682 | | |
| 15683 | | > size stickRadius 0.05 |
| 15684 | | |
| 15685 | | Changed 4167 bond radii |
| 15686 | | |
| 15687 | | > size #1:138 stickRadius 0.2 |
| 15688 | | |
| 15689 | | Changed 7 bond radii |
| 15690 | | |
| 15691 | | > size #2:176 stickRadius 0.2 |
| 15692 | | |
| 15693 | | Changed 7 bond radii |
| 15694 | | |
| 15695 | | > view sel-residues pad -1 |
| 15696 | | |
| 15697 | | > ~select |
| 15698 | | |
| 15699 | | Nothing selected |
| 15700 | | |
| 15701 | | > save fig3.jpg |
| 15702 | | |
| 15703 | | > sel-ca |
| 15704 | | |
| 15705 | | 13 atoms, 1 model selected |
| 15706 | | 26 atoms, 2 models selected |
| 15707 | | |
| 15708 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 15709 | | |
| 15710 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 15711 | | |
| 15712 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 15713 | | > bgColor white offset 0,0,0 |
| 15714 | | |
| 15715 | | > view sel-residues pad -1 |
| 15716 | | |
| 15717 | | > sel-ca |
| 15718 | | |
| 15719 | | 13 atoms, 1 model selected |
| 15720 | | 26 atoms, 2 models selected |
| 15721 | | |
| 15722 | | > align #2 & sel toAtoms #1 & sel |
| 15723 | | |
| 15724 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 15725 | | |
| 15726 | | > ~select |
| 15727 | | |
| 15728 | | Nothing selected |
| 15729 | | |
| 15730 | | > save fig4.jpg |
| 15731 | | |
| 15732 | | > sel-ca |
| 15733 | | |
| 15734 | | 13 atoms, 1 model selected |
| 15735 | | 26 atoms, 2 models selected |
| 15736 | | |
| 15737 | | > ribbon sel |
| 15738 | | |
| 15739 | | > ~select |
| 15740 | | |
| 15741 | | Nothing selected |
| 15742 | | |
| 15743 | | > save fig5.jpg |
| 15744 | | |
| 15745 | | executed script.view.cxc |
| 15746 | | |
| 15747 | | > open "/Users/admin/Dropbox (Technion |
| 15748 | | > Dropbox)/PROJECTS/alexB/chimerax/fig5.jpg" |
| 15749 | | |
| 15750 | | Unrecognized file suffix '.jpg' |
| 15751 | | |
| 15752 | | > open "/Users/admin/Dropbox (Technion |
| 15753 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 15754 | | |
| 15755 | | > close |
| 15756 | | |
| 15757 | | > graphics bgColor white |
| 15758 | | |
| 15759 | | > open 1WMB |
| 15760 | | |
| 15761 | | 1wmb title: |
| 15762 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 15763 | | info...] |
| 15764 | | |
| 15765 | | Chain information for 1wmb #1 |
| 15766 | | --- |
| 15767 | | Chain | Description |
| 15768 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 15769 | | |
| 15770 | | Non-standard residues in 1wmb #1 |
| 15771 | | --- |
| 15772 | | CAC — cacodylate ion (dimethylarsinate) |
| 15773 | | MG — magnesium ion |
| 15774 | | |
| 15775 | | 1wmb mmCIF Assemblies |
| 15776 | | --- |
| 15777 | | 1| author_and_software_defined_assembly |
| 15778 | | |
| 15779 | | |
| 15780 | | > open 3I3O |
| 15781 | | |
| 15782 | | 3i3o title: |
| 15783 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 15784 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 15785 | | info...] |
| 15786 | | |
| 15787 | | Chain information for 3i3o #2 |
| 15788 | | --- |
| 15789 | | Chain | Description |
| 15790 | | A B C D E F G H | Short chain dehydrogenase |
| 15791 | | |
| 15792 | | Non-standard residues in 3i3o #2 |
| 15793 | | --- |
| 15794 | | CAC — cacodylate ion (dimethylarsinate) |
| 15795 | | CL — chloride ion |
| 15796 | | MG — magnesium ion |
| 15797 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 15798 | | |
| 15799 | | 3i3o mmCIF Assemblies |
| 15800 | | --- |
| 15801 | | 1| author_and_software_defined_assembly |
| 15802 | | 2| author_and_software_defined_assembly |
| 15803 | | |
| 15804 | | |
| 15805 | | > delete ~/a |
| 15806 | | |
| 15807 | | > delete solvent |
| 15808 | | |
| 15809 | | > mmaker #2 to #1 |
| 15810 | | |
| 15811 | | Parameters |
| 15812 | | --- |
| 15813 | | Chain pairing | bb |
| 15814 | | Alignment algorithm | Needleman-Wunsch |
| 15815 | | Similarity matrix | BLOSUM-62 |
| 15816 | | SS fraction | 0.3 |
| 15817 | | Gap open (HH/SS/other) | 18/18/6 |
| 15818 | | Gap extend | 1 |
| 15819 | | SS matrix | | | H | S | O |
| 15820 | | ---|---|---|--- |
| 15821 | | H | 6 | -9 | -6 |
| 15822 | | S | | 6 | -6 |
| 15823 | | O | | | 4 |
| 15824 | | Iteration cutoff | 2 |
| 15825 | | |
| 15826 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 15827 | | score = 499.7 |
| 15828 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 15829 | | 3.736) |
| 15830 | | |
| 15831 | | |
| 15832 | | > color #1 green |
| 15833 | | |
| 15834 | | > color #2 tan |
| 15835 | | |
| 15836 | | > color ~C byatom |
| 15837 | | |
| 15838 | | > ~display |
| 15839 | | |
| 15840 | | > display #1:138 #2:176 |
| 15841 | | |
| 15842 | | > style stick |
| 15843 | | |
| 15844 | | Changed 4099 atom styles |
| 15845 | | |
| 15846 | | > ribbon |
| 15847 | | |
| 15848 | | > transparency 60 target r |
| 15849 | | |
| 15850 | | > view |
| 15851 | | |
| 15852 | | > size #1:138 #2:176 stickRadius 0.3 |
| 15853 | | |
| 15854 | | Changed 14 bond radii |
| 15855 | | |
| 15856 | | > save fig1.jpg |
| 15857 | | |
| 15858 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 15859 | | |
| 15860 | | > sel-ca |
| 15861 | | |
| 15862 | | 13 atoms, 1 model selected |
| 15863 | | 26 atoms, 2 models selected |
| 15864 | | |
| 15865 | | > display sel-residues |
| 15866 | | |
| 15867 | | > color ~C byatom |
| 15868 | | |
| 15869 | | > style stick |
| 15870 | | |
| 15871 | | Changed 4099 atom styles |
| 15872 | | |
| 15873 | | > view #1:138 :< 5 pad -1 |
| 15874 | | |
| 15875 | | > hbonds #1:138 & #1 name hb1 color green |
| 15876 | | |
| 15877 | | 3 hydrogen bonds found |
| 15878 | | |
| 15879 | | > hbonds #2:176 & #2 name hb2 color tan |
| 15880 | | |
| 15881 | | 4 hydrogen bonds found |
| 15882 | | |
| 15883 | | > transparency 90 target r |
| 15884 | | |
| 15885 | | > label #1:138 #2:176 offset 1,-1,1 |
| 15886 | | |
| 15887 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 15888 | | |
| 15889 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 15890 | | |
| 15891 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 15892 | | > bgColor white offset 0,0,0 |
| 15893 | | |
| 15894 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 15895 | | > bgColor white offset 0,0.7,0 |
| 15896 | | |
| 15897 | | > ~select |
| 15898 | | |
| 15899 | | Nothing selected |
| 15900 | | |
| 15901 | | > save fig2.jpg |
| 15902 | | |
| 15903 | | > sel-ca |
| 15904 | | |
| 15905 | | 13 atoms, 1 model selected |
| 15906 | | 26 atoms, 2 models selected |
| 15907 | | |
| 15908 | | > ~ribbon |
| 15909 | | |
| 15910 | | > size stickRadius 0.05 |
| 15911 | | |
| 15912 | | Changed 4167 bond radii |
| 15913 | | |
| 15914 | | > size #1:138 stickRadius 0.2 |
| 15915 | | |
| 15916 | | Changed 7 bond radii |
| 15917 | | |
| 15918 | | > size #2:176 stickRadius 0.2 |
| 15919 | | |
| 15920 | | Changed 7 bond radii |
| 15921 | | |
| 15922 | | > view sel-residues pad -1 |
| 15923 | | |
| 15924 | | > ~select |
| 15925 | | |
| 15926 | | Nothing selected |
| 15927 | | |
| 15928 | | > save fig3.jpg |
| 15929 | | |
| 15930 | | > sel-ca |
| 15931 | | |
| 15932 | | 13 atoms, 1 model selected |
| 15933 | | 26 atoms, 2 models selected |
| 15934 | | |
| 15935 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 15936 | | |
| 15937 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 15938 | | |
| 15939 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color green |
| 15940 | | > bgColor white offset 0,0,0 |
| 15941 | | |
| 15942 | | > view sel-residues pad -1 |
| 15943 | | |
| 15944 | | > sel-ca |
| 15945 | | |
| 15946 | | 13 atoms, 1 model selected |
| 15947 | | 26 atoms, 2 models selected |
| 15948 | | |
| 15949 | | > align #2 & sel toAtoms #1 & sel |
| 15950 | | |
| 15951 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 15952 | | |
| 15953 | | > ~select |
| 15954 | | |
| 15955 | | Nothing selected |
| 15956 | | |
| 15957 | | > save fig4.jpg |
| 15958 | | |
| 15959 | | > sel-ca |
| 15960 | | |
| 15961 | | 13 atoms, 1 model selected |
| 15962 | | 26 atoms, 2 models selected |
| 15963 | | |
| 15964 | | > ribbon sel |
| 15965 | | |
| 15966 | | > ~select |
| 15967 | | |
| 15968 | | Nothing selected |
| 15969 | | |
| 15970 | | > save fig5.jpg |
| 15971 | | |
| 15972 | | executed script.view.cxc |
| 15973 | | |
| 15974 | | > open "/Users/admin/Dropbox (Technion |
| 15975 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 15976 | | |
| 15977 | | > close |
| 15978 | | |
| 15979 | | > graphics bgColor white |
| 15980 | | |
| 15981 | | > open 1WMB |
| 15982 | | |
| 15983 | | 1wmb title: |
| 15984 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 15985 | | info...] |
| 15986 | | |
| 15987 | | Chain information for 1wmb #1 |
| 15988 | | --- |
| 15989 | | Chain | Description |
| 15990 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 15991 | | |
| 15992 | | Non-standard residues in 1wmb #1 |
| 15993 | | --- |
| 15994 | | CAC — cacodylate ion (dimethylarsinate) |
| 15995 | | MG — magnesium ion |
| 15996 | | |
| 15997 | | 1wmb mmCIF Assemblies |
| 15998 | | --- |
| 15999 | | 1| author_and_software_defined_assembly |
| 16000 | | |
| 16001 | | |
| 16002 | | > open 3I3O |
| 16003 | | |
| 16004 | | 3i3o title: |
| 16005 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 16006 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 16007 | | info...] |
| 16008 | | |
| 16009 | | Chain information for 3i3o #2 |
| 16010 | | --- |
| 16011 | | Chain | Description |
| 16012 | | A B C D E F G H | Short chain dehydrogenase |
| 16013 | | |
| 16014 | | Non-standard residues in 3i3o #2 |
| 16015 | | --- |
| 16016 | | CAC — cacodylate ion (dimethylarsinate) |
| 16017 | | CL — chloride ion |
| 16018 | | MG — magnesium ion |
| 16019 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 16020 | | |
| 16021 | | 3i3o mmCIF Assemblies |
| 16022 | | --- |
| 16023 | | 1| author_and_software_defined_assembly |
| 16024 | | 2| author_and_software_defined_assembly |
| 16025 | | |
| 16026 | | |
| 16027 | | > delete ~/a |
| 16028 | | |
| 16029 | | > delete solvent |
| 16030 | | |
| 16031 | | > mmaker #2 to #1 |
| 16032 | | |
| 16033 | | Parameters |
| 16034 | | --- |
| 16035 | | Chain pairing | bb |
| 16036 | | Alignment algorithm | Needleman-Wunsch |
| 16037 | | Similarity matrix | BLOSUM-62 |
| 16038 | | SS fraction | 0.3 |
| 16039 | | Gap open (HH/SS/other) | 18/18/6 |
| 16040 | | Gap extend | 1 |
| 16041 | | SS matrix | | | H | S | O |
| 16042 | | ---|---|---|--- |
| 16043 | | H | 6 | -9 | -6 |
| 16044 | | S | | 6 | -6 |
| 16045 | | O | | | 4 |
| 16046 | | Iteration cutoff | 2 |
| 16047 | | |
| 16048 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 16049 | | score = 499.7 |
| 16050 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 16051 | | 3.736) |
| 16052 | | |
| 16053 | | |
| 16054 | | > color #1 green |
| 16055 | | |
| 16056 | | > color #2 tan |
| 16057 | | |
| 16058 | | > color ~C byatom |
| 16059 | | |
| 16060 | | > ~display |
| 16061 | | |
| 16062 | | > display #1:138 #2:176 |
| 16063 | | |
| 16064 | | > style stick |
| 16065 | | |
| 16066 | | Changed 4099 atom styles |
| 16067 | | |
| 16068 | | > ribbon |
| 16069 | | |
| 16070 | | > transparency 60 target r |
| 16071 | | |
| 16072 | | > view |
| 16073 | | |
| 16074 | | > size #1:138 #2:176 stickRadius 0.3 |
| 16075 | | |
| 16076 | | Changed 14 bond radii |
| 16077 | | |
| 16078 | | > save fig1.jpg |
| 16079 | | |
| 16080 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 16081 | | |
| 16082 | | > sel-ca |
| 16083 | | |
| 16084 | | 13 atoms, 1 model selected |
| 16085 | | 26 atoms, 2 models selected |
| 16086 | | |
| 16087 | | > display sel-residues |
| 16088 | | |
| 16089 | | > color ~C byatom |
| 16090 | | |
| 16091 | | > style stick |
| 16092 | | |
| 16093 | | Changed 4099 atom styles |
| 16094 | | |
| 16095 | | > view #1:138 :< 5 pad -1 |
| 16096 | | |
| 16097 | | > hbonds #1:138 & #1 name hb1 color green |
| 16098 | | |
| 16099 | | 3 hydrogen bonds found |
| 16100 | | |
| 16101 | | > hbonds #2:176 & #2 name hb2 color tan |
| 16102 | | |
| 16103 | | 4 hydrogen bonds found |
| 16104 | | |
| 16105 | | > transparency 90 target r |
| 16106 | | |
| 16107 | | > label #1:138 #2:176 offset 1,-1,1 |
| 16108 | | |
| 16109 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 16110 | | |
| 16111 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 16112 | | |
| 16113 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 16114 | | > bgColor white offset 0,0.7,0 |
| 16115 | | |
| 16116 | | > ~select |
| 16117 | | |
| 16118 | | Nothing selected |
| 16119 | | |
| 16120 | | > save fig2.jpg |
| 16121 | | |
| 16122 | | > sel-ca |
| 16123 | | |
| 16124 | | 13 atoms, 1 model selected |
| 16125 | | 26 atoms, 2 models selected |
| 16126 | | |
| 16127 | | > ~ribbon |
| 16128 | | |
| 16129 | | > size stickRadius 0.05 |
| 16130 | | |
| 16131 | | Changed 4167 bond radii |
| 16132 | | |
| 16133 | | > size #1:138 stickRadius 0.2 |
| 16134 | | |
| 16135 | | Changed 7 bond radii |
| 16136 | | |
| 16137 | | > size #2:176 stickRadius 0.2 |
| 16138 | | |
| 16139 | | Changed 7 bond radii |
| 16140 | | |
| 16141 | | > view sel-residues pad -1 |
| 16142 | | |
| 16143 | | > ~select |
| 16144 | | |
| 16145 | | Nothing selected |
| 16146 | | |
| 16147 | | > save fig3.jpg |
| 16148 | | |
| 16149 | | > sel-ca |
| 16150 | | |
| 16151 | | 13 atoms, 1 model selected |
| 16152 | | 26 atoms, 2 models selected |
| 16153 | | |
| 16154 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 16155 | | |
| 16156 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 16157 | | |
| 16158 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f},{number} height 0.5 color |
| 16159 | | > green bgColor white offset 0,0,0 |
| 16160 | | |
| 16161 | | > view sel-residues pad -1 |
| 16162 | | |
| 16163 | | > sel-ca |
| 16164 | | |
| 16165 | | 13 atoms, 1 model selected |
| 16166 | | 26 atoms, 2 models selected |
| 16167 | | |
| 16168 | | > align #2 & sel toAtoms #1 & sel |
| 16169 | | |
| 16170 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 16171 | | |
| 16172 | | > ~select |
| 16173 | | |
| 16174 | | Nothing selected |
| 16175 | | |
| 16176 | | > save fig4.jpg |
| 16177 | | |
| 16178 | | > sel-ca |
| 16179 | | |
| 16180 | | 13 atoms, 1 model selected |
| 16181 | | 26 atoms, 2 models selected |
| 16182 | | |
| 16183 | | > ribbon sel |
| 16184 | | |
| 16185 | | > ~select |
| 16186 | | |
| 16187 | | Nothing selected |
| 16188 | | |
| 16189 | | > save fig5.jpg |
| 16190 | | |
| 16191 | | executed script.view.cxc |
| 16192 | | |
| 16193 | | > open "/Users/admin/Dropbox (Technion |
| 16194 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 16195 | | |
| 16196 | | > close |
| 16197 | | |
| 16198 | | > graphics bgColor white |
| 16199 | | |
| 16200 | | > open 1WMB |
| 16201 | | |
| 16202 | | 1wmb title: |
| 16203 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 16204 | | info...] |
| 16205 | | |
| 16206 | | Chain information for 1wmb #1 |
| 16207 | | --- |
| 16208 | | Chain | Description |
| 16209 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 16210 | | |
| 16211 | | Non-standard residues in 1wmb #1 |
| 16212 | | --- |
| 16213 | | CAC — cacodylate ion (dimethylarsinate) |
| 16214 | | MG — magnesium ion |
| 16215 | | |
| 16216 | | 1wmb mmCIF Assemblies |
| 16217 | | --- |
| 16218 | | 1| author_and_software_defined_assembly |
| 16219 | | |
| 16220 | | |
| 16221 | | > open 3I3O |
| 16222 | | |
| 16223 | | 3i3o title: |
| 16224 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 16225 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 16226 | | info...] |
| 16227 | | |
| 16228 | | Chain information for 3i3o #2 |
| 16229 | | --- |
| 16230 | | Chain | Description |
| 16231 | | A B C D E F G H | Short chain dehydrogenase |
| 16232 | | |
| 16233 | | Non-standard residues in 3i3o #2 |
| 16234 | | --- |
| 16235 | | CAC — cacodylate ion (dimethylarsinate) |
| 16236 | | CL — chloride ion |
| 16237 | | MG — magnesium ion |
| 16238 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 16239 | | |
| 16240 | | 3i3o mmCIF Assemblies |
| 16241 | | --- |
| 16242 | | 1| author_and_software_defined_assembly |
| 16243 | | 2| author_and_software_defined_assembly |
| 16244 | | |
| 16245 | | |
| 16246 | | > delete ~/a |
| 16247 | | |
| 16248 | | > delete solvent |
| 16249 | | |
| 16250 | | > mmaker #2 to #1 |
| 16251 | | |
| 16252 | | Parameters |
| 16253 | | --- |
| 16254 | | Chain pairing | bb |
| 16255 | | Alignment algorithm | Needleman-Wunsch |
| 16256 | | Similarity matrix | BLOSUM-62 |
| 16257 | | SS fraction | 0.3 |
| 16258 | | Gap open (HH/SS/other) | 18/18/6 |
| 16259 | | Gap extend | 1 |
| 16260 | | SS matrix | | | H | S | O |
| 16261 | | ---|---|---|--- |
| 16262 | | H | 6 | -9 | -6 |
| 16263 | | S | | 6 | -6 |
| 16264 | | O | | | 4 |
| 16265 | | Iteration cutoff | 2 |
| 16266 | | |
| 16267 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 16268 | | score = 499.7 |
| 16269 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 16270 | | 3.736) |
| 16271 | | |
| 16272 | | |
| 16273 | | > color #1 green |
| 16274 | | |
| 16275 | | > color #2 tan |
| 16276 | | |
| 16277 | | > color ~C byatom |
| 16278 | | |
| 16279 | | > ~display |
| 16280 | | |
| 16281 | | > display #1:138 #2:176 |
| 16282 | | |
| 16283 | | > style stick |
| 16284 | | |
| 16285 | | Changed 4099 atom styles |
| 16286 | | |
| 16287 | | > ribbon |
| 16288 | | |
| 16289 | | > transparency 60 target r |
| 16290 | | |
| 16291 | | > view |
| 16292 | | |
| 16293 | | > size #1:138 #2:176 stickRadius 0.3 |
| 16294 | | |
| 16295 | | Changed 14 bond radii |
| 16296 | | |
| 16297 | | > save fig1.jpg |
| 16298 | | |
| 16299 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 16300 | | |
| 16301 | | > sel-ca |
| 16302 | | |
| 16303 | | 13 atoms, 1 model selected |
| 16304 | | 26 atoms, 2 models selected |
| 16305 | | |
| 16306 | | > display sel-residues |
| 16307 | | |
| 16308 | | > color ~C byatom |
| 16309 | | |
| 16310 | | > style stick |
| 16311 | | |
| 16312 | | Changed 4099 atom styles |
| 16313 | | |
| 16314 | | > view #1:138 :< 5 pad -1 |
| 16315 | | |
| 16316 | | > hbonds #1:138 & #1 name hb1 color green |
| 16317 | | |
| 16318 | | 3 hydrogen bonds found |
| 16319 | | |
| 16320 | | > hbonds #2:176 & #2 name hb2 color tan |
| 16321 | | |
| 16322 | | 4 hydrogen bonds found |
| 16323 | | |
| 16324 | | > transparency 90 target r |
| 16325 | | |
| 16326 | | > label #1:138 #2:176 offset 1,-1,1 |
| 16327 | | |
| 16328 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 16329 | | |
| 16330 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 16331 | | |
| 16332 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 16333 | | > bgColor white offset 0,0.7,0 |
| 16334 | | |
| 16335 | | > ~select |
| 16336 | | |
| 16337 | | Nothing selected |
| 16338 | | |
| 16339 | | > save fig2.jpg |
| 16340 | | |
| 16341 | | > sel-ca |
| 16342 | | |
| 16343 | | 13 atoms, 1 model selected |
| 16344 | | 26 atoms, 2 models selected |
| 16345 | | |
| 16346 | | > ~ribbon |
| 16347 | | |
| 16348 | | > size stickRadius 0.05 |
| 16349 | | |
| 16350 | | Changed 4167 bond radii |
| 16351 | | |
| 16352 | | > size #1:138 stickRadius 0.2 |
| 16353 | | |
| 16354 | | Changed 7 bond radii |
| 16355 | | |
| 16356 | | > size #2:176 stickRadius 0.2 |
| 16357 | | |
| 16358 | | Changed 7 bond radii |
| 16359 | | |
| 16360 | | > view sel-residues pad -1 |
| 16361 | | |
| 16362 | | > ~select |
| 16363 | | |
| 16364 | | Nothing selected |
| 16365 | | |
| 16366 | | > save fig3.jpg |
| 16367 | | |
| 16368 | | > sel-ca |
| 16369 | | |
| 16370 | | 13 atoms, 1 model selected |
| 16371 | | 26 atoms, 2 models selected |
| 16372 | | |
| 16373 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 16374 | | |
| 16375 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 16376 | | |
| 16377 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f},{0.number} height 0.5 |
| 16378 | | > color green bgColor white offset 0,0,0 |
| 16379 | | |
| 16380 | | > view sel-residues pad -1 |
| 16381 | | |
| 16382 | | > sel-ca |
| 16383 | | |
| 16384 | | 13 atoms, 1 model selected |
| 16385 | | 26 atoms, 2 models selected |
| 16386 | | |
| 16387 | | > align #2 & sel toAtoms #1 & sel |
| 16388 | | |
| 16389 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 16390 | | |
| 16391 | | > ~select |
| 16392 | | |
| 16393 | | Nothing selected |
| 16394 | | |
| 16395 | | > save fig4.jpg |
| 16396 | | |
| 16397 | | > sel-ca |
| 16398 | | |
| 16399 | | 13 atoms, 1 model selected |
| 16400 | | 26 atoms, 2 models selected |
| 16401 | | |
| 16402 | | > ribbon sel |
| 16403 | | |
| 16404 | | > ~select |
| 16405 | | |
| 16406 | | Nothing selected |
| 16407 | | |
| 16408 | | > save fig5.jpg |
| 16409 | | |
| 16410 | | executed script.view.cxc |
| 16411 | | |
| 16412 | | > open "/Users/admin/Dropbox (Technion |
| 16413 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 16414 | | |
| 16415 | | > close |
| 16416 | | |
| 16417 | | > graphics bgColor white |
| 16418 | | |
| 16419 | | > open 1WMB |
| 16420 | | |
| 16421 | | 1wmb title: |
| 16422 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 16423 | | info...] |
| 16424 | | |
| 16425 | | Chain information for 1wmb #1 |
| 16426 | | --- |
| 16427 | | Chain | Description |
| 16428 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 16429 | | |
| 16430 | | Non-standard residues in 1wmb #1 |
| 16431 | | --- |
| 16432 | | CAC — cacodylate ion (dimethylarsinate) |
| 16433 | | MG — magnesium ion |
| 16434 | | |
| 16435 | | 1wmb mmCIF Assemblies |
| 16436 | | --- |
| 16437 | | 1| author_and_software_defined_assembly |
| 16438 | | |
| 16439 | | |
| 16440 | | > open 3I3O |
| 16441 | | |
| 16442 | | 3i3o title: |
| 16443 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 16444 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 16445 | | info...] |
| 16446 | | |
| 16447 | | Chain information for 3i3o #2 |
| 16448 | | --- |
| 16449 | | Chain | Description |
| 16450 | | A B C D E F G H | Short chain dehydrogenase |
| 16451 | | |
| 16452 | | Non-standard residues in 3i3o #2 |
| 16453 | | --- |
| 16454 | | CAC — cacodylate ion (dimethylarsinate) |
| 16455 | | CL — chloride ion |
| 16456 | | MG — magnesium ion |
| 16457 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 16458 | | |
| 16459 | | 3i3o mmCIF Assemblies |
| 16460 | | --- |
| 16461 | | 1| author_and_software_defined_assembly |
| 16462 | | 2| author_and_software_defined_assembly |
| 16463 | | |
| 16464 | | |
| 16465 | | > delete ~/a |
| 16466 | | |
| 16467 | | > delete solvent |
| 16468 | | |
| 16469 | | > mmaker #2 to #1 |
| 16470 | | |
| 16471 | | Parameters |
| 16472 | | --- |
| 16473 | | Chain pairing | bb |
| 16474 | | Alignment algorithm | Needleman-Wunsch |
| 16475 | | Similarity matrix | BLOSUM-62 |
| 16476 | | SS fraction | 0.3 |
| 16477 | | Gap open (HH/SS/other) | 18/18/6 |
| 16478 | | Gap extend | 1 |
| 16479 | | SS matrix | | | H | S | O |
| 16480 | | ---|---|---|--- |
| 16481 | | H | 6 | -9 | -6 |
| 16482 | | S | | 6 | -6 |
| 16483 | | O | | | 4 |
| 16484 | | Iteration cutoff | 2 |
| 16485 | | |
| 16486 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 16487 | | score = 499.7 |
| 16488 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 16489 | | 3.736) |
| 16490 | | |
| 16491 | | |
| 16492 | | > color #1 green |
| 16493 | | |
| 16494 | | > color #2 tan |
| 16495 | | |
| 16496 | | > color ~C byatom |
| 16497 | | |
| 16498 | | > ~display |
| 16499 | | |
| 16500 | | > display #1:138 #2:176 |
| 16501 | | |
| 16502 | | > style stick |
| 16503 | | |
| 16504 | | Changed 4099 atom styles |
| 16505 | | |
| 16506 | | > ribbon |
| 16507 | | |
| 16508 | | > transparency 60 target r |
| 16509 | | |
| 16510 | | > view |
| 16511 | | |
| 16512 | | > size #1:138 #2:176 stickRadius 0.3 |
| 16513 | | |
| 16514 | | Changed 14 bond radii |
| 16515 | | |
| 16516 | | > save fig1.jpg |
| 16517 | | |
| 16518 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 16519 | | |
| 16520 | | > sel-ca |
| 16521 | | |
| 16522 | | 13 atoms, 1 model selected |
| 16523 | | 26 atoms, 2 models selected |
| 16524 | | |
| 16525 | | > display sel-residues |
| 16526 | | |
| 16527 | | > color ~C byatom |
| 16528 | | |
| 16529 | | > style stick |
| 16530 | | |
| 16531 | | Changed 4099 atom styles |
| 16532 | | |
| 16533 | | > view #1:138 :< 5 pad -1 |
| 16534 | | |
| 16535 | | > hbonds #1:138 & #1 name hb1 color green |
| 16536 | | |
| 16537 | | 3 hydrogen bonds found |
| 16538 | | |
| 16539 | | > hbonds #2:176 & #2 name hb2 color tan |
| 16540 | | |
| 16541 | | 4 hydrogen bonds found |
| 16542 | | |
| 16543 | | > transparency 90 target r |
| 16544 | | |
| 16545 | | > label #1:138 #2:176 offset 1,-1,1 |
| 16546 | | |
| 16547 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 16548 | | |
| 16549 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 16550 | | |
| 16551 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 16552 | | > bgColor white offset 0,0.7,0 |
| 16553 | | |
| 16554 | | > ~select |
| 16555 | | |
| 16556 | | Nothing selected |
| 16557 | | |
| 16558 | | > save fig2.jpg |
| 16559 | | |
| 16560 | | > sel-ca |
| 16561 | | |
| 16562 | | 13 atoms, 1 model selected |
| 16563 | | 26 atoms, 2 models selected |
| 16564 | | |
| 16565 | | > ~ribbon |
| 16566 | | |
| 16567 | | > size stickRadius 0.05 |
| 16568 | | |
| 16569 | | Changed 4167 bond radii |
| 16570 | | |
| 16571 | | > size #1:138 stickRadius 0.2 |
| 16572 | | |
| 16573 | | Changed 7 bond radii |
| 16574 | | |
| 16575 | | > size #2:176 stickRadius 0.2 |
| 16576 | | |
| 16577 | | Changed 7 bond radii |
| 16578 | | |
| 16579 | | > view sel-residues pad -1 |
| 16580 | | |
| 16581 | | > ~select |
| 16582 | | |
| 16583 | | Nothing selected |
| 16584 | | |
| 16585 | | > save fig3.jpg |
| 16586 | | |
| 16587 | | > sel-ca |
| 16588 | | |
| 16589 | | 13 atoms, 1 model selected |
| 16590 | | 26 atoms, 2 models selected |
| 16591 | | |
| 16592 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 16593 | | |
| 16594 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 16595 | | |
| 16596 | | > label #1:138 residues text {0.phi:.1f},{0.psi:.1f},{0.number} height 1.5 |
| 16597 | | > color green bgColor white offset 0,0,0 |
| 16598 | | |
| 16599 | | > view sel-residues pad -1 |
| 16600 | | |
| 16601 | | > sel-ca |
| 16602 | | |
| 16603 | | 13 atoms, 1 model selected |
| 16604 | | 26 atoms, 2 models selected |
| 16605 | | |
| 16606 | | > align #2 & sel toAtoms #1 & sel |
| 16607 | | |
| 16608 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 16609 | | |
| 16610 | | > ~select |
| 16611 | | |
| 16612 | | Nothing selected |
| 16613 | | |
| 16614 | | > save fig4.jpg |
| 16615 | | |
| 16616 | | > sel-ca |
| 16617 | | |
| 16618 | | 13 atoms, 1 model selected |
| 16619 | | 26 atoms, 2 models selected |
| 16620 | | |
| 16621 | | > ribbon sel |
| 16622 | | |
| 16623 | | > ~select |
| 16624 | | |
| 16625 | | Nothing selected |
| 16626 | | |
| 16627 | | > save fig5.jpg |
| 16628 | | |
| 16629 | | executed script.view.cxc |
| 16630 | | |
| 16631 | | > open "/Users/admin/Dropbox (Technion |
| 16632 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 16633 | | |
| 16634 | | > close |
| 16635 | | |
| 16636 | | > graphics bgColor white |
| 16637 | | |
| 16638 | | > open 1WMB |
| 16639 | | |
| 16640 | | 1wmb title: |
| 16641 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 16642 | | info...] |
| 16643 | | |
| 16644 | | Chain information for 1wmb #1 |
| 16645 | | --- |
| 16646 | | Chain | Description |
| 16647 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 16648 | | |
| 16649 | | Non-standard residues in 1wmb #1 |
| 16650 | | --- |
| 16651 | | CAC — cacodylate ion (dimethylarsinate) |
| 16652 | | MG — magnesium ion |
| 16653 | | |
| 16654 | | 1wmb mmCIF Assemblies |
| 16655 | | --- |
| 16656 | | 1| author_and_software_defined_assembly |
| 16657 | | |
| 16658 | | |
| 16659 | | > open 3I3O |
| 16660 | | |
| 16661 | | 3i3o title: |
| 16662 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 16663 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 16664 | | info...] |
| 16665 | | |
| 16666 | | Chain information for 3i3o #2 |
| 16667 | | --- |
| 16668 | | Chain | Description |
| 16669 | | A B C D E F G H | Short chain dehydrogenase |
| 16670 | | |
| 16671 | | Non-standard residues in 3i3o #2 |
| 16672 | | --- |
| 16673 | | CAC — cacodylate ion (dimethylarsinate) |
| 16674 | | CL — chloride ion |
| 16675 | | MG — magnesium ion |
| 16676 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 16677 | | |
| 16678 | | 3i3o mmCIF Assemblies |
| 16679 | | --- |
| 16680 | | 1| author_and_software_defined_assembly |
| 16681 | | 2| author_and_software_defined_assembly |
| 16682 | | |
| 16683 | | |
| 16684 | | > delete ~/a |
| 16685 | | |
| 16686 | | > delete solvent |
| 16687 | | |
| 16688 | | > mmaker #2 to #1 |
| 16689 | | |
| 16690 | | Parameters |
| 16691 | | --- |
| 16692 | | Chain pairing | bb |
| 16693 | | Alignment algorithm | Needleman-Wunsch |
| 16694 | | Similarity matrix | BLOSUM-62 |
| 16695 | | SS fraction | 0.3 |
| 16696 | | Gap open (HH/SS/other) | 18/18/6 |
| 16697 | | Gap extend | 1 |
| 16698 | | SS matrix | | | H | S | O |
| 16699 | | ---|---|---|--- |
| 16700 | | H | 6 | -9 | -6 |
| 16701 | | S | | 6 | -6 |
| 16702 | | O | | | 4 |
| 16703 | | Iteration cutoff | 2 |
| 16704 | | |
| 16705 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 16706 | | score = 499.7 |
| 16707 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 16708 | | 3.736) |
| 16709 | | |
| 16710 | | |
| 16711 | | > color #1 green |
| 16712 | | |
| 16713 | | > color #2 tan |
| 16714 | | |
| 16715 | | > color ~C byatom |
| 16716 | | |
| 16717 | | > ~display |
| 16718 | | |
| 16719 | | > display #1:138 #2:176 |
| 16720 | | |
| 16721 | | > style stick |
| 16722 | | |
| 16723 | | Changed 4099 atom styles |
| 16724 | | |
| 16725 | | > ribbon |
| 16726 | | |
| 16727 | | > transparency 60 target r |
| 16728 | | |
| 16729 | | > view |
| 16730 | | |
| 16731 | | > size #1:138 #2:176 stickRadius 0.3 |
| 16732 | | |
| 16733 | | Changed 14 bond radii |
| 16734 | | |
| 16735 | | > save fig1.jpg |
| 16736 | | |
| 16737 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 16738 | | |
| 16739 | | > sel-ca |
| 16740 | | |
| 16741 | | 13 atoms, 1 model selected |
| 16742 | | 26 atoms, 2 models selected |
| 16743 | | |
| 16744 | | > display sel-residues |
| 16745 | | |
| 16746 | | > color ~C byatom |
| 16747 | | |
| 16748 | | > style stick |
| 16749 | | |
| 16750 | | Changed 4099 atom styles |
| 16751 | | |
| 16752 | | > view #1:138 :< 5 pad -1 |
| 16753 | | |
| 16754 | | > hbonds #1:138 & #1 name hb1 color green |
| 16755 | | |
| 16756 | | 3 hydrogen bonds found |
| 16757 | | |
| 16758 | | > hbonds #2:176 & #2 name hb2 color tan |
| 16759 | | |
| 16760 | | 4 hydrogen bonds found |
| 16761 | | |
| 16762 | | > transparency 90 target r |
| 16763 | | |
| 16764 | | > label #1:138 #2:176 offset 1,-1,1 |
| 16765 | | |
| 16766 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 16767 | | |
| 16768 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 16769 | | |
| 16770 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 16771 | | > bgColor white offset 0,0.7,0 |
| 16772 | | |
| 16773 | | > ~select |
| 16774 | | |
| 16775 | | Nothing selected |
| 16776 | | |
| 16777 | | > save fig2.jpg |
| 16778 | | |
| 16779 | | > sel-ca |
| 16780 | | |
| 16781 | | 13 atoms, 1 model selected |
| 16782 | | 26 atoms, 2 models selected |
| 16783 | | |
| 16784 | | > ~ribbon |
| 16785 | | |
| 16786 | | > size stickRadius 0.05 |
| 16787 | | |
| 16788 | | Changed 4167 bond radii |
| 16789 | | |
| 16790 | | > size #1:138 stickRadius 0.2 |
| 16791 | | |
| 16792 | | Changed 7 bond radii |
| 16793 | | |
| 16794 | | > size #2:176 stickRadius 0.2 |
| 16795 | | |
| 16796 | | Changed 7 bond radii |
| 16797 | | |
| 16798 | | > view sel-residues pad -1 |
| 16799 | | |
| 16800 | | > ~select |
| 16801 | | |
| 16802 | | Nothing selected |
| 16803 | | |
| 16804 | | > save fig3.jpg |
| 16805 | | |
| 16806 | | > sel-ca |
| 16807 | | |
| 16808 | | 13 atoms, 1 model selected |
| 16809 | | 26 atoms, 2 models selected |
| 16810 | | |
| 16811 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 16812 | | |
| 16813 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 16814 | | |
| 16815 | | > label #1:138 text {0.phi:.1f},{0.psi:.1f},{0.number} color green bgColor |
| 16816 | | > white offset 0,0,0 |
| 16817 | | |
| 16818 | | > view sel-residues pad -1 |
| 16819 | | |
| 16820 | | > sel-ca |
| 16821 | | |
| 16822 | | 13 atoms, 1 model selected |
| 16823 | | 26 atoms, 2 models selected |
| 16824 | | |
| 16825 | | > align #2 & sel toAtoms #1 & sel |
| 16826 | | |
| 16827 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 16828 | | |
| 16829 | | > ~select |
| 16830 | | |
| 16831 | | Nothing selected |
| 16832 | | |
| 16833 | | > save fig4.jpg |
| 16834 | | |
| 16835 | | > sel-ca |
| 16836 | | |
| 16837 | | 13 atoms, 1 model selected |
| 16838 | | 26 atoms, 2 models selected |
| 16839 | | |
| 16840 | | > ribbon sel |
| 16841 | | |
| 16842 | | > ~select |
| 16843 | | |
| 16844 | | Nothing selected |
| 16845 | | |
| 16846 | | > save fig5.jpg |
| 16847 | | |
| 16848 | | executed script.view.cxc |
| 16849 | | |
| 16850 | | > open "/Users/admin/Dropbox (Technion |
| 16851 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 16852 | | |
| 16853 | | > close |
| 16854 | | |
| 16855 | | > graphics bgColor white |
| 16856 | | |
| 16857 | | > open 1WMB |
| 16858 | | |
| 16859 | | 1wmb title: |
| 16860 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 16861 | | info...] |
| 16862 | | |
| 16863 | | Chain information for 1wmb #1 |
| 16864 | | --- |
| 16865 | | Chain | Description |
| 16866 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 16867 | | |
| 16868 | | Non-standard residues in 1wmb #1 |
| 16869 | | --- |
| 16870 | | CAC — cacodylate ion (dimethylarsinate) |
| 16871 | | MG — magnesium ion |
| 16872 | | |
| 16873 | | 1wmb mmCIF Assemblies |
| 16874 | | --- |
| 16875 | | 1| author_and_software_defined_assembly |
| 16876 | | |
| 16877 | | |
| 16878 | | > open 3I3O |
| 16879 | | |
| 16880 | | 3i3o title: |
| 16881 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 16882 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 16883 | | info...] |
| 16884 | | |
| 16885 | | Chain information for 3i3o #2 |
| 16886 | | --- |
| 16887 | | Chain | Description |
| 16888 | | A B C D E F G H | Short chain dehydrogenase |
| 16889 | | |
| 16890 | | Non-standard residues in 3i3o #2 |
| 16891 | | --- |
| 16892 | | CAC — cacodylate ion (dimethylarsinate) |
| 16893 | | CL — chloride ion |
| 16894 | | MG — magnesium ion |
| 16895 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 16896 | | |
| 16897 | | 3i3o mmCIF Assemblies |
| 16898 | | --- |
| 16899 | | 1| author_and_software_defined_assembly |
| 16900 | | 2| author_and_software_defined_assembly |
| 16901 | | |
| 16902 | | |
| 16903 | | > delete ~/a |
| 16904 | | |
| 16905 | | > delete solvent |
| 16906 | | |
| 16907 | | > mmaker #2 to #1 |
| 16908 | | |
| 16909 | | Parameters |
| 16910 | | --- |
| 16911 | | Chain pairing | bb |
| 16912 | | Alignment algorithm | Needleman-Wunsch |
| 16913 | | Similarity matrix | BLOSUM-62 |
| 16914 | | SS fraction | 0.3 |
| 16915 | | Gap open (HH/SS/other) | 18/18/6 |
| 16916 | | Gap extend | 1 |
| 16917 | | SS matrix | | | H | S | O |
| 16918 | | ---|---|---|--- |
| 16919 | | H | 6 | -9 | -6 |
| 16920 | | S | | 6 | -6 |
| 16921 | | O | | | 4 |
| 16922 | | Iteration cutoff | 2 |
| 16923 | | |
| 16924 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 16925 | | score = 499.7 |
| 16926 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 16927 | | 3.736) |
| 16928 | | |
| 16929 | | |
| 16930 | | > color #1 green |
| 16931 | | |
| 16932 | | > color #2 tan |
| 16933 | | |
| 16934 | | > color ~C byatom |
| 16935 | | |
| 16936 | | > ~display |
| 16937 | | |
| 16938 | | > display #1:138 #2:176 |
| 16939 | | |
| 16940 | | > style stick |
| 16941 | | |
| 16942 | | Changed 4099 atom styles |
| 16943 | | |
| 16944 | | > ribbon |
| 16945 | | |
| 16946 | | > transparency 60 target r |
| 16947 | | |
| 16948 | | > view |
| 16949 | | |
| 16950 | | > size #1:138 #2:176 stickRadius 0.3 |
| 16951 | | |
| 16952 | | Changed 14 bond radii |
| 16953 | | |
| 16954 | | > save fig1.jpg |
| 16955 | | |
| 16956 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 16957 | | |
| 16958 | | > sel-ca |
| 16959 | | |
| 16960 | | 13 atoms, 1 model selected |
| 16961 | | 26 atoms, 2 models selected |
| 16962 | | |
| 16963 | | > display sel-residues |
| 16964 | | |
| 16965 | | > color ~C byatom |
| 16966 | | |
| 16967 | | > style stick |
| 16968 | | |
| 16969 | | Changed 4099 atom styles |
| 16970 | | |
| 16971 | | > view #1:138 :< 5 pad -1 |
| 16972 | | |
| 16973 | | > hbonds #1:138 & #1 name hb1 color green |
| 16974 | | |
| 16975 | | 3 hydrogen bonds found |
| 16976 | | |
| 16977 | | > hbonds #2:176 & #2 name hb2 color tan |
| 16978 | | |
| 16979 | | 4 hydrogen bonds found |
| 16980 | | |
| 16981 | | > transparency 90 target r |
| 16982 | | |
| 16983 | | > label #1:138 #2:176 offset 1,-1,1 |
| 16984 | | |
| 16985 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 16986 | | |
| 16987 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 16988 | | |
| 16989 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 16990 | | > bgColor white offset 0,0.7,0 |
| 16991 | | |
| 16992 | | > ~select |
| 16993 | | |
| 16994 | | Nothing selected |
| 16995 | | |
| 16996 | | > save fig2.jpg |
| 16997 | | |
| 16998 | | > sel-ca |
| 16999 | | |
| 17000 | | 13 atoms, 1 model selected |
| 17001 | | 26 atoms, 2 models selected |
| 17002 | | |
| 17003 | | > ~ribbon |
| 17004 | | |
| 17005 | | > size stickRadius 0.05 |
| 17006 | | |
| 17007 | | Changed 4167 bond radii |
| 17008 | | |
| 17009 | | > size #1:138 stickRadius 0.2 |
| 17010 | | |
| 17011 | | Changed 7 bond radii |
| 17012 | | |
| 17013 | | > size #2:176 stickRadius 0.2 |
| 17014 | | |
| 17015 | | Changed 7 bond radii |
| 17016 | | |
| 17017 | | > view sel-residues pad -1 |
| 17018 | | |
| 17019 | | > ~select |
| 17020 | | |
| 17021 | | Nothing selected |
| 17022 | | |
| 17023 | | > save fig3.jpg |
| 17024 | | |
| 17025 | | > sel-ca |
| 17026 | | |
| 17027 | | 13 atoms, 1 model selected |
| 17028 | | 26 atoms, 2 models selected |
| 17029 | | |
| 17030 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 17031 | | |
| 17032 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 17033 | | |
| 17034 | | > label #1:138 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f},{0.number}" |
| 17035 | | > color green bgColor white offset 0,0,0 |
| 17036 | | |
| 17037 | | > view sel-residues pad -1 |
| 17038 | | |
| 17039 | | > sel-ca |
| 17040 | | |
| 17041 | | 13 atoms, 1 model selected |
| 17042 | | 26 atoms, 2 models selected |
| 17043 | | |
| 17044 | | > align #2 & sel toAtoms #1 & sel |
| 17045 | | |
| 17046 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 17047 | | |
| 17048 | | > ~select |
| 17049 | | |
| 17050 | | Nothing selected |
| 17051 | | |
| 17052 | | > save fig4.jpg |
| 17053 | | |
| 17054 | | > sel-ca |
| 17055 | | |
| 17056 | | 13 atoms, 1 model selected |
| 17057 | | 26 atoms, 2 models selected |
| 17058 | | |
| 17059 | | > ribbon sel |
| 17060 | | |
| 17061 | | > ~select |
| 17062 | | |
| 17063 | | Nothing selected |
| 17064 | | |
| 17065 | | > save fig5.jpg |
| 17066 | | |
| 17067 | | executed script.view.cxc |
| 17068 | | |
| 17069 | | > open "/Users/admin/Dropbox (Technion |
| 17070 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 17071 | | |
| 17072 | | > close |
| 17073 | | |
| 17074 | | > graphics bgColor white |
| 17075 | | |
| 17076 | | > open 1WMB |
| 17077 | | |
| 17078 | | 1wmb title: |
| 17079 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 17080 | | info...] |
| 17081 | | |
| 17082 | | Chain information for 1wmb #1 |
| 17083 | | --- |
| 17084 | | Chain | Description |
| 17085 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 17086 | | |
| 17087 | | Non-standard residues in 1wmb #1 |
| 17088 | | --- |
| 17089 | | CAC — cacodylate ion (dimethylarsinate) |
| 17090 | | MG — magnesium ion |
| 17091 | | |
| 17092 | | 1wmb mmCIF Assemblies |
| 17093 | | --- |
| 17094 | | 1| author_and_software_defined_assembly |
| 17095 | | |
| 17096 | | |
| 17097 | | > open 3I3O |
| 17098 | | |
| 17099 | | 3i3o title: |
| 17100 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 17101 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 17102 | | info...] |
| 17103 | | |
| 17104 | | Chain information for 3i3o #2 |
| 17105 | | --- |
| 17106 | | Chain | Description |
| 17107 | | A B C D E F G H | Short chain dehydrogenase |
| 17108 | | |
| 17109 | | Non-standard residues in 3i3o #2 |
| 17110 | | --- |
| 17111 | | CAC — cacodylate ion (dimethylarsinate) |
| 17112 | | CL — chloride ion |
| 17113 | | MG — magnesium ion |
| 17114 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 17115 | | |
| 17116 | | 3i3o mmCIF Assemblies |
| 17117 | | --- |
| 17118 | | 1| author_and_software_defined_assembly |
| 17119 | | 2| author_and_software_defined_assembly |
| 17120 | | |
| 17121 | | |
| 17122 | | > delete ~/a |
| 17123 | | |
| 17124 | | > delete solvent |
| 17125 | | |
| 17126 | | > mmaker #2 to #1 |
| 17127 | | |
| 17128 | | Parameters |
| 17129 | | --- |
| 17130 | | Chain pairing | bb |
| 17131 | | Alignment algorithm | Needleman-Wunsch |
| 17132 | | Similarity matrix | BLOSUM-62 |
| 17133 | | SS fraction | 0.3 |
| 17134 | | Gap open (HH/SS/other) | 18/18/6 |
| 17135 | | Gap extend | 1 |
| 17136 | | SS matrix | | | H | S | O |
| 17137 | | ---|---|---|--- |
| 17138 | | H | 6 | -9 | -6 |
| 17139 | | S | | 6 | -6 |
| 17140 | | O | | | 4 |
| 17141 | | Iteration cutoff | 2 |
| 17142 | | |
| 17143 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 17144 | | score = 499.7 |
| 17145 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 17146 | | 3.736) |
| 17147 | | |
| 17148 | | |
| 17149 | | > color #1 green |
| 17150 | | |
| 17151 | | > color #2 tan |
| 17152 | | |
| 17153 | | > color ~C byatom |
| 17154 | | |
| 17155 | | > ~display |
| 17156 | | |
| 17157 | | > display #1:138 #2:176 |
| 17158 | | |
| 17159 | | > style stick |
| 17160 | | |
| 17161 | | Changed 4099 atom styles |
| 17162 | | |
| 17163 | | > ribbon |
| 17164 | | |
| 17165 | | > transparency 60 target r |
| 17166 | | |
| 17167 | | > view |
| 17168 | | |
| 17169 | | > size #1:138 #2:176 stickRadius 0.3 |
| 17170 | | |
| 17171 | | Changed 14 bond radii |
| 17172 | | |
| 17173 | | > save fig1.jpg |
| 17174 | | |
| 17175 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 17176 | | |
| 17177 | | > sel-ca |
| 17178 | | |
| 17179 | | 13 atoms, 1 model selected |
| 17180 | | 26 atoms, 2 models selected |
| 17181 | | |
| 17182 | | > display sel-residues |
| 17183 | | |
| 17184 | | > color ~C byatom |
| 17185 | | |
| 17186 | | > style stick |
| 17187 | | |
| 17188 | | Changed 4099 atom styles |
| 17189 | | |
| 17190 | | > view #1:138 :< 5 pad -1 |
| 17191 | | |
| 17192 | | > hbonds #1:138 & #1 name hb1 color green |
| 17193 | | |
| 17194 | | 3 hydrogen bonds found |
| 17195 | | |
| 17196 | | > hbonds #2:176 & #2 name hb2 color tan |
| 17197 | | |
| 17198 | | 4 hydrogen bonds found |
| 17199 | | |
| 17200 | | > transparency 90 target r |
| 17201 | | |
| 17202 | | > label #1:138 #2:176 offset 1,-1,1 |
| 17203 | | |
| 17204 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 17205 | | |
| 17206 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 17207 | | |
| 17208 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 17209 | | > bgColor white offset 0,0.7,0 |
| 17210 | | |
| 17211 | | > ~select |
| 17212 | | |
| 17213 | | Nothing selected |
| 17214 | | |
| 17215 | | > save fig2.jpg |
| 17216 | | |
| 17217 | | > sel-ca |
| 17218 | | |
| 17219 | | 13 atoms, 1 model selected |
| 17220 | | 26 atoms, 2 models selected |
| 17221 | | |
| 17222 | | > ~ribbon |
| 17223 | | |
| 17224 | | > size stickRadius 0.05 |
| 17225 | | |
| 17226 | | Changed 4167 bond radii |
| 17227 | | |
| 17228 | | > size #1:138 stickRadius 0.2 |
| 17229 | | |
| 17230 | | Changed 7 bond radii |
| 17231 | | |
| 17232 | | > size #2:176 stickRadius 0.2 |
| 17233 | | |
| 17234 | | Changed 7 bond radii |
| 17235 | | |
| 17236 | | > view sel-residues pad -1 |
| 17237 | | |
| 17238 | | > ~select |
| 17239 | | |
| 17240 | | Nothing selected |
| 17241 | | |
| 17242 | | > save fig3.jpg |
| 17243 | | |
| 17244 | | > sel-ca |
| 17245 | | |
| 17246 | | 13 atoms, 1 model selected |
| 17247 | | 26 atoms, 2 models selected |
| 17248 | | |
| 17249 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 17250 | | |
| 17251 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 17252 | | |
| 17253 | | > label #1:138 text {0.name}{0.number}-{0.phi:.1f},{0.psi:.1f} color green |
| 17254 | | > bgColor white offset 0,0,0 |
| 17255 | | |
| 17256 | | > view sel-residues pad -1 |
| 17257 | | |
| 17258 | | > sel-ca |
| 17259 | | |
| 17260 | | 13 atoms, 1 model selected |
| 17261 | | 26 atoms, 2 models selected |
| 17262 | | |
| 17263 | | > align #2 & sel toAtoms #1 & sel |
| 17264 | | |
| 17265 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 17266 | | |
| 17267 | | > ~select |
| 17268 | | |
| 17269 | | Nothing selected |
| 17270 | | |
| 17271 | | > save fig4.jpg |
| 17272 | | |
| 17273 | | > sel-ca |
| 17274 | | |
| 17275 | | 13 atoms, 1 model selected |
| 17276 | | 26 atoms, 2 models selected |
| 17277 | | |
| 17278 | | > ribbon sel |
| 17279 | | |
| 17280 | | > ~select |
| 17281 | | |
| 17282 | | Nothing selected |
| 17283 | | |
| 17284 | | > save fig5.jpg |
| 17285 | | |
| 17286 | | executed script.view.cxc |
| 17287 | | |
| 17288 | | > open "/Users/admin/Dropbox (Technion |
| 17289 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 17290 | | |
| 17291 | | > close |
| 17292 | | |
| 17293 | | > graphics bgColor white |
| 17294 | | |
| 17295 | | > open 1WMB |
| 17296 | | |
| 17297 | | 1wmb title: |
| 17298 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 17299 | | info...] |
| 17300 | | |
| 17301 | | Chain information for 1wmb #1 |
| 17302 | | --- |
| 17303 | | Chain | Description |
| 17304 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 17305 | | |
| 17306 | | Non-standard residues in 1wmb #1 |
| 17307 | | --- |
| 17308 | | CAC — cacodylate ion (dimethylarsinate) |
| 17309 | | MG — magnesium ion |
| 17310 | | |
| 17311 | | 1wmb mmCIF Assemblies |
| 17312 | | --- |
| 17313 | | 1| author_and_software_defined_assembly |
| 17314 | | |
| 17315 | | |
| 17316 | | > open 3I3O |
| 17317 | | |
| 17318 | | 3i3o title: |
| 17319 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 17320 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 17321 | | info...] |
| 17322 | | |
| 17323 | | Chain information for 3i3o #2 |
| 17324 | | --- |
| 17325 | | Chain | Description |
| 17326 | | A B C D E F G H | Short chain dehydrogenase |
| 17327 | | |
| 17328 | | Non-standard residues in 3i3o #2 |
| 17329 | | --- |
| 17330 | | CAC — cacodylate ion (dimethylarsinate) |
| 17331 | | CL — chloride ion |
| 17332 | | MG — magnesium ion |
| 17333 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 17334 | | |
| 17335 | | 3i3o mmCIF Assemblies |
| 17336 | | --- |
| 17337 | | 1| author_and_software_defined_assembly |
| 17338 | | 2| author_and_software_defined_assembly |
| 17339 | | |
| 17340 | | |
| 17341 | | > delete ~/a |
| 17342 | | |
| 17343 | | > delete solvent |
| 17344 | | |
| 17345 | | > mmaker #2 to #1 |
| 17346 | | |
| 17347 | | Parameters |
| 17348 | | --- |
| 17349 | | Chain pairing | bb |
| 17350 | | Alignment algorithm | Needleman-Wunsch |
| 17351 | | Similarity matrix | BLOSUM-62 |
| 17352 | | SS fraction | 0.3 |
| 17353 | | Gap open (HH/SS/other) | 18/18/6 |
| 17354 | | Gap extend | 1 |
| 17355 | | SS matrix | | | H | S | O |
| 17356 | | ---|---|---|--- |
| 17357 | | H | 6 | -9 | -6 |
| 17358 | | S | | 6 | -6 |
| 17359 | | O | | | 4 |
| 17360 | | Iteration cutoff | 2 |
| 17361 | | |
| 17362 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 17363 | | score = 499.7 |
| 17364 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 17365 | | 3.736) |
| 17366 | | |
| 17367 | | |
| 17368 | | > color #1 green |
| 17369 | | |
| 17370 | | > color #2 tan |
| 17371 | | |
| 17372 | | > color ~C byatom |
| 17373 | | |
| 17374 | | > ~display |
| 17375 | | |
| 17376 | | > display #1:138 #2:176 |
| 17377 | | |
| 17378 | | > style stick |
| 17379 | | |
| 17380 | | Changed 4099 atom styles |
| 17381 | | |
| 17382 | | > ribbon |
| 17383 | | |
| 17384 | | > transparency 60 target r |
| 17385 | | |
| 17386 | | > view |
| 17387 | | |
| 17388 | | > size #1:138 #2:176 stickRadius 0.3 |
| 17389 | | |
| 17390 | | Changed 14 bond radii |
| 17391 | | |
| 17392 | | > save fig1.jpg |
| 17393 | | |
| 17394 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 17395 | | |
| 17396 | | > sel-ca |
| 17397 | | |
| 17398 | | 13 atoms, 1 model selected |
| 17399 | | 26 atoms, 2 models selected |
| 17400 | | |
| 17401 | | > display sel-residues |
| 17402 | | |
| 17403 | | > color ~C byatom |
| 17404 | | |
| 17405 | | > style stick |
| 17406 | | |
| 17407 | | Changed 4099 atom styles |
| 17408 | | |
| 17409 | | > view #1:138 :< 5 pad -1 |
| 17410 | | |
| 17411 | | > hbonds #1:138 & #1 name hb1 color green |
| 17412 | | |
| 17413 | | 3 hydrogen bonds found |
| 17414 | | |
| 17415 | | > hbonds #2:176 & #2 name hb2 color tan |
| 17416 | | |
| 17417 | | 4 hydrogen bonds found |
| 17418 | | |
| 17419 | | > transparency 90 target r |
| 17420 | | |
| 17421 | | > label #1:138 #2:176 offset 1,-1,1 |
| 17422 | | |
| 17423 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 17424 | | |
| 17425 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 17426 | | |
| 17427 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 17428 | | > bgColor white offset 0,0.7,0 |
| 17429 | | |
| 17430 | | > ~select |
| 17431 | | |
| 17432 | | Nothing selected |
| 17433 | | |
| 17434 | | > save fig2.jpg |
| 17435 | | |
| 17436 | | > sel-ca |
| 17437 | | |
| 17438 | | 13 atoms, 1 model selected |
| 17439 | | 26 atoms, 2 models selected |
| 17440 | | |
| 17441 | | > ~ribbon |
| 17442 | | |
| 17443 | | > size stickRadius 0.05 |
| 17444 | | |
| 17445 | | Changed 4167 bond radii |
| 17446 | | |
| 17447 | | > size #1:138 stickRadius 0.2 |
| 17448 | | |
| 17449 | | Changed 7 bond radii |
| 17450 | | |
| 17451 | | > size #2:176 stickRadius 0.2 |
| 17452 | | |
| 17453 | | Changed 7 bond radii |
| 17454 | | |
| 17455 | | > view sel-residues pad -1 |
| 17456 | | |
| 17457 | | > ~select |
| 17458 | | |
| 17459 | | Nothing selected |
| 17460 | | |
| 17461 | | > save fig3.jpg |
| 17462 | | |
| 17463 | | > sel-ca |
| 17464 | | |
| 17465 | | 13 atoms, 1 model selected |
| 17466 | | 26 atoms, 2 models selected |
| 17467 | | |
| 17468 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 17469 | | |
| 17470 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 17471 | | |
| 17472 | | > label #1:138 text "{0.name}{0.number}> {0.phi:.1f},{0.psi:.1f}" color green |
| 17473 | | > bgColor white offset 0,0,0 |
| 17474 | | |
| 17475 | | > label #1:176 text "{0.name}{0.number}> {0.phi:.1f},{0.psi:.1f}" color green |
| 17476 | | > bgColor white offset 0,0,0 |
| 17477 | | |
| 17478 | | > view sel-residues pad -1 |
| 17479 | | |
| 17480 | | > sel-ca |
| 17481 | | |
| 17482 | | 13 atoms, 1 model selected |
| 17483 | | 26 atoms, 2 models selected |
| 17484 | | |
| 17485 | | > align #2 & sel toAtoms #1 & sel |
| 17486 | | |
| 17487 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 17488 | | |
| 17489 | | > ~select |
| 17490 | | |
| 17491 | | Nothing selected |
| 17492 | | |
| 17493 | | > save fig4.jpg |
| 17494 | | |
| 17495 | | > sel-ca |
| 17496 | | |
| 17497 | | 13 atoms, 1 model selected |
| 17498 | | 26 atoms, 2 models selected |
| 17499 | | |
| 17500 | | > ribbon sel |
| 17501 | | |
| 17502 | | > ~select |
| 17503 | | |
| 17504 | | Nothing selected |
| 17505 | | |
| 17506 | | > save fig5.jpg |
| 17507 | | |
| 17508 | | executed script.view.cxc |
| 17509 | | |
| 17510 | | > open "/Users/admin/Dropbox (Technion |
| 17511 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 17512 | | |
| 17513 | | > close |
| 17514 | | |
| 17515 | | > graphics bgColor white |
| 17516 | | |
| 17517 | | > open 1WMB |
| 17518 | | |
| 17519 | | 1wmb title: |
| 17520 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 17521 | | info...] |
| 17522 | | |
| 17523 | | Chain information for 1wmb #1 |
| 17524 | | --- |
| 17525 | | Chain | Description |
| 17526 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 17527 | | |
| 17528 | | Non-standard residues in 1wmb #1 |
| 17529 | | --- |
| 17530 | | CAC — cacodylate ion (dimethylarsinate) |
| 17531 | | MG — magnesium ion |
| 17532 | | |
| 17533 | | 1wmb mmCIF Assemblies |
| 17534 | | --- |
| 17535 | | 1| author_and_software_defined_assembly |
| 17536 | | |
| 17537 | | |
| 17538 | | > open 3I3O |
| 17539 | | |
| 17540 | | 3i3o title: |
| 17541 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 17542 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 17543 | | info...] |
| 17544 | | |
| 17545 | | Chain information for 3i3o #2 |
| 17546 | | --- |
| 17547 | | Chain | Description |
| 17548 | | A B C D E F G H | Short chain dehydrogenase |
| 17549 | | |
| 17550 | | Non-standard residues in 3i3o #2 |
| 17551 | | --- |
| 17552 | | CAC — cacodylate ion (dimethylarsinate) |
| 17553 | | CL — chloride ion |
| 17554 | | MG — magnesium ion |
| 17555 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 17556 | | |
| 17557 | | 3i3o mmCIF Assemblies |
| 17558 | | --- |
| 17559 | | 1| author_and_software_defined_assembly |
| 17560 | | 2| author_and_software_defined_assembly |
| 17561 | | |
| 17562 | | |
| 17563 | | > delete ~/a |
| 17564 | | |
| 17565 | | > delete solvent |
| 17566 | | |
| 17567 | | > mmaker #2 to #1 |
| 17568 | | |
| 17569 | | Parameters |
| 17570 | | --- |
| 17571 | | Chain pairing | bb |
| 17572 | | Alignment algorithm | Needleman-Wunsch |
| 17573 | | Similarity matrix | BLOSUM-62 |
| 17574 | | SS fraction | 0.3 |
| 17575 | | Gap open (HH/SS/other) | 18/18/6 |
| 17576 | | Gap extend | 1 |
| 17577 | | SS matrix | | | H | S | O |
| 17578 | | ---|---|---|--- |
| 17579 | | H | 6 | -9 | -6 |
| 17580 | | S | | 6 | -6 |
| 17581 | | O | | | 4 |
| 17582 | | Iteration cutoff | 2 |
| 17583 | | |
| 17584 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 17585 | | score = 499.7 |
| 17586 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 17587 | | 3.736) |
| 17588 | | |
| 17589 | | |
| 17590 | | > color #1 green |
| 17591 | | |
| 17592 | | > color #2 tan |
| 17593 | | |
| 17594 | | > color ~C byatom |
| 17595 | | |
| 17596 | | > ~display |
| 17597 | | |
| 17598 | | > display #1:138 #2:176 |
| 17599 | | |
| 17600 | | > style stick |
| 17601 | | |
| 17602 | | Changed 4099 atom styles |
| 17603 | | |
| 17604 | | > ribbon |
| 17605 | | |
| 17606 | | > transparency 60 target r |
| 17607 | | |
| 17608 | | > view |
| 17609 | | |
| 17610 | | > size #1:138 #2:176 stickRadius 0.3 |
| 17611 | | |
| 17612 | | Changed 14 bond radii |
| 17613 | | |
| 17614 | | > save fig1.jpg |
| 17615 | | |
| 17616 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 17617 | | |
| 17618 | | > sel-ca |
| 17619 | | |
| 17620 | | 13 atoms, 1 model selected |
| 17621 | | 26 atoms, 2 models selected |
| 17622 | | |
| 17623 | | > display sel-residues |
| 17624 | | |
| 17625 | | > color ~C byatom |
| 17626 | | |
| 17627 | | > style stick |
| 17628 | | |
| 17629 | | Changed 4099 atom styles |
| 17630 | | |
| 17631 | | > view #1:138 :< 5 pad -1 |
| 17632 | | |
| 17633 | | > hbonds #1:138 & #1 name hb1 color green |
| 17634 | | |
| 17635 | | 3 hydrogen bonds found |
| 17636 | | |
| 17637 | | > hbonds #2:176 & #2 name hb2 color tan |
| 17638 | | |
| 17639 | | 4 hydrogen bonds found |
| 17640 | | |
| 17641 | | > transparency 90 target r |
| 17642 | | |
| 17643 | | > label #1:138 #2:176 offset 1,-1,1 |
| 17644 | | |
| 17645 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 17646 | | |
| 17647 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 17648 | | |
| 17649 | | > label #2:176 residues text {0.phi:.1f},{0.psi:.1f} height 0.5 color tan |
| 17650 | | > bgColor white offset 0,0.7,0 |
| 17651 | | |
| 17652 | | > ~select |
| 17653 | | |
| 17654 | | Nothing selected |
| 17655 | | |
| 17656 | | > save fig2.jpg |
| 17657 | | |
| 17658 | | > sel-ca |
| 17659 | | |
| 17660 | | 13 atoms, 1 model selected |
| 17661 | | 26 atoms, 2 models selected |
| 17662 | | |
| 17663 | | > ~ribbon |
| 17664 | | |
| 17665 | | > size stickRadius 0.05 |
| 17666 | | |
| 17667 | | Changed 4167 bond radii |
| 17668 | | |
| 17669 | | > size #1:138 stickRadius 0.2 |
| 17670 | | |
| 17671 | | Changed 7 bond radii |
| 17672 | | |
| 17673 | | > size #2:176 stickRadius 0.2 |
| 17674 | | |
| 17675 | | Changed 7 bond radii |
| 17676 | | |
| 17677 | | > view sel-residues pad -1 |
| 17678 | | |
| 17679 | | > ~select |
| 17680 | | |
| 17681 | | Nothing selected |
| 17682 | | |
| 17683 | | > save fig3.jpg |
| 17684 | | |
| 17685 | | > sel-ca |
| 17686 | | |
| 17687 | | 13 atoms, 1 model selected |
| 17688 | | 26 atoms, 2 models selected |
| 17689 | | |
| 17690 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 17691 | | |
| 17692 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 17693 | | |
| 17694 | | > label #1:138 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.7 |
| 17695 | | > color green bgColor white offset 0,0,0 |
| 17696 | | |
| 17697 | | > label #1:176 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.7 |
| 17698 | | > color green bgColor white offset 0,0,0 |
| 17699 | | |
| 17700 | | > view sel-residues pad -1 |
| 17701 | | |
| 17702 | | > sel-ca |
| 17703 | | |
| 17704 | | 13 atoms, 1 model selected |
| 17705 | | 26 atoms, 2 models selected |
| 17706 | | |
| 17707 | | > align #2 & sel toAtoms #1 & sel |
| 17708 | | |
| 17709 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 17710 | | |
| 17711 | | > ~select |
| 17712 | | |
| 17713 | | Nothing selected |
| 17714 | | |
| 17715 | | > save fig4.jpg |
| 17716 | | |
| 17717 | | > sel-ca |
| 17718 | | |
| 17719 | | 13 atoms, 1 model selected |
| 17720 | | 26 atoms, 2 models selected |
| 17721 | | |
| 17722 | | > ribbon sel |
| 17723 | | |
| 17724 | | > ~select |
| 17725 | | |
| 17726 | | Nothing selected |
| 17727 | | |
| 17728 | | > save fig5.jpg |
| 17729 | | |
| 17730 | | executed script.view.cxc |
| 17731 | | |
| 17732 | | > open "/Users/admin/Dropbox (Technion |
| 17733 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 17734 | | |
| 17735 | | > close |
| 17736 | | |
| 17737 | | > graphics bgColor white |
| 17738 | | |
| 17739 | | > open 1WMB |
| 17740 | | |
| 17741 | | 1wmb title: |
| 17742 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 17743 | | info...] |
| 17744 | | |
| 17745 | | Chain information for 1wmb #1 |
| 17746 | | --- |
| 17747 | | Chain | Description |
| 17748 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 17749 | | |
| 17750 | | Non-standard residues in 1wmb #1 |
| 17751 | | --- |
| 17752 | | CAC — cacodylate ion (dimethylarsinate) |
| 17753 | | MG — magnesium ion |
| 17754 | | |
| 17755 | | 1wmb mmCIF Assemblies |
| 17756 | | --- |
| 17757 | | 1| author_and_software_defined_assembly |
| 17758 | | |
| 17759 | | |
| 17760 | | > open 3I3O |
| 17761 | | |
| 17762 | | 3i3o title: |
| 17763 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 17764 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 17765 | | info...] |
| 17766 | | |
| 17767 | | Chain information for 3i3o #2 |
| 17768 | | --- |
| 17769 | | Chain | Description |
| 17770 | | A B C D E F G H | Short chain dehydrogenase |
| 17771 | | |
| 17772 | | Non-standard residues in 3i3o #2 |
| 17773 | | --- |
| 17774 | | CAC — cacodylate ion (dimethylarsinate) |
| 17775 | | CL — chloride ion |
| 17776 | | MG — magnesium ion |
| 17777 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 17778 | | |
| 17779 | | 3i3o mmCIF Assemblies |
| 17780 | | --- |
| 17781 | | 1| author_and_software_defined_assembly |
| 17782 | | 2| author_and_software_defined_assembly |
| 17783 | | |
| 17784 | | |
| 17785 | | > delete ~/a |
| 17786 | | |
| 17787 | | > delete solvent |
| 17788 | | |
| 17789 | | > mmaker #2 to #1 |
| 17790 | | |
| 17791 | | Parameters |
| 17792 | | --- |
| 17793 | | Chain pairing | bb |
| 17794 | | Alignment algorithm | Needleman-Wunsch |
| 17795 | | Similarity matrix | BLOSUM-62 |
| 17796 | | SS fraction | 0.3 |
| 17797 | | Gap open (HH/SS/other) | 18/18/6 |
| 17798 | | Gap extend | 1 |
| 17799 | | SS matrix | | | H | S | O |
| 17800 | | ---|---|---|--- |
| 17801 | | H | 6 | -9 | -6 |
| 17802 | | S | | 6 | -6 |
| 17803 | | O | | | 4 |
| 17804 | | Iteration cutoff | 2 |
| 17805 | | |
| 17806 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 17807 | | score = 499.7 |
| 17808 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 17809 | | 3.736) |
| 17810 | | |
| 17811 | | |
| 17812 | | > color #1 green |
| 17813 | | |
| 17814 | | > color #2 tan |
| 17815 | | |
| 17816 | | > color ~C byatom |
| 17817 | | |
| 17818 | | > ~display |
| 17819 | | |
| 17820 | | > display #1:138 #2:176 |
| 17821 | | |
| 17822 | | > style stick |
| 17823 | | |
| 17824 | | Changed 4099 atom styles |
| 17825 | | |
| 17826 | | > ribbon |
| 17827 | | |
| 17828 | | > transparency 60 target r |
| 17829 | | |
| 17830 | | > view |
| 17831 | | |
| 17832 | | > size #1:138 #2:176 stickRadius 0.3 |
| 17833 | | |
| 17834 | | Changed 14 bond radii |
| 17835 | | |
| 17836 | | > save fig1.jpg |
| 17837 | | |
| 17838 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 17839 | | |
| 17840 | | > sel-ca |
| 17841 | | |
| 17842 | | 13 atoms, 1 model selected |
| 17843 | | 26 atoms, 2 models selected |
| 17844 | | |
| 17845 | | > display sel-residues |
| 17846 | | |
| 17847 | | > color ~C byatom |
| 17848 | | |
| 17849 | | > style stick |
| 17850 | | |
| 17851 | | Changed 4099 atom styles |
| 17852 | | |
| 17853 | | > view #1:138 :< 5 pad -1 |
| 17854 | | |
| 17855 | | > hbonds #1:138 & #1 name hb1 color green |
| 17856 | | |
| 17857 | | 3 hydrogen bonds found |
| 17858 | | |
| 17859 | | > hbonds #2:176 & #2 name hb2 color tan |
| 17860 | | |
| 17861 | | 4 hydrogen bonds found |
| 17862 | | |
| 17863 | | > transparency 90 target r |
| 17864 | | |
| 17865 | | > label #1:138 #2:176 offset 1,-1,1 |
| 17866 | | |
| 17867 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 17868 | | |
| 17869 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 17870 | | |
| 17871 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 17872 | | |
| 17873 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 17874 | | |
| 17875 | | > label #1:138 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.6 |
| 17876 | | > color green bgColor white offset 0,0,0 |
| 17877 | | |
| 17878 | | > label #1:176 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.6 |
| 17879 | | > color green bgColor white offset 0,0,0 |
| 17880 | | |
| 17881 | | > ~select |
| 17882 | | |
| 17883 | | Nothing selected |
| 17884 | | |
| 17885 | | > save fig2.jpg |
| 17886 | | |
| 17887 | | > sel-ca |
| 17888 | | |
| 17889 | | 13 atoms, 1 model selected |
| 17890 | | 26 atoms, 2 models selected |
| 17891 | | |
| 17892 | | > ~ribbon |
| 17893 | | |
| 17894 | | > size stickRadius 0.05 |
| 17895 | | |
| 17896 | | Changed 4167 bond radii |
| 17897 | | |
| 17898 | | > size #1:138 stickRadius 0.2 |
| 17899 | | |
| 17900 | | Changed 7 bond radii |
| 17901 | | |
| 17902 | | > size #2:176 stickRadius 0.2 |
| 17903 | | |
| 17904 | | Changed 7 bond radii |
| 17905 | | |
| 17906 | | > view sel-residues pad -1 |
| 17907 | | |
| 17908 | | > ~select |
| 17909 | | |
| 17910 | | Nothing selected |
| 17911 | | |
| 17912 | | > save fig3.jpg |
| 17913 | | |
| 17914 | | > sel-ca |
| 17915 | | |
| 17916 | | 13 atoms, 1 model selected |
| 17917 | | 26 atoms, 2 models selected |
| 17918 | | |
| 17919 | | > view sel-residues pad -1 |
| 17920 | | |
| 17921 | | > sel-ca |
| 17922 | | |
| 17923 | | 13 atoms, 1 model selected |
| 17924 | | 26 atoms, 2 models selected |
| 17925 | | |
| 17926 | | > align #2 & sel toAtoms #1 & sel |
| 17927 | | |
| 17928 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 17929 | | |
| 17930 | | > ~select |
| 17931 | | |
| 17932 | | Nothing selected |
| 17933 | | |
| 17934 | | > save fig4.jpg |
| 17935 | | |
| 17936 | | > sel-ca |
| 17937 | | |
| 17938 | | 13 atoms, 1 model selected |
| 17939 | | 26 atoms, 2 models selected |
| 17940 | | |
| 17941 | | > ribbon sel |
| 17942 | | |
| 17943 | | > ~select |
| 17944 | | |
| 17945 | | Nothing selected |
| 17946 | | |
| 17947 | | > save fig5.jpg |
| 17948 | | |
| 17949 | | executed script.view.cxc |
| 17950 | | |
| 17951 | | > open "/Users/admin/Dropbox (Technion |
| 17952 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 17953 | | |
| 17954 | | > close |
| 17955 | | |
| 17956 | | > graphics bgColor white |
| 17957 | | |
| 17958 | | > open 1WMB |
| 17959 | | |
| 17960 | | 1wmb title: |
| 17961 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 17962 | | info...] |
| 17963 | | |
| 17964 | | Chain information for 1wmb #1 |
| 17965 | | --- |
| 17966 | | Chain | Description |
| 17967 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 17968 | | |
| 17969 | | Non-standard residues in 1wmb #1 |
| 17970 | | --- |
| 17971 | | CAC — cacodylate ion (dimethylarsinate) |
| 17972 | | MG — magnesium ion |
| 17973 | | |
| 17974 | | 1wmb mmCIF Assemblies |
| 17975 | | --- |
| 17976 | | 1| author_and_software_defined_assembly |
| 17977 | | |
| 17978 | | |
| 17979 | | > open 3I3O |
| 17980 | | |
| 17981 | | 3i3o title: |
| 17982 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 17983 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 17984 | | info...] |
| 17985 | | |
| 17986 | | Chain information for 3i3o #2 |
| 17987 | | --- |
| 17988 | | Chain | Description |
| 17989 | | A B C D E F G H | Short chain dehydrogenase |
| 17990 | | |
| 17991 | | Non-standard residues in 3i3o #2 |
| 17992 | | --- |
| 17993 | | CAC — cacodylate ion (dimethylarsinate) |
| 17994 | | CL — chloride ion |
| 17995 | | MG — magnesium ion |
| 17996 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 17997 | | |
| 17998 | | 3i3o mmCIF Assemblies |
| 17999 | | --- |
| 18000 | | 1| author_and_software_defined_assembly |
| 18001 | | 2| author_and_software_defined_assembly |
| 18002 | | |
| 18003 | | |
| 18004 | | > delete ~/a |
| 18005 | | |
| 18006 | | > delete solvent |
| 18007 | | |
| 18008 | | > mmaker #2 to #1 |
| 18009 | | |
| 18010 | | Parameters |
| 18011 | | --- |
| 18012 | | Chain pairing | bb |
| 18013 | | Alignment algorithm | Needleman-Wunsch |
| 18014 | | Similarity matrix | BLOSUM-62 |
| 18015 | | SS fraction | 0.3 |
| 18016 | | Gap open (HH/SS/other) | 18/18/6 |
| 18017 | | Gap extend | 1 |
| 18018 | | SS matrix | | | H | S | O |
| 18019 | | ---|---|---|--- |
| 18020 | | H | 6 | -9 | -6 |
| 18021 | | S | | 6 | -6 |
| 18022 | | O | | | 4 |
| 18023 | | Iteration cutoff | 2 |
| 18024 | | |
| 18025 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 18026 | | score = 499.7 |
| 18027 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 18028 | | 3.736) |
| 18029 | | |
| 18030 | | |
| 18031 | | > color #1 green |
| 18032 | | |
| 18033 | | > color #2 tan |
| 18034 | | |
| 18035 | | > color ~C byatom |
| 18036 | | |
| 18037 | | > ~display |
| 18038 | | |
| 18039 | | > display #1:138 #2:176 |
| 18040 | | |
| 18041 | | > style stick |
| 18042 | | |
| 18043 | | Changed 4099 atom styles |
| 18044 | | |
| 18045 | | > ribbon |
| 18046 | | |
| 18047 | | > transparency 60 target r |
| 18048 | | |
| 18049 | | > view |
| 18050 | | |
| 18051 | | > size #1:138 #2:176 stickRadius 0.3 |
| 18052 | | |
| 18053 | | Changed 14 bond radii |
| 18054 | | |
| 18055 | | > save fig1.jpg |
| 18056 | | |
| 18057 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 18058 | | |
| 18059 | | > sel-ca |
| 18060 | | |
| 18061 | | 13 atoms, 1 model selected |
| 18062 | | 26 atoms, 2 models selected |
| 18063 | | |
| 18064 | | > display sel-residues |
| 18065 | | |
| 18066 | | > color ~C byatom |
| 18067 | | |
| 18068 | | > style stick |
| 18069 | | |
| 18070 | | Changed 4099 atom styles |
| 18071 | | |
| 18072 | | > view #1:138 :< 5 pad -1 |
| 18073 | | |
| 18074 | | > hbonds #1:138 & #1 name hb1 color green |
| 18075 | | |
| 18076 | | 3 hydrogen bonds found |
| 18077 | | |
| 18078 | | > hbonds #2:176 & #2 name hb2 color tan |
| 18079 | | |
| 18080 | | 4 hydrogen bonds found |
| 18081 | | |
| 18082 | | > transparency 90 target r |
| 18083 | | |
| 18084 | | > label #1:138 #2:176 offset 1,-1,1 |
| 18085 | | |
| 18086 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 18087 | | |
| 18088 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 18089 | | |
| 18090 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 18091 | | |
| 18092 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 18093 | | |
| 18094 | | > label #1:138 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.5 |
| 18095 | | > color green bgColor white offset 0,0,0 |
| 18096 | | |
| 18097 | | > label #1:176 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.5 |
| 18098 | | > color green bgColor white offset 0,0.7,0 |
| 18099 | | |
| 18100 | | > ~select |
| 18101 | | |
| 18102 | | Nothing selected |
| 18103 | | |
| 18104 | | > save fig2.jpg |
| 18105 | | |
| 18106 | | > sel-ca |
| 18107 | | |
| 18108 | | 13 atoms, 1 model selected |
| 18109 | | 26 atoms, 2 models selected |
| 18110 | | |
| 18111 | | > ~ribbon |
| 18112 | | |
| 18113 | | > size stickRadius 0.05 |
| 18114 | | |
| 18115 | | Changed 4167 bond radii |
| 18116 | | |
| 18117 | | > size #1:138 stickRadius 0.2 |
| 18118 | | |
| 18119 | | Changed 7 bond radii |
| 18120 | | |
| 18121 | | > size #2:176 stickRadius 0.2 |
| 18122 | | |
| 18123 | | Changed 7 bond radii |
| 18124 | | |
| 18125 | | > view sel-residues pad -1 |
| 18126 | | |
| 18127 | | > ~select |
| 18128 | | |
| 18129 | | Nothing selected |
| 18130 | | |
| 18131 | | > save fig3.jpg |
| 18132 | | |
| 18133 | | > sel-ca |
| 18134 | | |
| 18135 | | 13 atoms, 1 model selected |
| 18136 | | 26 atoms, 2 models selected |
| 18137 | | |
| 18138 | | > view sel-residues pad -1 |
| 18139 | | |
| 18140 | | > sel-ca |
| 18141 | | |
| 18142 | | 13 atoms, 1 model selected |
| 18143 | | 26 atoms, 2 models selected |
| 18144 | | |
| 18145 | | > align #2 & sel toAtoms #1 & sel |
| 18146 | | |
| 18147 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 18148 | | |
| 18149 | | > ~select |
| 18150 | | |
| 18151 | | Nothing selected |
| 18152 | | |
| 18153 | | > save fig4.jpg |
| 18154 | | |
| 18155 | | > sel-ca |
| 18156 | | |
| 18157 | | 13 atoms, 1 model selected |
| 18158 | | 26 atoms, 2 models selected |
| 18159 | | |
| 18160 | | > ribbon sel |
| 18161 | | |
| 18162 | | > ~select |
| 18163 | | |
| 18164 | | Nothing selected |
| 18165 | | |
| 18166 | | > save fig5.jpg |
| 18167 | | |
| 18168 | | executed script.view.cxc |
| 18169 | | |
| 18170 | | > open "/Users/admin/Dropbox (Technion |
| 18171 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 18172 | | |
| 18173 | | > close |
| 18174 | | |
| 18175 | | > graphics bgColor white |
| 18176 | | |
| 18177 | | > open 1WMB |
| 18178 | | |
| 18179 | | 1wmb title: |
| 18180 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 18181 | | info...] |
| 18182 | | |
| 18183 | | Chain information for 1wmb #1 |
| 18184 | | --- |
| 18185 | | Chain | Description |
| 18186 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 18187 | | |
| 18188 | | Non-standard residues in 1wmb #1 |
| 18189 | | --- |
| 18190 | | CAC — cacodylate ion (dimethylarsinate) |
| 18191 | | MG — magnesium ion |
| 18192 | | |
| 18193 | | 1wmb mmCIF Assemblies |
| 18194 | | --- |
| 18195 | | 1| author_and_software_defined_assembly |
| 18196 | | |
| 18197 | | |
| 18198 | | > open 3I3O |
| 18199 | | |
| 18200 | | 3i3o title: |
| 18201 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 18202 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 18203 | | info...] |
| 18204 | | |
| 18205 | | Chain information for 3i3o #2 |
| 18206 | | --- |
| 18207 | | Chain | Description |
| 18208 | | A B C D E F G H | Short chain dehydrogenase |
| 18209 | | |
| 18210 | | Non-standard residues in 3i3o #2 |
| 18211 | | --- |
| 18212 | | CAC — cacodylate ion (dimethylarsinate) |
| 18213 | | CL — chloride ion |
| 18214 | | MG — magnesium ion |
| 18215 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 18216 | | |
| 18217 | | 3i3o mmCIF Assemblies |
| 18218 | | --- |
| 18219 | | 1| author_and_software_defined_assembly |
| 18220 | | 2| author_and_software_defined_assembly |
| 18221 | | |
| 18222 | | |
| 18223 | | > delete ~/a |
| 18224 | | |
| 18225 | | > delete solvent |
| 18226 | | |
| 18227 | | > mmaker #2 to #1 |
| 18228 | | |
| 18229 | | Parameters |
| 18230 | | --- |
| 18231 | | Chain pairing | bb |
| 18232 | | Alignment algorithm | Needleman-Wunsch |
| 18233 | | Similarity matrix | BLOSUM-62 |
| 18234 | | SS fraction | 0.3 |
| 18235 | | Gap open (HH/SS/other) | 18/18/6 |
| 18236 | | Gap extend | 1 |
| 18237 | | SS matrix | | | H | S | O |
| 18238 | | ---|---|---|--- |
| 18239 | | H | 6 | -9 | -6 |
| 18240 | | S | | 6 | -6 |
| 18241 | | O | | | 4 |
| 18242 | | Iteration cutoff | 2 |
| 18243 | | |
| 18244 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 18245 | | score = 499.7 |
| 18246 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 18247 | | 3.736) |
| 18248 | | |
| 18249 | | |
| 18250 | | > color #1 green |
| 18251 | | |
| 18252 | | > color #2 tan |
| 18253 | | |
| 18254 | | > color ~C byatom |
| 18255 | | |
| 18256 | | > ~display |
| 18257 | | |
| 18258 | | > display #1:138 #2:176 |
| 18259 | | |
| 18260 | | > style stick |
| 18261 | | |
| 18262 | | Changed 4099 atom styles |
| 18263 | | |
| 18264 | | > ribbon |
| 18265 | | |
| 18266 | | > transparency 60 target r |
| 18267 | | |
| 18268 | | > view |
| 18269 | | |
| 18270 | | > size #1:138 #2:176 stickRadius 0.3 |
| 18271 | | |
| 18272 | | Changed 14 bond radii |
| 18273 | | |
| 18274 | | > save fig1.jpg |
| 18275 | | |
| 18276 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 18277 | | |
| 18278 | | > sel-ca |
| 18279 | | |
| 18280 | | 13 atoms, 1 model selected |
| 18281 | | 26 atoms, 2 models selected |
| 18282 | | |
| 18283 | | > display sel-residues |
| 18284 | | |
| 18285 | | > color ~C byatom |
| 18286 | | |
| 18287 | | > style stick |
| 18288 | | |
| 18289 | | Changed 4099 atom styles |
| 18290 | | |
| 18291 | | > view #1:138 :< 5 pad -1 |
| 18292 | | |
| 18293 | | > hbonds #1:138 & #1 name hb1 color green |
| 18294 | | |
| 18295 | | 3 hydrogen bonds found |
| 18296 | | |
| 18297 | | > hbonds #2:176 & #2 name hb2 color tan |
| 18298 | | |
| 18299 | | 4 hydrogen bonds found |
| 18300 | | |
| 18301 | | > transparency 90 target r |
| 18302 | | |
| 18303 | | > label #1:138 #2:176 offset 1,-1,1 |
| 18304 | | |
| 18305 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 18306 | | |
| 18307 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 18308 | | |
| 18309 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 18310 | | |
| 18311 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 18312 | | |
| 18313 | | > label #1:138 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.5 |
| 18314 | | > color green bgColor white offset 0,0,0 |
| 18315 | | |
| 18316 | | > label #2:176 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.5 |
| 18317 | | > color green bgColor white offset 0,0.7,0 |
| 18318 | | |
| 18319 | | > ~select |
| 18320 | | |
| 18321 | | Nothing selected |
| 18322 | | |
| 18323 | | > save fig2.jpg |
| 18324 | | |
| 18325 | | > sel-ca |
| 18326 | | |
| 18327 | | 13 atoms, 1 model selected |
| 18328 | | 26 atoms, 2 models selected |
| 18329 | | |
| 18330 | | > ~ribbon |
| 18331 | | |
| 18332 | | > size stickRadius 0.05 |
| 18333 | | |
| 18334 | | Changed 4167 bond radii |
| 18335 | | |
| 18336 | | > size #1:138 stickRadius 0.2 |
| 18337 | | |
| 18338 | | Changed 7 bond radii |
| 18339 | | |
| 18340 | | > size #2:176 stickRadius 0.2 |
| 18341 | | |
| 18342 | | Changed 7 bond radii |
| 18343 | | |
| 18344 | | > view sel-residues pad -1 |
| 18345 | | |
| 18346 | | > ~select |
| 18347 | | |
| 18348 | | Nothing selected |
| 18349 | | |
| 18350 | | > save fig3.jpg |
| 18351 | | |
| 18352 | | > sel-ca |
| 18353 | | |
| 18354 | | 13 atoms, 1 model selected |
| 18355 | | 26 atoms, 2 models selected |
| 18356 | | |
| 18357 | | > view sel-residues pad -1 |
| 18358 | | |
| 18359 | | > sel-ca |
| 18360 | | |
| 18361 | | 13 atoms, 1 model selected |
| 18362 | | 26 atoms, 2 models selected |
| 18363 | | |
| 18364 | | > align #2 & sel toAtoms #1 & sel |
| 18365 | | |
| 18366 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 18367 | | |
| 18368 | | > ~select |
| 18369 | | |
| 18370 | | Nothing selected |
| 18371 | | |
| 18372 | | > save fig4.jpg |
| 18373 | | |
| 18374 | | > sel-ca |
| 18375 | | |
| 18376 | | 13 atoms, 1 model selected |
| 18377 | | 26 atoms, 2 models selected |
| 18378 | | |
| 18379 | | > ribbon sel |
| 18380 | | |
| 18381 | | > ~select |
| 18382 | | |
| 18383 | | Nothing selected |
| 18384 | | |
| 18385 | | > save fig5.jpg |
| 18386 | | |
| 18387 | | executed script.view.cxc |
| 18388 | | |
| 18389 | | > open "/Users/admin/Dropbox (Technion |
| 18390 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 18391 | | |
| 18392 | | > close |
| 18393 | | |
| 18394 | | > graphics bgColor white |
| 18395 | | |
| 18396 | | > open 1WMB |
| 18397 | | |
| 18398 | | 1wmb title: |
| 18399 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 18400 | | info...] |
| 18401 | | |
| 18402 | | Chain information for 1wmb #1 |
| 18403 | | --- |
| 18404 | | Chain | Description |
| 18405 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 18406 | | |
| 18407 | | Non-standard residues in 1wmb #1 |
| 18408 | | --- |
| 18409 | | CAC — cacodylate ion (dimethylarsinate) |
| 18410 | | MG — magnesium ion |
| 18411 | | |
| 18412 | | 1wmb mmCIF Assemblies |
| 18413 | | --- |
| 18414 | | 1| author_and_software_defined_assembly |
| 18415 | | |
| 18416 | | |
| 18417 | | > open 3I3O |
| 18418 | | |
| 18419 | | 3i3o title: |
| 18420 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 18421 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 18422 | | info...] |
| 18423 | | |
| 18424 | | Chain information for 3i3o #2 |
| 18425 | | --- |
| 18426 | | Chain | Description |
| 18427 | | A B C D E F G H | Short chain dehydrogenase |
| 18428 | | |
| 18429 | | Non-standard residues in 3i3o #2 |
| 18430 | | --- |
| 18431 | | CAC — cacodylate ion (dimethylarsinate) |
| 18432 | | CL — chloride ion |
| 18433 | | MG — magnesium ion |
| 18434 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 18435 | | |
| 18436 | | 3i3o mmCIF Assemblies |
| 18437 | | --- |
| 18438 | | 1| author_and_software_defined_assembly |
| 18439 | | 2| author_and_software_defined_assembly |
| 18440 | | |
| 18441 | | |
| 18442 | | > delete ~/a |
| 18443 | | |
| 18444 | | > delete solvent |
| 18445 | | |
| 18446 | | > mmaker #2 to #1 |
| 18447 | | |
| 18448 | | Parameters |
| 18449 | | --- |
| 18450 | | Chain pairing | bb |
| 18451 | | Alignment algorithm | Needleman-Wunsch |
| 18452 | | Similarity matrix | BLOSUM-62 |
| 18453 | | SS fraction | 0.3 |
| 18454 | | Gap open (HH/SS/other) | 18/18/6 |
| 18455 | | Gap extend | 1 |
| 18456 | | SS matrix | | | H | S | O |
| 18457 | | ---|---|---|--- |
| 18458 | | H | 6 | -9 | -6 |
| 18459 | | S | | 6 | -6 |
| 18460 | | O | | | 4 |
| 18461 | | Iteration cutoff | 2 |
| 18462 | | |
| 18463 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 18464 | | score = 499.7 |
| 18465 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 18466 | | 3.736) |
| 18467 | | |
| 18468 | | |
| 18469 | | > color #1 green |
| 18470 | | |
| 18471 | | > color #2 tan |
| 18472 | | |
| 18473 | | > color ~C byatom |
| 18474 | | |
| 18475 | | > ~display |
| 18476 | | |
| 18477 | | > display #1:138 #2:176 |
| 18478 | | |
| 18479 | | > style stick |
| 18480 | | |
| 18481 | | Changed 4099 atom styles |
| 18482 | | |
| 18483 | | > ribbon |
| 18484 | | |
| 18485 | | > transparency 60 target r |
| 18486 | | |
| 18487 | | > view |
| 18488 | | |
| 18489 | | > size #1:138 #2:176 stickRadius 0.3 |
| 18490 | | |
| 18491 | | Changed 14 bond radii |
| 18492 | | |
| 18493 | | > save fig1.jpg |
| 18494 | | |
| 18495 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 18496 | | |
| 18497 | | > sel-ca |
| 18498 | | |
| 18499 | | 13 atoms, 1 model selected |
| 18500 | | 26 atoms, 2 models selected |
| 18501 | | |
| 18502 | | > display sel-residues |
| 18503 | | |
| 18504 | | > color ~C byatom |
| 18505 | | |
| 18506 | | > style stick |
| 18507 | | |
| 18508 | | Changed 4099 atom styles |
| 18509 | | |
| 18510 | | > view #1:138 :< 5 pad -1 |
| 18511 | | |
| 18512 | | > hbonds #1:138 & #1 name hb1 color green |
| 18513 | | |
| 18514 | | 3 hydrogen bonds found |
| 18515 | | |
| 18516 | | > hbonds #2:176 & #2 name hb2 color tan |
| 18517 | | |
| 18518 | | 4 hydrogen bonds found |
| 18519 | | |
| 18520 | | > transparency 90 target r |
| 18521 | | |
| 18522 | | > label #1:138 #2:176 offset 1,-1,1 |
| 18523 | | |
| 18524 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 18525 | | |
| 18526 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 18527 | | |
| 18528 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 18529 | | |
| 18530 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 18531 | | |
| 18532 | | > label #1:138 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.5 |
| 18533 | | > color green bgColor white offset 0,0,0 |
| 18534 | | |
| 18535 | | > label #2:176 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.5 |
| 18536 | | > color tan bgColor white offset 0,0.7,0 |
| 18537 | | |
| 18538 | | > ~select |
| 18539 | | |
| 18540 | | Nothing selected |
| 18541 | | |
| 18542 | | > save fig2.jpg |
| 18543 | | |
| 18544 | | > sel-ca |
| 18545 | | |
| 18546 | | 13 atoms, 1 model selected |
| 18547 | | 26 atoms, 2 models selected |
| 18548 | | |
| 18549 | | > ~ribbon |
| 18550 | | |
| 18551 | | > size stickRadius 0.05 |
| 18552 | | |
| 18553 | | Changed 4167 bond radii |
| 18554 | | |
| 18555 | | > size #1:138 stickRadius 0.2 |
| 18556 | | |
| 18557 | | Changed 7 bond radii |
| 18558 | | |
| 18559 | | > size #2:176 stickRadius 0.2 |
| 18560 | | |
| 18561 | | Changed 7 bond radii |
| 18562 | | |
| 18563 | | > view sel-residues pad -1 |
| 18564 | | |
| 18565 | | > ~select |
| 18566 | | |
| 18567 | | Nothing selected |
| 18568 | | |
| 18569 | | > save fig3.jpg |
| 18570 | | |
| 18571 | | > sel-ca |
| 18572 | | |
| 18573 | | 13 atoms, 1 model selected |
| 18574 | | 26 atoms, 2 models selected |
| 18575 | | |
| 18576 | | > view sel-residues pad -1 |
| 18577 | | |
| 18578 | | > sel-ca |
| 18579 | | |
| 18580 | | 13 atoms, 1 model selected |
| 18581 | | 26 atoms, 2 models selected |
| 18582 | | |
| 18583 | | > align #2 & sel toAtoms #1 & sel |
| 18584 | | |
| 18585 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 18586 | | |
| 18587 | | > ~select |
| 18588 | | |
| 18589 | | Nothing selected |
| 18590 | | |
| 18591 | | > save fig4.jpg |
| 18592 | | |
| 18593 | | > sel-ca |
| 18594 | | |
| 18595 | | 13 atoms, 1 model selected |
| 18596 | | 26 atoms, 2 models selected |
| 18597 | | |
| 18598 | | > ribbon sel |
| 18599 | | |
| 18600 | | > ~select |
| 18601 | | |
| 18602 | | Nothing selected |
| 18603 | | |
| 18604 | | > save fig5.jpg |
| 18605 | | |
| 18606 | | executed script.view.cxc |
| 18607 | | |
| 18608 | | > open "/Users/admin/Dropbox (Technion |
| 18609 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 18610 | | |
| 18611 | | > close |
| 18612 | | |
| 18613 | | > graphics bgColor white |
| 18614 | | |
| 18615 | | > open 1WMB |
| 18616 | | |
| 18617 | | 1wmb title: |
| 18618 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 18619 | | info...] |
| 18620 | | |
| 18621 | | Chain information for 1wmb #1 |
| 18622 | | --- |
| 18623 | | Chain | Description |
| 18624 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 18625 | | |
| 18626 | | Non-standard residues in 1wmb #1 |
| 18627 | | --- |
| 18628 | | CAC — cacodylate ion (dimethylarsinate) |
| 18629 | | MG — magnesium ion |
| 18630 | | |
| 18631 | | 1wmb mmCIF Assemblies |
| 18632 | | --- |
| 18633 | | 1| author_and_software_defined_assembly |
| 18634 | | |
| 18635 | | |
| 18636 | | > open 3I3O |
| 18637 | | |
| 18638 | | 3i3o title: |
| 18639 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 18640 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 18641 | | info...] |
| 18642 | | |
| 18643 | | Chain information for 3i3o #2 |
| 18644 | | --- |
| 18645 | | Chain | Description |
| 18646 | | A B C D E F G H | Short chain dehydrogenase |
| 18647 | | |
| 18648 | | Non-standard residues in 3i3o #2 |
| 18649 | | --- |
| 18650 | | CAC — cacodylate ion (dimethylarsinate) |
| 18651 | | CL — chloride ion |
| 18652 | | MG — magnesium ion |
| 18653 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 18654 | | |
| 18655 | | 3i3o mmCIF Assemblies |
| 18656 | | --- |
| 18657 | | 1| author_and_software_defined_assembly |
| 18658 | | 2| author_and_software_defined_assembly |
| 18659 | | |
| 18660 | | |
| 18661 | | > delete ~/a |
| 18662 | | |
| 18663 | | > delete solvent |
| 18664 | | |
| 18665 | | > mmaker #2 to #1 |
| 18666 | | |
| 18667 | | Parameters |
| 18668 | | --- |
| 18669 | | Chain pairing | bb |
| 18670 | | Alignment algorithm | Needleman-Wunsch |
| 18671 | | Similarity matrix | BLOSUM-62 |
| 18672 | | SS fraction | 0.3 |
| 18673 | | Gap open (HH/SS/other) | 18/18/6 |
| 18674 | | Gap extend | 1 |
| 18675 | | SS matrix | | | H | S | O |
| 18676 | | ---|---|---|--- |
| 18677 | | H | 6 | -9 | -6 |
| 18678 | | S | | 6 | -6 |
| 18679 | | O | | | 4 |
| 18680 | | Iteration cutoff | 2 |
| 18681 | | |
| 18682 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 18683 | | score = 499.7 |
| 18684 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 18685 | | 3.736) |
| 18686 | | |
| 18687 | | |
| 18688 | | > color #1 green |
| 18689 | | |
| 18690 | | > color #2 tan |
| 18691 | | |
| 18692 | | > color ~C byatom |
| 18693 | | |
| 18694 | | > ~display |
| 18695 | | |
| 18696 | | > display #1:138 #2:176 |
| 18697 | | |
| 18698 | | > style stick |
| 18699 | | |
| 18700 | | Changed 4099 atom styles |
| 18701 | | |
| 18702 | | > ribbon |
| 18703 | | |
| 18704 | | > transparency 60 target r |
| 18705 | | |
| 18706 | | > view |
| 18707 | | |
| 18708 | | > size #1:138 #2:176 stickRadius 0.3 |
| 18709 | | |
| 18710 | | Changed 14 bond radii |
| 18711 | | |
| 18712 | | > save fig1.jpg |
| 18713 | | |
| 18714 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 18715 | | |
| 18716 | | > sel-ca |
| 18717 | | |
| 18718 | | 13 atoms, 1 model selected |
| 18719 | | 26 atoms, 2 models selected |
| 18720 | | |
| 18721 | | > display sel-residues |
| 18722 | | |
| 18723 | | > color ~C byatom |
| 18724 | | |
| 18725 | | > style stick |
| 18726 | | |
| 18727 | | Changed 4099 atom styles |
| 18728 | | |
| 18729 | | > view #1:138 :< 5 pad -1 |
| 18730 | | |
| 18731 | | > hbonds #1:138 & #1 name hb1 color green |
| 18732 | | |
| 18733 | | 3 hydrogen bonds found |
| 18734 | | |
| 18735 | | > hbonds #2:176 & #2 name hb2 color tan |
| 18736 | | |
| 18737 | | 4 hydrogen bonds found |
| 18738 | | |
| 18739 | | > transparency 90 target r |
| 18740 | | |
| 18741 | | > label #1:138 #2:176 offset 1,-1,1 |
| 18742 | | |
| 18743 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 18744 | | |
| 18745 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 18746 | | |
| 18747 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 18748 | | |
| 18749 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 18750 | | |
| 18751 | | > label #1:138 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.5 |
| 18752 | | > color green bgColor white offset 0,0,0 |
| 18753 | | |
| 18754 | | > label #2:176 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.5 |
| 18755 | | > color tan bgColor white offset 0,0.7,0 |
| 18756 | | |
| 18757 | | > ~select |
| 18758 | | |
| 18759 | | Nothing selected |
| 18760 | | |
| 18761 | | > save fig2.jpg |
| 18762 | | |
| 18763 | | > sel-ca |
| 18764 | | |
| 18765 | | 13 atoms, 1 model selected |
| 18766 | | 26 atoms, 2 models selected |
| 18767 | | |
| 18768 | | > ~ribbon |
| 18769 | | |
| 18770 | | > size stickRadius 0.05 |
| 18771 | | |
| 18772 | | Changed 4167 bond radii |
| 18773 | | |
| 18774 | | > size #1:138 stickRadius 0.2 |
| 18775 | | |
| 18776 | | Changed 7 bond radii |
| 18777 | | |
| 18778 | | > size #2:176 stickRadius 0.2 |
| 18779 | | |
| 18780 | | Changed 7 bond radii |
| 18781 | | |
| 18782 | | > view sel-residues pad -1 |
| 18783 | | |
| 18784 | | > ~select |
| 18785 | | |
| 18786 | | Nothing selected |
| 18787 | | |
| 18788 | | > save fig3.jpg |
| 18789 | | |
| 18790 | | > sel-ca |
| 18791 | | |
| 18792 | | 13 atoms, 1 model selected |
| 18793 | | 26 atoms, 2 models selected |
| 18794 | | |
| 18795 | | > view sel-residues pad -1 |
| 18796 | | |
| 18797 | | > sel-ca |
| 18798 | | |
| 18799 | | 13 atoms, 1 model selected |
| 18800 | | 26 atoms, 2 models selected |
| 18801 | | |
| 18802 | | > align #2 & sel toAtoms #1 & sel |
| 18803 | | |
| 18804 | | RMSD between 13 atom pairs is 0.455 angstroms |
| 18805 | | |
| 18806 | | > ~select |
| 18807 | | |
| 18808 | | Nothing selected |
| 18809 | | |
| 18810 | | > save fig4.jpg |
| 18811 | | |
| 18812 | | > sel-ca |
| 18813 | | |
| 18814 | | 13 atoms, 1 model selected |
| 18815 | | 26 atoms, 2 models selected |
| 18816 | | |
| 18817 | | > ribbon sel |
| 18818 | | |
| 18819 | | > ~select |
| 18820 | | |
| 18821 | | Nothing selected |
| 18822 | | |
| 18823 | | > save fig5.jpg |
| 18824 | | |
| 18825 | | executed script.view.cxc |
| 18826 | | |
| 18827 | | > open "/Users/admin/Dropbox (Technion |
| 18828 | | > Dropbox)/PROJECTS/alexB/chimerax/script.view.cxc" |
| 18829 | | |
| 18830 | | > close |
| 18831 | | |
| 18832 | | > graphics bgColor white |
| 18833 | | |
| 18834 | | > open 1WMB |
| 18835 | | |
| 18836 | | 1wmb title: |
| 18837 | | Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase [more |
| 18838 | | info...] |
| 18839 | | |
| 18840 | | Chain information for 1wmb #1 |
| 18841 | | --- |
| 18842 | | Chain | Description |
| 18843 | | A B | D(-)-3-hydroxybutyrate dehydrogenase |
| 18844 | | |
| 18845 | | Non-standard residues in 1wmb #1 |
| 18846 | | --- |
| 18847 | | CAC — cacodylate ion (dimethylarsinate) |
| 18848 | | MG — magnesium ion |
| 18849 | | |
| 18850 | | 1wmb mmCIF Assemblies |
| 18851 | | --- |
| 18852 | | 1| author_and_software_defined_assembly |
| 18853 | | |
| 18854 | | |
| 18855 | | > open 3I3O |
| 18856 | | |
| 18857 | | 3i3o title: |
| 18858 | | 2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from |
| 18859 | | Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone [more |
| 18860 | | info...] |
| 18861 | | |
| 18862 | | Chain information for 3i3o #2 |
| 18863 | | --- |
| 18864 | | Chain | Description |
| 18865 | | A B C D E F G H | Short chain dehydrogenase |
| 18866 | | |
| 18867 | | Non-standard residues in 3i3o #2 |
| 18868 | | --- |
| 18869 | | CAC — cacodylate ion (dimethylarsinate) |
| 18870 | | CL — chloride ion |
| 18871 | | MG — magnesium ion |
| 18872 | | NAE — nicotinamide adenine dinucleotide acetone adduct |
| 18873 | | |
| 18874 | | 3i3o mmCIF Assemblies |
| 18875 | | --- |
| 18876 | | 1| author_and_software_defined_assembly |
| 18877 | | 2| author_and_software_defined_assembly |
| 18878 | | |
| 18879 | | |
| 18880 | | > delete ~/a |
| 18881 | | |
| 18882 | | > delete solvent |
| 18883 | | |
| 18884 | | > mmaker #2 to #1 |
| 18885 | | |
| 18886 | | Parameters |
| 18887 | | --- |
| 18888 | | Chain pairing | bb |
| 18889 | | Alignment algorithm | Needleman-Wunsch |
| 18890 | | Similarity matrix | BLOSUM-62 |
| 18891 | | SS fraction | 0.3 |
| 18892 | | Gap open (HH/SS/other) | 18/18/6 |
| 18893 | | Gap extend | 1 |
| 18894 | | SS matrix | | | H | S | O |
| 18895 | | ---|---|---|--- |
| 18896 | | H | 6 | -9 | -6 |
| 18897 | | S | | 6 | -6 |
| 18898 | | O | | | 4 |
| 18899 | | Iteration cutoff | 2 |
| 18900 | | |
| 18901 | | Matchmaker 1wmb, chain A (#1) with 3i3o, chain A (#2), sequence alignment |
| 18902 | | score = 499.7 |
| 18903 | | RMSD between 190 pruned atom pairs is 0.961 angstroms; (across all 245 pairs: |
| 18904 | | 3.736) |
| 18905 | | |
| 18906 | | |
| 18907 | | > color #1 green |
| 18908 | | |
| 18909 | | > color #2 tan |
| 18910 | | |
| 18911 | | > color ~C byatom |
| 18912 | | |
| 18913 | | > ~display |
| 18914 | | |
| 18915 | | > display #1:138 #2:176 |
| 18916 | | |
| 18917 | | > style stick |
| 18918 | | |
| 18919 | | Changed 4099 atom styles |
| 18920 | | |
| 18921 | | > ribbon |
| 18922 | | |
| 18923 | | > transparency 60 target r |
| 18924 | | |
| 18925 | | > view |
| 18926 | | |
| 18927 | | > size #1:138 #2:176 stickRadius 0.3 |
| 18928 | | |
| 18929 | | Changed 14 bond radii |
| 18930 | | |
| 18931 | | > save fig1.jpg |
| 18932 | | |
| 18933 | | > alias sel-ca sel #1@ca & #1:138@ca @< 7.5; sel #1,2@ca & sel @< 2 |
| 18934 | | |
| 18935 | | > sel-ca |
| 18936 | | |
| 18937 | | 13 atoms, 1 model selected |
| 18938 | | 26 atoms, 2 models selected |
| 18939 | | |
| 18940 | | > display sel-residues |
| 18941 | | |
| 18942 | | > color ~C byatom |
| 18943 | | |
| 18944 | | > style stick |
| 18945 | | |
| 18946 | | Changed 4099 atom styles |
| 18947 | | |
| 18948 | | > view #1:138 :< 5 pad -1 |
| 18949 | | |
| 18950 | | > hbonds #1:138 & #1 name hb1 color green |
| 18951 | | |
| 18952 | | 3 hydrogen bonds found |
| 18953 | | |
| 18954 | | > hbonds #2:176 & #2 name hb2 color tan |
| 18955 | | |
| 18956 | | 4 hydrogen bonds found |
| 18957 | | |
| 18958 | | > transparency 90 target r |
| 18959 | | |
| 18960 | | > label #1:138 #2:176 offset 1,-1,1 |
| 18961 | | |
| 18962 | | > 2dlabels text 1WMB color green size 40 xpos .03 ypos .90 |
| 18963 | | |
| 18964 | | > 2dlabels text 3I3O color tan size 40 xpos .03 ypos .82 |
| 18965 | | |
| 18966 | | > label sel-residues & #1 height 0.4 offset 0,0,0 color green bgColor white |
| 18967 | | |
| 18968 | | > label sel-residues & #2 height 0.4 offset 0,0.7,0 color tan bgColor white |
| 18969 | | |
| 18970 | | > label #1:138 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.5 |
| 18971 | | > color green bgColor white offset 0,0,0 |
| 18972 | | |
| 18973 | | > label #2:176 text "{0.name} {0.number} {0.phi:.1f},{0.psi:.1f}" height 0.5 |
| 18974 | | > color tan bgColor white offset 0,0.7,0 |
| 18975 | | |
| 18976 | | > ~select |
| 18977 | | |
| 18978 | | Nothing selected |
| 18979 | | |
| 18980 | | > save fig2.jpg |
| | 3038 | |
| | 3039 | [had to truncate log due to ticket-length limitation] |
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