Changes between Initial Version and Version 1 of Ticket #19316


Ignore:
Timestamp:
Nov 7, 2025, 1:09:19 PM (35 hours ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #19316

    • Property Cc Eric Pettersen added
    • Property Component Unassigned → Build System
    • Property Owner set to Zach Pearson
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → ffmpeg: Permission denied

  • Ticket #19316 – Description

    initial v1  
    30413041See log for complete Python traceback. 
    30423042 
    3043 Traceback (most recent call last): 
    3044 File
    3045 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3046 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3047 self.status(self._last_message, self._last_color) 
    3048 File
    3049 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3050 packages/chimerax/ui/statusbar.py", line 164, in status 
    3051 r.draw_background() 
    3052 File
    3053 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3054 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3055 GL.glClear(flags) 
    3056 File "src/errorchecker.pyx", line 59, in
    3057 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3058 OpenGL.error.GLError: GLError( 
    3059 err = 1286, 
    3060 description = b'invalid framebuffer operation', 
    3061 baseOperation = glClear, 
    3062 cArguments = (16640,) 
    3063 ) 
    3064  
    3065 OpenGL.error.GLError: GLError( 
    3066 err = 1286, 
    3067 description = b'invalid framebuffer operation', 
    3068 baseOperation = glClear, 
    3069 cArguments = (16640,) 
    3070 ) 
    3071  
    3072 File "src/errorchecker.pyx", line 59, in
    3073 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3074  
    3075 See log for complete Python traceback. 
    3076  
    3077 Traceback (most recent call last): 
    3078 File
    3079 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3080 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3081 self.status(self._last_message, self._last_color) 
    3082 File
    3083 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3084 packages/chimerax/ui/statusbar.py", line 164, in status 
    3085 r.draw_background() 
    3086 File
    3087 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3088 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3089 GL.glClear(flags) 
    3090 File "src/errorchecker.pyx", line 59, in
    3091 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3092 OpenGL.error.GLError: GLError( 
    3093 err = 1286, 
    3094 description = b'invalid framebuffer operation', 
    3095 baseOperation = glClear, 
    3096 cArguments = (16640,) 
    3097 ) 
    3098  
    3099 OpenGL.error.GLError: GLError( 
    3100 err = 1286, 
    3101 description = b'invalid framebuffer operation', 
    3102 baseOperation = glClear, 
    3103 cArguments = (16640,) 
    3104 ) 
    3105  
    3106 File "src/errorchecker.pyx", line 59, in
    3107 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3108  
    3109 See log for complete Python traceback. 
    3110  
    3111 Traceback (most recent call last): 
    3112 File
    3113 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3114 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3115 self.status(self._last_message, self._last_color) 
    3116 File
    3117 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3118 packages/chimerax/ui/statusbar.py", line 164, in status 
    3119 r.draw_background() 
    3120 File
    3121 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3122 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3123 GL.glClear(flags) 
    3124 File "src/errorchecker.pyx", line 59, in
    3125 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3126 OpenGL.error.GLError: GLError( 
    3127 err = 1286, 
    3128 description = b'invalid framebuffer operation', 
    3129 baseOperation = glClear, 
    3130 cArguments = (16640,) 
    3131 ) 
    3132  
    3133 OpenGL.error.GLError: GLError( 
    3134 err = 1286, 
    3135 description = b'invalid framebuffer operation', 
    3136 baseOperation = glClear, 
    3137 cArguments = (16640,) 
    3138 ) 
    3139  
    3140 File "src/errorchecker.pyx", line 59, in
    3141 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3142  
    3143 See log for complete Python traceback. 
    3144  
    3145 Traceback (most recent call last): 
    3146 File
    3147 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3148 packages/chimerax/ui/gui.py", line 172, in _update_color_scheme 
    3149 self.session.logger.status(msg) 
    3150 File
    3151 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3152 packages/chimerax/core/logger.py", line 522, in status 
    3153 StatusLogger.status(self, msg, **kw) 
    3154 File
    3155 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3156 packages/chimerax/core/logger.py", line 220, in status 
    3157 if l.status(msg, color, secondary) and getattr( 
    3158 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    3159 File
    3160 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3161 packages/chimerax/ui/gui.py", line 1085, in status 
    3162 sbar.status(msg, color, secondary) 
    3163 File
    3164 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3165 packages/chimerax/ui/statusbar.py", line 164, in status 
    3166 r.draw_background() 
    3167 File
    3168 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3169 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3170 GL.glClear(flags) 
    3171 File "src/errorchecker.pyx", line 59, in
    3172 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3173 OpenGL.error.GLError: GLError( 
    3174 err = 1286, 
    3175 description = b'invalid framebuffer operation', 
    3176 baseOperation = glClear, 
    3177 cArguments = (16640,) 
    3178 ) 
    3179  
    3180 OpenGL.error.GLError: GLError( 
    3181 err = 1286, 
    3182 description = b'invalid framebuffer operation', 
    3183 baseOperation = glClear, 
    3184 cArguments = (16640,) 
    3185 ) 
    3186  
    3187 File "src/errorchecker.pyx", line 59, in
    3188 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3189  
    3190 See log for complete Python traceback. 
    3191  
    3192 Traceback (most recent call last): 
    3193 File
    3194 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3195 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3196 self.status(self._last_message, self._last_color) 
    3197 File
    3198 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3199 packages/chimerax/ui/statusbar.py", line 164, in status 
    3200 r.draw_background() 
    3201 File
    3202 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3203 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3204 GL.glClear(flags) 
    3205 File "src/errorchecker.pyx", line 59, in
    3206 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3207 OpenGL.error.GLError: GLError( 
    3208 err = 1286, 
    3209 description = b'invalid framebuffer operation', 
    3210 baseOperation = glClear, 
    3211 cArguments = (16640,) 
    3212 ) 
    3213  
    3214 OpenGL.error.GLError: GLError( 
    3215 err = 1286, 
    3216 description = b'invalid framebuffer operation', 
    3217 baseOperation = glClear, 
    3218 cArguments = (16640,) 
    3219 ) 
    3220  
    3221 File "src/errorchecker.pyx", line 59, in
    3222 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3223  
    3224 See log for complete Python traceback. 
    3225  
    3226 Traceback (most recent call last): 
    3227 File
    3228 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3229 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3230 self.status(self._last_message, self._last_color) 
    3231 File
    3232 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3233 packages/chimerax/ui/statusbar.py", line 164, in status 
    3234 r.draw_background() 
    3235 File
    3236 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3237 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3238 GL.glClear(flags) 
    3239 File "src/errorchecker.pyx", line 59, in
    3240 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3241 OpenGL.error.GLError: GLError( 
    3242 err = 1286, 
    3243 description = b'invalid framebuffer operation', 
    3244 baseOperation = glClear, 
    3245 cArguments = (16640,) 
    3246 ) 
    3247  
    3248 OpenGL.error.GLError: GLError( 
    3249 err = 1286, 
    3250 description = b'invalid framebuffer operation', 
    3251 baseOperation = glClear, 
    3252 cArguments = (16640,) 
    3253 ) 
    3254  
    3255 File "src/errorchecker.pyx", line 59, in
    3256 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3257  
    3258 See log for complete Python traceback. 
    3259  
    3260 Traceback (most recent call last): 
    3261 File
    3262 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3263 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3264 self.status(self._last_message, self._last_color) 
    3265 File
    3266 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3267 packages/chimerax/ui/statusbar.py", line 164, in status 
    3268 r.draw_background() 
    3269 File
    3270 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3271 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3272 GL.glClear(flags) 
    3273 File "src/errorchecker.pyx", line 59, in
    3274 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3275 OpenGL.error.GLError: GLError( 
    3276 err = 1286, 
    3277 description = b'invalid framebuffer operation', 
    3278 baseOperation = glClear, 
    3279 cArguments = (16640,) 
    3280 ) 
    3281  
    3282 OpenGL.error.GLError: GLError( 
    3283 err = 1286, 
    3284 description = b'invalid framebuffer operation', 
    3285 baseOperation = glClear, 
    3286 cArguments = (16640,) 
    3287 ) 
    3288  
    3289 File "src/errorchecker.pyx", line 59, in
    3290 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3291  
    3292 See log for complete Python traceback. 
    3293  
    3294 Traceback (most recent call last): 
    3295 File
    3296 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3297 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3298 self.status(self._last_message, self._last_color) 
    3299 File
    3300 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3301 packages/chimerax/ui/statusbar.py", line 164, in status 
    3302 r.draw_background() 
    3303 File
    3304 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3305 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3306 GL.glClear(flags) 
    3307 File "src/errorchecker.pyx", line 59, in
    3308 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3309 OpenGL.error.GLError: GLError( 
    3310 err = 1286, 
    3311 description = b'invalid framebuffer operation', 
    3312 baseOperation = glClear, 
    3313 cArguments = (16640,) 
    3314 ) 
    3315  
    3316 OpenGL.error.GLError: GLError( 
    3317 err = 1286, 
    3318 description = b'invalid framebuffer operation', 
    3319 baseOperation = glClear, 
    3320 cArguments = (16640,) 
    3321 ) 
    3322  
    3323 File "src/errorchecker.pyx", line 59, in
    3324 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3325  
    3326 See log for complete Python traceback. 
    3327  
    3328 Traceback (most recent call last): 
    3329 File
    3330 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3331 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3332 self.status(self._last_message, self._last_color) 
    3333 File
    3334 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3335 packages/chimerax/ui/statusbar.py", line 164, in status 
    3336 r.draw_background() 
    3337 File
    3338 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3339 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3340 GL.glClear(flags) 
    3341 File "src/errorchecker.pyx", line 59, in
    3342 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3343 OpenGL.error.GLError: GLError( 
    3344 err = 1286, 
    3345 description = b'invalid framebuffer operation', 
    3346 baseOperation = glClear, 
    3347 cArguments = (16640,) 
    3348 ) 
    3349  
    3350 OpenGL.error.GLError: GLError( 
    3351 err = 1286, 
    3352 description = b'invalid framebuffer operation', 
    3353 baseOperation = glClear, 
    3354 cArguments = (16640,) 
    3355 ) 
    3356  
    3357 File "src/errorchecker.pyx", line 59, in
    3358 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3359  
    3360 See log for complete Python traceback. 
    3361  
    3362 Traceback (most recent call last): 
    3363 File
    3364 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3365 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3366 self.status(self._last_message, self._last_color) 
    3367 File
    3368 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3369 packages/chimerax/ui/statusbar.py", line 164, in status 
    3370 r.draw_background() 
    3371 File
    3372 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3373 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3374 GL.glClear(flags) 
    3375 File "src/errorchecker.pyx", line 59, in
    3376 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3377 OpenGL.error.GLError: GLError( 
    3378 err = 1286, 
    3379 description = b'invalid framebuffer operation', 
    3380 baseOperation = glClear, 
    3381 cArguments = (16640,) 
    3382 ) 
    3383  
    3384 OpenGL.error.GLError: GLError( 
    3385 err = 1286, 
    3386 description = b'invalid framebuffer operation', 
    3387 baseOperation = glClear, 
    3388 cArguments = (16640,) 
    3389 ) 
    3390  
    3391 File "src/errorchecker.pyx", line 59, in
    3392 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3393  
    3394 See log for complete Python traceback. 
    3395  
    3396 Traceback (most recent call last): 
    3397 File
    3398 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3399 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3400 self.status(self._last_message, self._last_color) 
    3401 File
    3402 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3403 packages/chimerax/ui/statusbar.py", line 164, in status 
    3404 r.draw_background() 
    3405 File
    3406 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3407 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3408 GL.glClear(flags) 
    3409 File "src/errorchecker.pyx", line 59, in
    3410 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3411 OpenGL.error.GLError: GLError( 
    3412 err = 1286, 
    3413 description = b'invalid framebuffer operation', 
    3414 baseOperation = glClear, 
    3415 cArguments = (16640,) 
    3416 ) 
    3417  
    3418 OpenGL.error.GLError: GLError( 
    3419 err = 1286, 
    3420 description = b'invalid framebuffer operation', 
    3421 baseOperation = glClear, 
    3422 cArguments = (16640,) 
    3423 ) 
    3424  
    3425 File "src/errorchecker.pyx", line 59, in
    3426 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3427  
    3428 See log for complete Python traceback. 
    3429  
    3430 Traceback (most recent call last): 
    3431 File
    3432 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3433 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3434 self.status(self._last_message, self._last_color) 
    3435 File
    3436 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3437 packages/chimerax/ui/statusbar.py", line 164, in status 
    3438 r.draw_background() 
    3439 File
    3440 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3441 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3442 GL.glClear(flags) 
    3443 File "src/errorchecker.pyx", line 59, in
    3444 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3445 OpenGL.error.GLError: GLError( 
    3446 err = 1286, 
    3447 description = b'invalid framebuffer operation', 
    3448 baseOperation = glClear, 
    3449 cArguments = (16640,) 
    3450 ) 
    3451  
    3452 OpenGL.error.GLError: GLError( 
    3453 err = 1286, 
    3454 description = b'invalid framebuffer operation', 
    3455 baseOperation = glClear, 
    3456 cArguments = (16640,) 
    3457 ) 
    3458  
    3459 File "src/errorchecker.pyx", line 59, in
    3460 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3461  
    3462 See log for complete Python traceback. 
    3463  
    3464 Traceback (most recent call last): 
    3465 File
    3466 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3467 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3468 self.status(self._last_message, self._last_color) 
    3469 File
    3470 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3471 packages/chimerax/ui/statusbar.py", line 164, in status 
    3472 r.draw_background() 
    3473 File
    3474 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3475 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3476 GL.glClear(flags) 
    3477 File "src/errorchecker.pyx", line 59, in
    3478 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3479 OpenGL.error.GLError: GLError( 
    3480 err = 1286, 
    3481 description = b'invalid framebuffer operation', 
    3482 baseOperation = glClear, 
    3483 cArguments = (16640,) 
    3484 ) 
    3485  
    3486 OpenGL.error.GLError: GLError( 
    3487 err = 1286, 
    3488 description = b'invalid framebuffer operation', 
    3489 baseOperation = glClear, 
    3490 cArguments = (16640,) 
    3491 ) 
    3492  
    3493 File "src/errorchecker.pyx", line 59, in
    3494 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3495  
    3496 See log for complete Python traceback. 
    3497  
    3498 Desktop color scheme is light 
    3499 Traceback (most recent call last): 
    3500 File
    3501 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3502 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3503 self.status(self._last_message, self._last_color) 
    3504 File
    3505 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3506 packages/chimerax/ui/statusbar.py", line 164, in status 
    3507 r.draw_background() 
    3508 File
    3509 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3510 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3511 GL.glClear(flags) 
    3512 File "src/errorchecker.pyx", line 59, in
    3513 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3514 OpenGL.error.GLError: GLError( 
    3515 err = 1286, 
    3516 description = b'invalid framebuffer operation', 
    3517 baseOperation = glClear, 
    3518 cArguments = (16640,) 
    3519 ) 
    3520  
    3521 OpenGL.error.GLError: GLError( 
    3522 err = 1286, 
    3523 description = b'invalid framebuffer operation', 
    3524 baseOperation = glClear, 
    3525 cArguments = (16640,) 
    3526 ) 
    3527  
    3528 File "src/errorchecker.pyx", line 59, in
    3529 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3530  
    3531 See log for complete Python traceback. 
    3532  
    3533 Traceback (most recent call last): 
    3534 File
    3535 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3536 packages/chimerax/ui/gui.py", line 873, in customEvent 
    3537 func(*args, **kw) 
    3538 File
    3539 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3540 packages/chimerax/core/logger.py", line 522, in status 
    3541 StatusLogger.status(self, msg, **kw) 
    3542 File
    3543 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3544 packages/chimerax/core/logger.py", line 220, in status 
    3545 if l.status(msg, color, secondary) and getattr( 
    3546 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    3547 File
    3548 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3549 packages/chimerax/ui/gui.py", line 1085, in status 
    3550 sbar.status(msg, color, secondary) 
    3551 File
    3552 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3553 packages/chimerax/ui/statusbar.py", line 164, in status 
    3554 r.draw_background() 
    3555 File
    3556 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3557 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3558 GL.glClear(flags) 
    3559 File "src/errorchecker.pyx", line 59, in
    3560 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3561 OpenGL.error.GLError: GLError( 
    3562 err = 1286, 
    3563 description = b'invalid framebuffer operation', 
    3564 baseOperation = glClear, 
    3565 cArguments = (16640,) 
    3566 ) 
    3567  
    3568 OpenGL.error.GLError: GLError( 
    3569 err = 1286, 
    3570 description = b'invalid framebuffer operation', 
    3571 baseOperation = glClear, 
    3572 cArguments = (16640,) 
    3573 ) 
    3574  
    3575 File "src/errorchecker.pyx", line 59, in
    3576 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3577  
    3578 See log for complete Python traceback. 
    3579  
    3580 Traceback (most recent call last): 
    3581 File
    3582 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3583 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3584 self.status(self._last_message, self._last_color) 
    3585 File
    3586 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3587 packages/chimerax/ui/statusbar.py", line 164, in status 
    3588 r.draw_background() 
    3589 File
    3590 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3591 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3592 GL.glClear(flags) 
    3593 File "src/errorchecker.pyx", line 59, in
    3594 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3595 OpenGL.error.GLError: GLError( 
    3596 err = 1286, 
    3597 description = b'invalid framebuffer operation', 
    3598 baseOperation = glClear, 
    3599 cArguments = (16640,) 
    3600 ) 
    3601  
    3602 OpenGL.error.GLError: GLError( 
    3603 err = 1286, 
    3604 description = b'invalid framebuffer operation', 
    3605 baseOperation = glClear, 
    3606 cArguments = (16640,) 
    3607 ) 
    3608  
    3609 File "src/errorchecker.pyx", line 59, in
    3610 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3611  
    3612 See log for complete Python traceback. 
    3613  
    3614 Traceback (most recent call last): 
    3615 File
    3616 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3617 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3618 self.status(self._last_message, self._last_color) 
    3619 File
    3620 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3621 packages/chimerax/ui/statusbar.py", line 164, in status 
    3622 r.draw_background() 
    3623 File
    3624 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3625 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3626 GL.glClear(flags) 
    3627 File "src/errorchecker.pyx", line 59, in
    3628 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3629 OpenGL.error.GLError: GLError( 
    3630 err = 1286, 
    3631 description = b'invalid framebuffer operation', 
    3632 baseOperation = glClear, 
    3633 cArguments = (16640,) 
    3634 ) 
    3635  
    3636 OpenGL.error.GLError: GLError( 
    3637 err = 1286, 
    3638 description = b'invalid framebuffer operation', 
    3639 baseOperation = glClear, 
    3640 cArguments = (16640,) 
    3641 ) 
    3642  
    3643 File "src/errorchecker.pyx", line 59, in
    3644 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3645  
    3646 See log for complete Python traceback. 
    3647  
    3648 Traceback (most recent call last): 
    3649 File
    3650 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3651 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3652 self.status(self._last_message, self._last_color) 
    3653 File
    3654 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3655 packages/chimerax/ui/statusbar.py", line 164, in status 
    3656 r.draw_background() 
    3657 File
    3658 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3659 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3660 GL.glClear(flags) 
    3661 File "src/errorchecker.pyx", line 59, in
    3662 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3663 OpenGL.error.GLError: GLError( 
    3664 err = 1286, 
    3665 description = b'invalid framebuffer operation', 
    3666 baseOperation = glClear, 
    3667 cArguments = (16640,) 
    3668 ) 
    3669  
    3670 OpenGL.error.GLError: GLError( 
    3671 err = 1286, 
    3672 description = b'invalid framebuffer operation', 
    3673 baseOperation = glClear, 
    3674 cArguments = (16640,) 
    3675 ) 
    3676  
    3677 File "src/errorchecker.pyx", line 59, in
    3678 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3679  
    3680 See log for complete Python traceback. 
    3681  
    3682 Traceback (most recent call last): 
    3683 File
    3684 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3685 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3686 self.status(self._last_message, self._last_color) 
    3687 File
    3688 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3689 packages/chimerax/ui/statusbar.py", line 164, in status 
    3690 r.draw_background() 
    3691 File
    3692 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3693 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3694 GL.glClear(flags) 
    3695 File "src/errorchecker.pyx", line 59, in
    3696 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3697 OpenGL.error.GLError: GLError( 
    3698 err = 1286, 
    3699 description = b'invalid framebuffer operation', 
    3700 baseOperation = glClear, 
    3701 cArguments = (16640,) 
    3702 ) 
    3703  
    3704 OpenGL.error.GLError: GLError( 
    3705 err = 1286, 
    3706 description = b'invalid framebuffer operation', 
    3707 baseOperation = glClear, 
    3708 cArguments = (16640,) 
    3709 ) 
    3710  
    3711 File "src/errorchecker.pyx", line 59, in
    3712 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3713  
    3714 See log for complete Python traceback. 
    3715  
    3716 Traceback (most recent call last): 
    3717 File
    3718 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3719 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3720 self.status(self._last_message, self._last_color) 
    3721 File
    3722 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3723 packages/chimerax/ui/statusbar.py", line 164, in status 
    3724 r.draw_background() 
    3725 File
    3726 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3727 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3728 GL.glClear(flags) 
    3729 File "src/errorchecker.pyx", line 59, in
    3730 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3731 OpenGL.error.GLError: GLError( 
    3732 err = 1286, 
    3733 description = b'invalid framebuffer operation', 
    3734 baseOperation = glClear, 
    3735 cArguments = (16640,) 
    3736 ) 
    3737  
    3738 OpenGL.error.GLError: GLError( 
    3739 err = 1286, 
    3740 description = b'invalid framebuffer operation', 
    3741 baseOperation = glClear, 
    3742 cArguments = (16640,) 
    3743 ) 
    3744  
    3745 File "src/errorchecker.pyx", line 59, in
    3746 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3747  
    3748 See log for complete Python traceback. 
    3749  
    3750 Traceback (most recent call last): 
    3751 File
    3752 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3753 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3754 self.status(self._last_message, self._last_color) 
    3755 File
    3756 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3757 packages/chimerax/ui/statusbar.py", line 164, in status 
    3758 r.draw_background() 
    3759 File
    3760 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3761 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3762 GL.glClear(flags) 
    3763 File "src/errorchecker.pyx", line 59, in
    3764 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3765 OpenGL.error.GLError: GLError( 
    3766 err = 1286, 
    3767 description = b'invalid framebuffer operation', 
    3768 baseOperation = glClear, 
    3769 cArguments = (16640,) 
    3770 ) 
    3771  
    3772 OpenGL.error.GLError: GLError( 
    3773 err = 1286, 
    3774 description = b'invalid framebuffer operation', 
    3775 baseOperation = glClear, 
    3776 cArguments = (16640,) 
    3777 ) 
    3778  
    3779 File "src/errorchecker.pyx", line 59, in
    3780 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3781  
    3782 See log for complete Python traceback. 
    3783  
    3784 Traceback (most recent call last): 
    3785 File
    3786 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3787 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3788 self.status(self._last_message, self._last_color) 
    3789 File
    3790 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3791 packages/chimerax/ui/statusbar.py", line 164, in status 
    3792 r.draw_background() 
    3793 File
    3794 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3795 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3796 GL.glClear(flags) 
    3797 File "src/errorchecker.pyx", line 59, in
    3798 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3799 OpenGL.error.GLError: GLError( 
    3800 err = 1286, 
    3801 description = b'invalid framebuffer operation', 
    3802 baseOperation = glClear, 
    3803 cArguments = (16640,) 
    3804 ) 
    3805  
    3806 OpenGL.error.GLError: GLError( 
    3807 err = 1286, 
    3808 description = b'invalid framebuffer operation', 
    3809 baseOperation = glClear, 
    3810 cArguments = (16640,) 
    3811 ) 
    3812  
    3813 File "src/errorchecker.pyx", line 59, in
    3814 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3815  
    3816 See log for complete Python traceback. 
    3817  
    3818 Traceback (most recent call last): 
    3819 File
    3820 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3821 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3822 self.status(self._last_message, self._last_color) 
    3823 File
    3824 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3825 packages/chimerax/ui/statusbar.py", line 164, in status 
    3826 r.draw_background() 
    3827 File
    3828 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3829 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3830 GL.glClear(flags) 
    3831 File "src/errorchecker.pyx", line 59, in
    3832 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3833 OpenGL.error.GLError: GLError( 
    3834 err = 1286, 
    3835 description = b'invalid framebuffer operation', 
    3836 baseOperation = glClear, 
    3837 cArguments = (16640,) 
    3838 ) 
    3839  
    3840 OpenGL.error.GLError: GLError( 
    3841 err = 1286, 
    3842 description = b'invalid framebuffer operation', 
    3843 baseOperation = glClear, 
    3844 cArguments = (16640,) 
    3845 ) 
    3846  
    3847 File "src/errorchecker.pyx", line 59, in
    3848 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3849  
    3850 See log for complete Python traceback. 
    3851  
    3852 Traceback (most recent call last): 
    3853 File
    3854 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3855 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3856 self.status(self._last_message, self._last_color) 
    3857 File
    3858 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3859 packages/chimerax/ui/statusbar.py", line 164, in status 
    3860 r.draw_background() 
    3861 File
    3862 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3863 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3864 GL.glClear(flags) 
    3865 File "src/errorchecker.pyx", line 59, in
    3866 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3867 OpenGL.error.GLError: GLError( 
    3868 err = 1286, 
    3869 description = b'invalid framebuffer operation', 
    3870 baseOperation = glClear, 
    3871 cArguments = (16640,) 
    3872 ) 
    3873  
    3874 OpenGL.error.GLError: GLError( 
    3875 err = 1286, 
    3876 description = b'invalid framebuffer operation', 
    3877 baseOperation = glClear, 
    3878 cArguments = (16640,) 
    3879 ) 
    3880  
    3881 File "src/errorchecker.pyx", line 59, in
    3882 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3883  
    3884 See log for complete Python traceback. 
    3885  
    3886 Traceback (most recent call last): 
    3887 File
    3888 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3889 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3890 self.status(self._last_message, self._last_color) 
    3891 File
    3892 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3893 packages/chimerax/ui/statusbar.py", line 164, in status 
    3894 r.draw_background() 
    3895 File
    3896 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3897 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3898 GL.glClear(flags) 
    3899 File "src/errorchecker.pyx", line 59, in
    3900 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3901 OpenGL.error.GLError: GLError( 
    3902 err = 1286, 
    3903 description = b'invalid framebuffer operation', 
    3904 baseOperation = glClear, 
    3905 cArguments = (16640,) 
    3906 ) 
    3907  
    3908 OpenGL.error.GLError: GLError( 
    3909 err = 1286, 
    3910 description = b'invalid framebuffer operation', 
    3911 baseOperation = glClear, 
    3912 cArguments = (16640,) 
    3913 ) 
    3914  
    3915 File "src/errorchecker.pyx", line 59, in
    3916 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3917  
    3918 See log for complete Python traceback. 
    3919  
    3920 Traceback (most recent call last): 
    3921 File
    3922 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3923 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3924 self.status(self._last_message, self._last_color) 
    3925 File
    3926 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3927 packages/chimerax/ui/statusbar.py", line 164, in status 
    3928 r.draw_background() 
    3929 File
    3930 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3931 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3932 GL.glClear(flags) 
    3933 File "src/errorchecker.pyx", line 59, in
    3934 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3935 OpenGL.error.GLError: GLError( 
    3936 err = 1286, 
    3937 description = b'invalid framebuffer operation', 
    3938 baseOperation = glClear, 
    3939 cArguments = (16640,) 
    3940 ) 
    3941  
    3942 OpenGL.error.GLError: GLError( 
    3943 err = 1286, 
    3944 description = b'invalid framebuffer operation', 
    3945 baseOperation = glClear, 
    3946 cArguments = (16640,) 
    3947 ) 
    3948  
    3949 File "src/errorchecker.pyx", line 59, in
    3950 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3951  
    3952 See log for complete Python traceback. 
    3953  
    3954 Traceback (most recent call last): 
    3955 File
    3956 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3957 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3958 self.status(self._last_message, self._last_color) 
    3959 File
    3960 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3961 packages/chimerax/ui/statusbar.py", line 164, in status 
    3962 r.draw_background() 
    3963 File
    3964 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3965 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3966 GL.glClear(flags) 
    3967 File "src/errorchecker.pyx", line 59, in
    3968 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3969 OpenGL.error.GLError: GLError( 
    3970 err = 1286, 
    3971 description = b'invalid framebuffer operation', 
    3972 baseOperation = glClear, 
    3973 cArguments = (16640,) 
    3974 ) 
    3975  
    3976 OpenGL.error.GLError: GLError( 
    3977 err = 1286, 
    3978 description = b'invalid framebuffer operation', 
    3979 baseOperation = glClear, 
    3980 cArguments = (16640,) 
    3981 ) 
    3982  
    3983 File "src/errorchecker.pyx", line 59, in
    3984 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3985  
    3986 See log for complete Python traceback. 
    3987  
    3988 Traceback (most recent call last): 
    3989 File
    3990 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3991 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3992 self.status(self._last_message, self._last_color) 
    3993 File
    3994 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3995 packages/chimerax/ui/statusbar.py", line 164, in status 
    3996 r.draw_background() 
    3997 File
    3998 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3999 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4000 GL.glClear(flags) 
    4001 File "src/errorchecker.pyx", line 59, in
    4002 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4003 OpenGL.error.GLError: GLError( 
    4004 err = 1286, 
    4005 description = b'invalid framebuffer operation', 
    4006 baseOperation = glClear, 
    4007 cArguments = (16640,) 
    4008 ) 
    4009  
    4010 OpenGL.error.GLError: GLError( 
    4011 err = 1286, 
    4012 description = b'invalid framebuffer operation', 
    4013 baseOperation = glClear, 
    4014 cArguments = (16640,) 
    4015 ) 
    4016  
    4017 File "src/errorchecker.pyx", line 59, in
    4018 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4019  
    4020 See log for complete Python traceback. 
    4021  
    4022 Traceback (most recent call last): 
    4023 File
    4024 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4025 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4026 self.status(self._last_message, self._last_color) 
    4027 File
    4028 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4029 packages/chimerax/ui/statusbar.py", line 164, in status 
    4030 r.draw_background() 
    4031 File
    4032 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4033 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4034 GL.glClear(flags) 
    4035 File "src/errorchecker.pyx", line 59, in
    4036 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4037 OpenGL.error.GLError: GLError( 
    4038 err = 1286, 
    4039 description = b'invalid framebuffer operation', 
    4040 baseOperation = glClear, 
    4041 cArguments = (16640,) 
    4042 ) 
    4043  
    4044 OpenGL.error.GLError: GLError( 
    4045 err = 1286, 
    4046 description = b'invalid framebuffer operation', 
    4047 baseOperation = glClear, 
    4048 cArguments = (16640,) 
    4049 ) 
    4050  
    4051 File "src/errorchecker.pyx", line 59, in
    4052 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4053  
    4054 See log for complete Python traceback. 
    4055  
    4056 Traceback (most recent call last): 
    4057 File
    4058 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4059 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4060 self.status(self._last_message, self._last_color) 
    4061 File
    4062 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4063 packages/chimerax/ui/statusbar.py", line 164, in status 
    4064 r.draw_background() 
    4065 File
    4066 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4067 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4068 GL.glClear(flags) 
    4069 File "src/errorchecker.pyx", line 59, in
    4070 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4071 OpenGL.error.GLError: GLError( 
    4072 err = 1286, 
    4073 description = b'invalid framebuffer operation', 
    4074 baseOperation = glClear, 
    4075 cArguments = (16640,) 
    4076 ) 
    4077  
    4078 OpenGL.error.GLError: GLError( 
    4079 err = 1286, 
    4080 description = b'invalid framebuffer operation', 
    4081 baseOperation = glClear, 
    4082 cArguments = (16640,) 
    4083 ) 
    4084  
    4085 File "src/errorchecker.pyx", line 59, in
    4086 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4087  
    4088 See log for complete Python traceback. 
    4089  
    4090 Traceback (most recent call last): 
    4091 File
    4092 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4093 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4094 self.status(self._last_message, self._last_color) 
    4095 File
    4096 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4097 packages/chimerax/ui/statusbar.py", line 164, in status 
    4098 r.draw_background() 
    4099 File
    4100 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4101 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4102 GL.glClear(flags) 
    4103 File "src/errorchecker.pyx", line 59, in
    4104 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4105 OpenGL.error.GLError: GLError( 
    4106 err = 1286, 
    4107 description = b'invalid framebuffer operation', 
    4108 baseOperation = glClear, 
    4109 cArguments = (16640,) 
    4110 ) 
    4111  
    4112 OpenGL.error.GLError: GLError( 
    4113 err = 1286, 
    4114 description = b'invalid framebuffer operation', 
    4115 baseOperation = glClear, 
    4116 cArguments = (16640,) 
    4117 ) 
    4118  
    4119 File "src/errorchecker.pyx", line 59, in
    4120 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4121  
    4122 See log for complete Python traceback. 
    4123  
    4124 Traceback (most recent call last): 
    4125 File
    4126 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4127 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4128 self.status(self._last_message, self._last_color) 
    4129 File
    4130 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4131 packages/chimerax/ui/statusbar.py", line 164, in status 
    4132 r.draw_background() 
    4133 File
    4134 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4135 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4136 GL.glClear(flags) 
    4137 File "src/errorchecker.pyx", line 59, in
    4138 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4139 OpenGL.error.GLError: GLError( 
    4140 err = 1286, 
    4141 description = b'invalid framebuffer operation', 
    4142 baseOperation = glClear, 
    4143 cArguments = (16640,) 
    4144 ) 
    4145  
    4146 OpenGL.error.GLError: GLError( 
    4147 err = 1286, 
    4148 description = b'invalid framebuffer operation', 
    4149 baseOperation = glClear, 
    4150 cArguments = (16640,) 
    4151 ) 
    4152  
    4153 File "src/errorchecker.pyx", line 59, in
    4154 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4155  
    4156 See log for complete Python traceback. 
    4157  
    4158 Traceback (most recent call last): 
    4159 File
    4160 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4161 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4162 self.status(self._last_message, self._last_color) 
    4163 File
    4164 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4165 packages/chimerax/ui/statusbar.py", line 164, in status 
    4166 r.draw_background() 
    4167 File
    4168 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4169 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4170 GL.glClear(flags) 
    4171 File "src/errorchecker.pyx", line 59, in
    4172 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4173 OpenGL.error.GLError: GLError( 
    4174 err = 1286, 
    4175 description = b'invalid framebuffer operation', 
    4176 baseOperation = glClear, 
    4177 cArguments = (16640,) 
    4178 ) 
    4179  
    4180 OpenGL.error.GLError: GLError( 
    4181 err = 1286, 
    4182 description = b'invalid framebuffer operation', 
    4183 baseOperation = glClear, 
    4184 cArguments = (16640,) 
    4185 ) 
    4186  
    4187 File "src/errorchecker.pyx", line 59, in
    4188 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4189  
    4190 See log for complete Python traceback. 
    4191  
    4192 
    4193 > hide #!1 models
    4194 
    4195 > hide #4 models
    4196 
    4197 > hide #6 models
    4198 
    4199 > hide #7 models
    4200 
    4201 > show #6 models
    4202 
    4203 > hide #6 models
    4204 
    4205 > select clear
    4206 
    4207 Traceback (most recent call last): 
    4208 File
    4209 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4210 packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda> 
    4211 gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
    4212 "mouse_up") 
    4213 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4214 File
    4215 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4216 packages/chimerax/mouse_modes/mousemodes.py", line 556, in
    4217 _dispatch_mouse_event 
    4218 f(MouseEvent(event, modifiers=modifiers)) 
    4219 File
    4220 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4221 packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up 
    4222 mouse_select(event, mode, self.session, self.view) 
    4223 File
    4224 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4225 packages/chimerax/mouse_modes/std_modes.py", line 210, in mouse_select 
    4226 select_pick(session, pick, mode) 
    4227 File
    4228 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4229 packages/chimerax/mouse_modes/std_modes.py", line 227, in select_pick 
    4230 session.logger.status('cleared selection') 
    4231 File
    4232 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4233 packages/chimerax/core/logger.py", line 522, in status 
    4234 StatusLogger.status(self, msg, **kw) 
    4235 File
    4236 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4237 packages/chimerax/core/logger.py", line 220, in status 
    4238 if l.status(msg, color, secondary) and getattr( 
    4239 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4240 File
    4241 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4242 packages/chimerax/ui/gui.py", line 1085, in status 
    4243 sbar.status(msg, color, secondary) 
    4244 File
    4245 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4246 packages/chimerax/ui/statusbar.py", line 164, in status 
    4247 r.draw_background() 
    4248 File
    4249 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4250 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4251 GL.glClear(flags) 
    4252 File "src/errorchecker.pyx", line 59, in
    4253 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4254 OpenGL.error.GLError: GLError( 
    4255 err = 1286, 
    4256 description = b'invalid framebuffer operation', 
    4257 baseOperation = glClear, 
    4258 cArguments = (16640,) 
    4259 ) 
    4260  
    4261 OpenGL.error.GLError: GLError( 
    4262 err = 1286, 
    4263 description = b'invalid framebuffer operation', 
    4264 baseOperation = glClear, 
    4265 cArguments = (16640,) 
    4266 ) 
    4267  
    4268 File "src/errorchecker.pyx", line 59, in
    4269 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4270  
    4271 See log for complete Python traceback. 
    4272  
    4273 
    4274 > select #5/H:39
    4275 
    4276 17 atoms, 16 bonds, 1 residue, 1 model selected 
    4277 Traceback (most recent call last): 
    4278 File
    4279 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4280 packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda> 
    4281 gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
    4282 "mouse_up") 
    4283 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4284 File
    4285 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4286 packages/chimerax/mouse_modes/mousemodes.py", line 556, in
    4287 _dispatch_mouse_event 
    4288 f(MouseEvent(event, modifiers=modifiers)) 
    4289 File
    4290 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4291 packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up 
    4292 mouse_select(event, mode, self.session, self.view) 
    4293 File
    4294 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4295 packages/chimerax/mouse_modes/std_modes.py", line 210, in mouse_select 
    4296 select_pick(session, pick, mode) 
    4297 File
    4298 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4299 packages/chimerax/mouse_modes/std_modes.py", line 241, in select_pick 
    4300 run(session, 'select %s' % spec) 
    4301 File
    4302 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4303 packages/chimerax/core/commands/run.py", line 49, in run 
    4304 results = command.run(text, log=log, return_json=return_json) 
    4305 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4306 File
    4307 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4308 packages/chimerax/core/commands/cli.py", line 3221, in run 
    4309 result = ci.function(session, **kw_args) 
    4310 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4311 File
    4312 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4313 packages/chimerax/std_commands/select.py", line 62, in select 
    4314 report_selection(session) 
    4315 File
    4316 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4317 packages/chimerax/std_commands/select.py", line 192, in report_selection 
    4318 session.logger.status(', '.join(lines) + ' selected', log = True) 
    4319 File
    4320 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4321 packages/chimerax/core/logger.py", line 522, in status 
    4322 StatusLogger.status(self, msg, **kw) 
    4323 File
    4324 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4325 packages/chimerax/core/logger.py", line 220, in status 
    4326 if l.status(msg, color, secondary) and getattr( 
    4327 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4328 File
    4329 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4330 packages/chimerax/ui/gui.py", line 1085, in status 
    4331 sbar.status(msg, color, secondary) 
    4332 File
    4333 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4334 packages/chimerax/ui/statusbar.py", line 164, in status 
    4335 r.draw_background() 
    4336 File
    4337 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4338 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4339 GL.glClear(flags) 
    4340 File "src/errorchecker.pyx", line 59, in
    4341 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4342 OpenGL.error.GLError: GLError( 
    4343 err = 1286, 
    4344 description = b'invalid framebuffer operation', 
    4345 baseOperation = glClear, 
    4346 cArguments = (16640,) 
    4347 ) 
    4348  
    4349 OpenGL.error.GLError: GLError( 
    4350 err = 1286, 
    4351 description = b'invalid framebuffer operation', 
    4352 baseOperation = glClear, 
    4353 cArguments = (16640,) 
    4354 ) 
    4355  
    4356 File "src/errorchecker.pyx", line 59, in
    4357 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4358  
    4359 See log for complete Python traceback. 
    4360  
    4361 
    4362 > select add #5/G:93
    4363 
    4364 33 atoms, 31 bonds, 2 residues, 1 model selected 
    4365 Traceback (most recent call last): 
    4366 File
    4367 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4368 packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda> 
    4369 gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
    4370 "mouse_up") 
    4371 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4372 File
    4373 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4374 packages/chimerax/mouse_modes/mousemodes.py", line 556, in
    4375 _dispatch_mouse_event 
    4376 f(MouseEvent(event, modifiers=modifiers)) 
    4377 File
    4378 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4379 packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up 
    4380 mouse_select(event, mode, self.session, self.view) 
    4381 File
    4382 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4383 packages/chimerax/mouse_modes/std_modes.py", line 210, in mouse_select 
    4384 select_pick(session, pick, mode) 
    4385 File
    4386 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4387 packages/chimerax/mouse_modes/std_modes.py", line 245, in select_pick 
    4388 run(session, 'select %s %s' % (operation, spec)) 
    4389 File
    4390 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4391 packages/chimerax/core/commands/run.py", line 49, in run 
    4392 results = command.run(text, log=log, return_json=return_json) 
    4393 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4394 File
    4395 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4396 packages/chimerax/core/commands/cli.py", line 3221, in run 
    4397 result = ci.function(session, **kw_args) 
    4398 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4399 File
    4400 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4401 packages/chimerax/std_commands/select.py", line 120, in select_add 
    4402 report_selection(session) 
    4403 File
    4404 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4405 packages/chimerax/std_commands/select.py", line 192, in report_selection 
    4406 session.logger.status(', '.join(lines) + ' selected', log = True) 
    4407 File
    4408 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4409 packages/chimerax/core/logger.py", line 522, in status 
    4410 StatusLogger.status(self, msg, **kw) 
    4411 File
    4412 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4413 packages/chimerax/core/logger.py", line 220, in status 
    4414 if l.status(msg, color, secondary) and getattr( 
    4415 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4416 File
    4417 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4418 packages/chimerax/ui/gui.py", line 1085, in status 
    4419 sbar.status(msg, color, secondary) 
    4420 File
    4421 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4422 packages/chimerax/ui/statusbar.py", line 164, in status 
    4423 r.draw_background() 
    4424 File
    4425 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4426 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4427 GL.glClear(flags) 
    4428 File "src/errorchecker.pyx", line 59, in
    4429 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4430 OpenGL.error.GLError: GLError( 
    4431 err = 1286, 
    4432 description = b'invalid framebuffer operation', 
    4433 baseOperation = glClear, 
    4434 cArguments = (16640,) 
    4435 ) 
    4436  
    4437 OpenGL.error.GLError: GLError( 
    4438 err = 1286, 
    4439 description = b'invalid framebuffer operation', 
    4440 baseOperation = glClear, 
    4441 cArguments = (16640,) 
    4442 ) 
    4443  
    4444 File "src/errorchecker.pyx", line 59, in
    4445 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4446  
    4447 See log for complete Python traceback. 
    4448  
    4449 
    4450 > select up
    4451 
    4452 218 atoms, 221 bonds, 13 residues, 1 model selected 
    4453 Traceback (most recent call last): 
    4454 File
    4455 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4456 packages/chimerax/ui/gui.py", line 393, in forward_keystroke 
    4457 run(self.session, 'select up') 
    4458 File
    4459 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4460 packages/chimerax/core/commands/run.py", line 49, in run 
    4461 results = command.run(text, log=log, return_json=return_json) 
    4462 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4463 File
    4464 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4465 packages/chimerax/core/commands/cli.py", line 3221, in run 
    4466 result = ci.function(session, **kw_args) 
    4467 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4468 File
    4469 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4470 packages/chimerax/std_commands/select.py", line 145, in select_up 
    4471 report_selection(session) 
    4472 File
    4473 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4474 packages/chimerax/std_commands/select.py", line 192, in report_selection 
    4475 session.logger.status(', '.join(lines) + ' selected', log = True) 
    4476 File
    4477 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4478 packages/chimerax/core/logger.py", line 522, in status 
    4479 StatusLogger.status(self, msg, **kw) 
    4480 File
    4481 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4482 packages/chimerax/core/logger.py", line 220, in status 
    4483 if l.status(msg, color, secondary) and getattr( 
    4484 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4485 File
    4486 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4487 packages/chimerax/ui/gui.py", line 1085, in status 
    4488 sbar.status(msg, color, secondary) 
    4489 File
    4490 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4491 packages/chimerax/ui/statusbar.py", line 164, in status 
    4492 r.draw_background() 
    4493 File
    4494 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4495 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4496 GL.glClear(flags) 
    4497 File "src/errorchecker.pyx", line 59, in
    4498 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4499 OpenGL.error.GLError: GLError( 
    4500 err = 1286, 
    4501 description = b'invalid framebuffer operation', 
    4502 baseOperation = glClear, 
    4503 cArguments = (16640,) 
    4504 ) 
    4505  
    4506 OpenGL.error.GLError: GLError( 
    4507 err = 1286, 
    4508 description = b'invalid framebuffer operation', 
    4509 baseOperation = glClear, 
    4510 cArguments = (16640,) 
    4511 ) 
    4512  
    4513 File "src/errorchecker.pyx", line 59, in
    4514 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4515  
    4516 See log for complete Python traceback. 
    4517  
    4518 
    4519 > select up
    4520 
    4521 3494 atoms, 3537 bonds, 236 residues, 1 model selected 
    4522 Traceback (most recent call last): 
    4523 File
    4524 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4525 packages/chimerax/ui/gui.py", line 393, in forward_keystroke 
    4526 run(self.session, 'select up') 
    4527 File
    4528 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4529 packages/chimerax/core/commands/run.py", line 49, in run 
    4530 results = command.run(text, log=log, return_json=return_json) 
    4531 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4532 File
    4533 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4534 packages/chimerax/core/commands/cli.py", line 3221, in run 
    4535 result = ci.function(session, **kw_args) 
    4536 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4537 File
    4538 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4539 packages/chimerax/std_commands/select.py", line 145, in select_up 
    4540 report_selection(session) 
    4541 File
    4542 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4543 packages/chimerax/std_commands/select.py", line 192, in report_selection 
    4544 session.logger.status(', '.join(lines) + ' selected', log = True) 
    4545 File
    4546 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4547 packages/chimerax/core/logger.py", line 522, in status 
    4548 StatusLogger.status(self, msg, **kw) 
    4549 File
    4550 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4551 packages/chimerax/core/logger.py", line 220, in status 
    4552 if l.status(msg, color, secondary) and getattr( 
    4553 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4554 File
    4555 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4556 packages/chimerax/ui/gui.py", line 1085, in status 
    4557 sbar.status(msg, color, secondary) 
    4558 File
    4559 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4560 packages/chimerax/ui/statusbar.py", line 164, in status 
    4561 r.draw_background() 
    4562 File
    4563 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4564 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4565 GL.glClear(flags) 
    4566 File "src/errorchecker.pyx", line 59, in
    4567 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4568 OpenGL.error.GLError: GLError( 
    4569 err = 1286, 
    4570 description = b'invalid framebuffer operation', 
    4571 baseOperation = glClear, 
    4572 cArguments = (16640,) 
    4573 ) 
    4574  
    4575 OpenGL.error.GLError: GLError( 
    4576 err = 1286, 
    4577 description = b'invalid framebuffer operation', 
    4578 baseOperation = glClear, 
    4579 cArguments = (16640,) 
    4580 ) 
    4581  
    4582 File "src/errorchecker.pyx", line 59, in
    4583 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4584  
    4585 See log for complete Python traceback. 
    4586  
    4587 
    4588 > show #6 models
    4589 
    4590 > show #7 models
    4591 
    4592 > show #4 models
    4593 
    4594 > ui tool show Matchmaker
    4595 
    4596 [Repeated 1 time(s)]
    4597 
    4598 > matchmaker #4,6-7 to #5 & sel
    4599 
    4600 Parameters 
    4601 --- 
    4602 Chain pairing | bb 
    4603 Alignment algorithm | Needleman-Wunsch 
    4604 Similarity matrix | BLOSUM-62 
    4605 SS fraction | 0.3 
    4606 Gap open (HH/SS/other) | 18/18/6 
    4607 Gap extend | 1 
    4608 SS matrix |  |  | H | S | O 
    4609 ---|---|---|--- 
    4610 H | 6 | -9 | -6 
    4611 S |  | 6 | -6 
    4612 O |  |  | 4 
    4613 Iteration cutoff | 2 
    4614  
    4615 Matchmaker design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
    4616 (#4), sequence alignment score = 665.8 
    4617 Traceback (most recent call last): 
    4618 File
    4619 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4620 packages/chimerax/match_maker/tool.py", line 175, in <lambda> 
    4621 bbox.button(qbbox.Apply).clicked.connect(lambda *args:
    4622 self.run_matchmaker(apply=True)) 
    4623 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4624 File
    4625 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4626 packages/chimerax/match_maker/tool.py", line 312, in run_matchmaker 
    4627 run(self.session, cmd) 
    4628 File
    4629 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4630 packages/chimerax/core/commands/run.py", line 49, in run 
    4631 results = command.run(text, log=log, return_json=return_json) 
    4632 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4633 File
    4634 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4635 packages/chimerax/core/commands/cli.py", line 3221, in run 
    4636 result = ci.function(session, **kw_args) 
    4637 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4638 File
    4639 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4640 packages/chimerax/match_maker/match.py", line 777, in cmd_match 
    4641 ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
    4642 gap_extend, 
    4643 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4644 File
    4645 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4646 packages/chimerax/match_maker/match.py", line 552, in match 
    4647 logger.status("Matchmaker %s (#%s) with %s (#%s)," 
    4648 File
    4649 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4650 packages/chimerax/core/logger.py", line 522, in status 
    4651 StatusLogger.status(self, msg, **kw) 
    4652 File
    4653 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4654 packages/chimerax/core/logger.py", line 220, in status 
    4655 if l.status(msg, color, secondary) and getattr( 
    4656 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4657 File
    4658 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4659 packages/chimerax/ui/gui.py", line 1085, in status 
    4660 sbar.status(msg, color, secondary) 
    4661 File
    4662 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4663 packages/chimerax/ui/statusbar.py", line 164, in status 
    4664 r.draw_background() 
    4665 File
    4666 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4667 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4668 GL.glClear(flags) 
    4669 File "src/errorchecker.pyx", line 59, in
    4670 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4671 OpenGL.error.GLError: GLError( 
    4672 err = 1286, 
    4673 description = b'invalid framebuffer operation', 
    4674 baseOperation = glClear, 
    4675 cArguments = (16640,) 
    4676 ) 
    4677  
    4678 OpenGL.error.GLError: GLError( 
    4679 err = 1286, 
    4680 description = b'invalid framebuffer operation', 
    4681 baseOperation = glClear, 
    4682 cArguments = (16640,) 
    4683 ) 
    4684  
    4685 File "src/errorchecker.pyx", line 59, in
    4686 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4687  
    4688 See log for complete Python traceback. 
    4689  
    4690 
    4691 > save /Users/oswanson/Desktop/Primocalins/Structures/initial_models.cxs
    4692 
    4693 ——— End of log from Fri Oct 31 13:49:15 2025 ———
    4694 
    4695 > view name session-start
    4696 
    4697 opened ChimeraX session 
    4698 
    4699 > ui tool show Matchmaker
    4700 
    4701 > matchmaker #4,6-7 to #5 & sel
    4702 
    4703 Parameters 
    4704 --- 
    4705 Chain pairing | bb 
    4706 Alignment algorithm | Needleman-Wunsch 
    4707 Similarity matrix | BLOSUM-62 
    4708 SS fraction | 0.3 
    4709 Gap open (HH/SS/other) | 18/18/6 
    4710 Gap extend | 1 
    4711 SS matrix |  |  | H | S | O 
    4712 ---|---|---|--- 
    4713 H | 6 | -9 | -6 
    4714 S |  | 6 | -6 
    4715 O |  |  | 4 
    4716 Iteration cutoff | 2 
    4717  
    4718 Matchmaker design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
    4719 (#4), sequence alignment score = 665.8 
    4720 RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
    4721 0.098) 
    4722  
    4723 Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
    4724 sequence alignment score = 665.8 
    4725 RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
    4726 0.168) 
    4727  
    4728 Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
    4729 sequence alignment score = 665.8 
    4730 RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
    4731 0.200) 
    4732  
    4733 
    4734 > select clear
    4735 
    4736 > hide #5 models
    4737 
    4738 > hide #4 models
    4739 
    4740 > hide #6 models
    4741 
    4742 > select #7/G:101
    4743 
    4744 24 atoms, 25 bonds, 1 residue, 1 model selected 
    4745 
    4746 > select up
    4747 
    4748 327 atoms, 336 bonds, 22 residues, 1 model selected 
    4749 
    4750 > select subtract #7/G:120
    4751 
    4752 320 atoms, 329 bonds, 21 residues, 1 model selected 
    4753 
    4754 > select #7/G:23
    4755 
    4756 22 atoms, 21 bonds, 1 residue, 1 model selected 
    4757 
    4758 > select up
    4759 
    4760 118 atoms, 117 bonds, 8 residues, 1 model selected 
    4761 
    4762 > select up
    4763 
    4764 1925 atoms, 1953 bonds, 126 residues, 1 model selected 
    4765 
    4766 > ui tool show "Color Actions"
    4767 
    4768 > color sel pale goldenrod
    4769 
    4770 > select #7/H:22
    4771 
    4772 10 atoms, 9 bonds, 1 residue, 1 model selected 
    4773 
    4774 > select up
    4775 
    4776 87 atoms, 86 bonds, 6 residues, 1 model selected 
    4777 
    4778 > select up
    4779 
    4780 1569 atoms, 1584 bonds, 110 residues, 1 model selected 
    4781 
    4782 > color sel cornsilk
    4783 
    4784 > color sel floral white
    4785 
    4786 > color sel light yellow
    4787 
    4788 > select clear
    4789 
    4790 Drag select of 1 residues 
    4791 
    4792 > select up
    4793 
    4794 327 atoms, 336 bonds, 22 residues, 1 model selected 
    4795 
    4796 > select subtract #7/G:113
    4797 
    4798 313 atoms, 321 bonds, 21 residues, 1 model selected 
    4799 
    4800 > select subtract #7/G:114
    4801 
    4802 293 atoms, 300 bonds, 20 residues, 1 model selected 
    4803 
    4804 > select subtract #7/G:116
    4805 
    4806 272 atoms, 277 bonds, 19 residues, 1 model selected 
    4807 
    4808 > select subtract #7/G:115
    4809 
    4810 260 atoms, 266 bonds, 18 residues, 1 model selected 
    4811 
    4812 > select subtract #7/G:117
    4813 
    4814 236 atoms, 240 bonds, 17 residues, 1 model selected 
    4815 
    4816 > select subtract #7/G:118
    4817 
    4818 229 atoms, 233 bonds, 16 residues, 1 model selected 
    4819 
    4820 > select subtract #7/G:120
    4821 
    4822 222 atoms, 226 bonds, 15 residues, 1 model selected 
    4823 
    4824 > select add #7/G:113
    4825 
    4826 236 atoms, 239 bonds, 16 residues, 1 model selected 
    4827 
    4828 > select add #7/G:114
    4829 
    4830 256 atoms, 259 bonds, 17 residues, 1 model selected 
    4831 
    4832 > select add #7/G:115
    4833 
    4834 268 atoms, 270 bonds, 18 residues, 1 model selected 
    4835 
    4836 > select add #7/G:116
    4837 
    4838 289 atoms, 291 bonds, 19 residues, 1 model selected 
    4839 
    4840 > select add #7/G:117
    4841 
    4842 313 atoms, 316 bonds, 20 residues, 1 model selected 
    4843 
    4844 > select add #7/G:98
    4845 
    4846 337 atoms, 339 bonds, 21 residues, 1 model selected 
    4847 
    4848 > select subtract #7/G:119
    4849 
    4850 320 atoms, 323 bonds, 20 residues, 1 model selected 
    4851 
    4852 > select subtract #7/G:117
    4853 
    4854 296 atoms, 298 bonds, 19 residues, 1 model selected 
    4855 
    4856 > color sel royal blue
    4857 
    4858 > color sel cornflower blue
    4859 
    4860 > color sel deep sky blue
    4861 
    4862 > lighting soft
    4863 
    4864 > lighting shadows true intensity 0.5
    4865 
    4866 > graphics silhouettes true
    4867 
    4868 > lighting shadows false
    4869 
    4870 > lighting soft
    4871 
    4872 > lighting full
    4873 
    4874 > lighting flat
    4875 
    4876 > lighting full
    4877 
    4878 > lighting soft
    4879 
    4880 > lighting shadows true intensity 0.5
    4881 
    4882 > lighting shadows false
    4883 
    4884 > lighting shadows true
    4885 
    4886 > lighting shadows false
    4887 
    4888 > lighting simple
    4889 
    4890 > lighting soft
    4891 
    4892 > ui tool show "Side View"
    4893 
    4894 > color sel deep sky blue
    4895 
    4896 > color sel light steel blue
    4897 
    4898 > color sel sky blue
    4899 
    4900 > color sel light sky blue
    4901 
    4902 > color sel light cyan
    4903 
    4904 > color sel sky blue
    4905 
    4906 > select clear
    4907 
    4908 > select #7/A:70
    4909 
    4910 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4911 
    4912 > select up
    4913 
    4914 155 atoms, 156 bonds, 9 residues, 1 model selected 
    4915 
    4916 > select up
    4917 
    4918 2806 atoms, 2845 bonds, 174 residues, 1 model selected 
    4919 
    4920 > show #!1 models
    4921 
    4922 > hide #!1 models
    4923 
    4924 > matchmaker #!1 to #5 & sel
    4925 
    4926 No 'to' model specified 
    4927 
    4928 > matchmaker #!1 to #5
    4929 
    4930 Parameters 
    4931 --- 
    4932 Chain pairing | bb 
    4933 Alignment algorithm | Needleman-Wunsch 
    4934 Similarity matrix | BLOSUM-62 
    4935 SS fraction | 0.3 
    4936 Gap open (HH/SS/other) | 18/18/6 
    4937 Gap extend | 1 
    4938 SS matrix |  |  | H | S | O 
    4939 ---|---|---|--- 
    4940 H | 6 | -9 | -6 
    4941 S |  | 6 | -6 
    4942 O |  |  | 4 
    4943 Iteration cutoff | 2 
    4944  
    4945 Matchmaker design_start.pdb, chain A (#5) with
    4946 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1), sequence alignment
    4947 score = 709.7 
    4948 RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 164 pairs:
    4949 1.402) 
    4950  
    4951 
    4952 > show #!1 models
    4953 
    4954 > hide #!1 models
    4955 
    4956 > show #5 models
    4957 
    4958 > hide #7 models
    4959 
    4960 > select #5/G:5
    4961 
    4962 16 atoms, 15 bonds, 1 residue, 1 model selected 
    4963 
    4964 > select up
    4965 
    4966 69 atoms, 68 bonds, 4 residues, 1 model selected 
    4967 
    4968 > select up
    4969 
    4970 1925 atoms, 1953 bonds, 126 residues, 1 model selected 
    4971 
    4972 > select up
    4973 
    4974 6339 atoms, 6419 bonds, 410 residues, 1 model selected 
    4975 
    4976 > select down
    4977 
    4978 1925 atoms, 1953 bonds, 126 residues, 1 model selected 
    4979 
    4980 > matchmaker #!1 to #5 & sel
    4981 
    4982 Parameters 
    4983 --- 
    4984 Chain pairing | bb 
    4985 Alignment algorithm | Needleman-Wunsch 
    4986 Similarity matrix | BLOSUM-62 
    4987 SS fraction | 0.3 
    4988 Gap open (HH/SS/other) | 18/18/6 
    4989 Gap extend | 1 
    4990 SS matrix |  |  | H | S | O 
    4991 ---|---|---|--- 
    4992 H | 6 | -9 | -6 
    4993 S |  | 6 | -6 
    4994 O |  |  | 4 
    4995 Iteration cutoff | 2 
    4996  
    4997 Matchmaker design_start.pdb, chain G (#5) with
    4998 231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
    4999 score = 638.8 
    5000 RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
    5001 0.817) 
    5002  
    5003 
    5004 > show #!1 models
    5005 
    5006 > hide #5 models
    5007 
    5008 > show #6 models
    5009 
    5010 > show #7 models
    5011 
    5012 > hide #7 models
    5013 
    5014 > hide #6 models
    5015 
    5016 > show #6 models
    5017 
    5018 > show #7 models
    5019 
    5020 > select clear
    5021 
    5022 > select #6/A:130
    5023 
    5024 21 atoms, 21 bonds, 1 residue, 1 model selected 
    5025 
    5026 > select up
    5027 
    5028 167 atoms, 170 bonds, 10 residues, 1 model selected 
    5029 
    5030 > select up
    5031 
    5032 2815 atoms, 2853 bonds, 174 residues, 1 model selected 
    5033 
    5034 > color sel pink
    5035 
    5036 > hide #!1 models
    5037 
    5038 > hide #7 models
    5039 
    5040 > select #6/G:5
    5041 
    5042 16 atoms, 15 bonds, 1 residue, 1 model selected 
    5043 
    5044 > select up
    5045 
    5046 69 atoms, 68 bonds, 4 residues, 1 model selected 
    5047 
    5048 > select up
    5049 
    5050 1925 atoms, 1953 bonds, 126 residues, 1 model selected 
    5051 
    5052 > color sel pale goldenrod
    5053 
    5054 > select #6/H:22
    5055 
    5056 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5057 
    5058 > select up
    5059 
    5060 87 atoms, 86 bonds, 6 residues, 1 model selected 
    5061 
    5062 > select up
    5063 
    5064 1569 atoms, 1584 bonds, 110 residues, 1 model selected 
    5065 
    5066 > color sel light yellow
    5067 
    5068 > select clear
    5069 
    5070 [Repeated 1 time(s)]
    5071 
    5072 > select #6/G:102
    5073 
    5074 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5075 
    5076 > select up
    5077 
    5078 327 atoms, 336 bonds, 22 residues, 1 model selected 
    5079 
    5080 > select #6/G:120
    5081 
    5082 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5083 
    5084 > select #6/G:103
    5085 
    5086 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5087 
    5088 > select up
    5089 
    5090 327 atoms, 336 bonds, 22 residues, 1 model selected 
    5091 
    5092 > select subtract #6/G:120
    5093 
    5094 320 atoms, 329 bonds, 21 residues, 1 model selected 
    5095 
    5096 > select subtract #6/G:119
    5097 
    5098 303 atoms, 312 bonds, 20 residues, 1 model selected 
    5099 
    5100 > select subtract #6/G:118
    5101 
    5102 296 atoms, 305 bonds, 19 residues, 1 model selected 
    5103 
    5104 > select subtract #6/G:117
    5105 
    5106 272 atoms, 279 bonds, 18 residues, 1 model selected 
    5107 
    5108 > color sel sky blue
    5109 
    5110 > select clear
    5111 
    5112 > show #7 models
    5113 
    5114 > hide #7 models
    5115 
    5116 > select #6/G:98
    5117 
    5118 24 atoms, 23 bonds, 1 residue, 1 model selected 
    5119 
    5120 > color sel sky blue
    5121 
    5122 > select clear
    5123 
    5124 > show #7 models
    5125 
    5126 > hide #6 models
    5127 
    5128 > show #6 models
    5129 
    5130 > hide #7 models
    5131 
    5132 > preset cartoons/nucleotides licorice/ovals
    5133 
    5134 Using preset: Cartoons/Nucleotides / Licorice/Ovals 
    5135 Changed 0 atom styles 
    5136 Preset expands to these ChimeraX commands:
    5137 
    5138    
    5139    
    5140     show nucleic
    5141     hide protein|solvent|H
    5142     surf hide
    5143     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    5144     ~worm
    5145     cartoon
    5146     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    5147     cartoon style ~(nucleic|strand) x round
    5148     cartoon style (nucleic|strand) x rect
    5149     cartoon style protein modeh default arrows f x round width 1 thick 1
    5150     cartoon style nucleic x round width 1.6 thick 1.6
    5151     nucleotides tube/slab shape ellipsoid
    5152 
    5153  
    5154 
    5155 > preset cartoons/nucleotides cylinders/stubs
    5156 
    5157 Using preset: Cartoons/Nucleotides / Cylinders/Stubs 
    5158 Changed 0 atom styles 
    5159 Preset expands to these ChimeraX commands:
    5160 
    5161    
    5162    
    5163     show nucleic
    5164     hide protein|solvent|H
    5165     surf hide
    5166     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    5167     ~worm
    5168     cartoon
    5169     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    5170     cartoon style ~(nucleic|strand) x round
    5171     cartoon style (nucleic|strand) x rect
    5172     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    5173     cartoon style nucleic x round width 1.6 thick 1.6
    5174     nucleotides stubs
    5175 
    5176  
    5177 
    5178 > preset cartoons/nucleotides ribbons/slabs
    5179 
    5180 Using preset: Cartoons/Nucleotides / Ribbons/Slabs 
    5181 Changed 0 atom styles 
    5182 Preset expands to these ChimeraX commands:
    5183 
    5184    
    5185    
    5186     show nucleic
    5187     hide protein|solvent|H
    5188     surf hide
    5189     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    5190     ~worm
    5191     cartoon
    5192     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    5193     cartoon style ~(nucleic|strand) x round
    5194     cartoon style (nucleic|strand) x rect
    5195     nucleotides tube/slab shape box
    5196 
    5197  
    5198 
    5199 > show #7 models
    5200 
    5201 > hide #6 models
    5202 
    5203 > show #6 models
    5204 
    5205 > hide #7 models
    5206 
    5207 > hide #6 models
    5208 
    5209 > show #4 models
    5210 
    5211 > show #6 models
    5212 
    5213 > hide #6 models
    5214 
    5215 > select #4/G:47
    5216 
    5217 24 atoms, 25 bonds, 1 residue, 1 model selected 
    5218 
    5219 > select up
    5220 
    5221 75 atoms, 76 bonds, 4 residues, 1 model selected 
    5222 
    5223 > select up
    5224 
    5225 1925 atoms, 1953 bonds, 126 residues, 1 model selected 
    5226 
    5227 > color sel pale goldenrod
    5228 
    5229 > select #4/H:87
    5230 
    5231 12 atoms, 11 bonds, 1 residue, 1 model selected 
    5232 
    5233 > select up
    5234 
    5235 124 atoms, 126 bonds, 9 residues, 1 model selected 
    5236 
    5237 > select up
    5238 
    5239 1569 atoms, 1584 bonds, 110 residues, 1 model selected 
    5240 
    5241 > color sel light yellow
    5242 
    5243 > select clear
    5244 
    5245 > select #4/G:101
    5246 
    5247 24 atoms, 25 bonds, 1 residue, 1 model selected 
    5248 
    5249 > select up
    5250 
    5251 327 atoms, 336 bonds, 22 residues, 1 model selected 
    5252 
    5253 > select #4/G:98
    5254 
    5255 24 atoms, 23 bonds, 1 residue, 1 model selected 
    5256 
    5257 > select clear
    5258 
    5259 > select #4/G:109
    5260 
    5261 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5262 
    5263 > select up
    5264 
    5265 327 atoms, 336 bonds, 22 residues, 1 model selected 
    5266 
    5267 > select add #4/G:98
    5268 
    5269 351 atoms, 359 bonds, 23 residues, 1 model selected 
    5270 
    5271 > select subtract #4/G:116
    5272 
    5273 330 atoms, 336 bonds, 22 residues, 1 model selected 
    5274 
    5275 > select subtract #4/G:117
    5276 
    5277 306 atoms, 310 bonds, 21 residues, 1 model selected 
    5278 
    5279 > select subtract #4/G:119
    5280 
    5281 289 atoms, 292 bonds, 20 residues, 1 model selected 
    5282 
    5283 > select add #4/G:95
    5284 
    5285 310 atoms, 313 bonds, 21 residues, 1 model selected 
    5286 
    5287 > select add #4/G:119
    5288 
    5289 327 atoms, 329 bonds, 22 residues, 1 model selected 
    5290 
    5291 > select subtract #4/G:95
    5292 
    5293 306 atoms, 308 bonds, 21 residues, 1 model selected 
    5294 
    5295 > select subtract #4/G:118
    5296 
    5297 299 atoms, 302 bonds, 20 residues, 1 model selected 
    5298 
    5299 > select subtract #4/G:119
    5300 
    5301 282 atoms, 286 bonds, 19 residues, 1 model selected 
    5302 
    5303 > select subtract #4/G:120
    5304 
    5305 275 atoms, 280 bonds, 18 residues, 1 model selected 
    5306 
    5307 > color sel sky blue
    5308 
    5309 > show #6 models
    5310 
    5311 > hide #6 models
    5312 
    5313 > show #7 models
    5314 
    5315 > hide #7 models
    5316 
    5317 > select clear
    5318 
    5319 > show #6 models
    5320 
    5321 > hide #6 models
    5322 
    5323 > show #!1 models
    5324 
    5325 > show #6 models
    5326 
    5327 > show #7 models
    5328 
    5329 > hide #4 models
    5330 
    5331 > hide #6 models
    5332 
    5333 > show #6 models
    5334 
    5335 > hide #!1 models
    5336 
    5337 > hide #7 models
    5338 
    5339 > show #7 models
    5340 
    5341 > hide #6 models
    5342 
    5343 > show #6 models
    5344 
    5345 > hide #7 models
    5346 
    5347 > show #4 models
    5348 
    5349 > hide #6 models
    5350 
    5351 > show #6 models
    5352 
    5353 > hide #4 models
    5354 
    5355 > show #7 models
    5356 
    5357 > hide #6 models
    5358 
    5359 > show #6 models
    5360 
    5361 > hide #6 models
    5362 
    5363 > show #5 models
    5364 
    5365 > hide #5 models
    5366 
    5367 > show #4 models
    5368 
    5369 > hide #4 models
    5370 
    5371 > show #6 models
    5372 
    5373 > select clear
    5374 
    5375 > select #6/A:76
    5376 
    5377 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5378 
    5379 > select up
    5380 
    5381 178 atoms, 180 bonds, 11 residues, 1 model selected 
    5382 
    5383 > select up
    5384 
    5385 2815 atoms, 2853 bonds, 174 residues, 1 model selected 
    5386 
    5387 > select up
    5388 
    5389 6309 atoms, 6390 bonds, 410 residues, 1 model selected 
    5390 
    5391 > select down
    5392 
    5393 2815 atoms, 2853 bonds, 174 residues, 1 model selected 
    5394 
    5395 > matchmaker #7 to #6 & sel
    5396 
    5397 Parameters 
    5398 --- 
    5399 Chain pairing | bb 
    5400 Alignment algorithm | Needleman-Wunsch 
    5401 Similarity matrix | BLOSUM-62 
    5402 SS fraction | 0.3 
    5403 Gap open (HH/SS/other) | 18/18/6 
    5404 Gap extend | 1 
    5405 SS matrix |  |  | H | S | O 
    5406 ---|---|---|--- 
    5407 H | 6 | -9 | -6 
    5408 S |  | 6 | -6 
    5409 O |  |  | 4 
    5410 Iteration cutoff | 2 
    5411  
    5412 Matchmaker RMSD4_NNK1.pdb, chain A (#6) with RMSD6_NNK1.pdb, chain A (#7),
    5413 sequence alignment score = 841.6 
    5414 RMSD between 174 pruned atom pairs is 0.233 angstroms; (across all 174 pairs:
    5415 0.233) 
    5416  
    5417 
    5418 > select clear
    5419 
    5420 > hide #7 models
    5421 
    5422 > hide #6 models
    5423 
    5424 > show #7 models
    5425 
    5426 > show #6 models
    5427 
    5428 > hide #7 models
    5429 
    5430 > show #7 models
    5431 
    5432 > hide #7 models
    5433 
    5434 > show #7 models
    5435 
    5436 > hide #6 models
    5437 
    5438 > show #6 models
    5439 
    5440 > hide #7 models
    5441 
    5442 > select clear
    5443 
    5444 > select #6/G:105
    5445 
    5446 21 atoms, 21 bonds, 1 residue, 1 model selected 
    5447 
    5448 > select up
    5449 
    5450 327 atoms, 336 bonds, 22 residues, 1 model selected 
    5451 
    5452 > ui tool show Contacts
    5453 
    5454 > contacts sel restrict cross interModel false intraMol false
    5455 > ignoreHiddenModels true select true color #ffd479 reveal true log true
    5456    
    5457    
    5458     Allowed overlap: -0.4
    5459     H-bond overlap reduction: 0.4
    5460     Ignore contacts between atoms separated by 4 bonds or less
    5461     Detect intra-residue contacts: False
    5462     Detect intra-molecule contacts: False
    5463    
    5464     98 contacts
    5465                  atom1                            atom2               overlap  distance
    5466     RMSD4_NNK1.pdb #6/G GLY 110 O    RMSD4_NNK1.pdb #6/H LEU 34 3HD1   0.347    2.133
    5467     RMSD4_NNK1.pdb #6/G ASP 107 H    RMSD4_NNK1.pdb #6/A GLU 79 OE1    0.259    1.821
    5468     RMSD4_NNK1.pdb #6/G PHE 114 H    RMSD4_NNK1.pdb #6/H TYR 38 OH     0.241    1.859
    5469     RMSD4_NNK1.pdb #6/G PHE 114 H    RMSD4_NNK1.pdb #6/H LEU 48 2HD1   0.178    1.822
    5470     RMSD4_NNK1.pdb #6/G PRO 112 O    RMSD4_NNK1.pdb #6/H TYR 38 HH     0.172    1.908
    5471     RMSD4_NNK1.pdb #6/G TYR 111 CE2  RMSD4_NNK1.pdb #6/H LEU 34 CD2    0.152    3.248
    5472     RMSD4_NNK1.pdb #6/G TYR 106 CD2  RMSD4_NNK1.pdb #6/A LEU 70 1HD2   0.132    2.568
    5473     RMSD4_NNK1.pdb #6/G ASP 115 OD1  RMSD4_NNK1.pdb #6/H TYR 51 HH     0.130    1.950
    5474     RMSD4_NNK1.pdb #6/G GLY 110 O    RMSD4_NNK1.pdb #6/H LEU 34 CD1    0.120    3.060
    5475     RMSD4_NNK1.pdb #6/G ASP 115 OD1  RMSD4_NNK1.pdb #6/H LEU 48 3HD1   0.112    2.368
    5476     RMSD4_NNK1.pdb #6/G TYR 111 CE2  RMSD4_NNK1.pdb #6/H LEU 34 1HD2   0.104    2.596
    5477     RMSD4_NNK1.pdb #6/G GLY 110 O    RMSD4_NNK1.pdb #6/H TYR 93 1HB    0.064    2.416
    5478     RMSD4_NNK1.pdb #6/G TYR 111 OH   RMSD4_NNK1.pdb #6/A VAL 77 3HG1   0.048    2.452
    5479     RMSD4_NNK1.pdb #6/G PHE 114 HD1  RMSD4_NNK1.pdb #6/H TYR 38 OH     0.047    2.453
    5480     RMSD4_NNK1.pdb #6/G ASP 115 CG   RMSD4_NNK1.pdb #6/H TYR 51 OH     0.031    3.169
    5481     RMSD4_NNK1.pdb #6/G TRP 117 CZ3  RMSD4_NNK1.pdb #6/H PRO 46 CG     0.022    3.378
    5482     RMSD4_NNK1.pdb #6/G PHE 114 H    RMSD4_NNK1.pdb #6/H LEU 48 CD1    0.008    2.692
    5483     RMSD4_NNK1.pdb #6/G PHE 114 CD1  RMSD4_NNK1.pdb #6/H TYR 38 OH     -0.013    3.213
    5484     RMSD4_NNK1.pdb #6/G TRP 117 CE3  RMSD4_NNK1.pdb #6/H PRO 46 CG     -0.014    3.414
    5485     RMSD4_NNK1.pdb #6/G TYR 106 CD2  RMSD4_NNK1.pdb #6/A LEU 70 CD2    -0.018    3.418
    5486     RMSD4_NNK1.pdb #6/G TYR 111 CD2  RMSD4_NNK1.pdb #6/H LEU 34 CD2    -0.019    3.419
    5487     RMSD4_NNK1.pdb #6/G TYR 111 CD2  RMSD4_NNK1.pdb #6/H LEU 34 2HD2   -0.019    2.719
    5488     RMSD4_NNK1.pdb #6/G PHE 114 N    RMSD4_NNK1.pdb #6/H LEU 48 2HD1   -0.033    2.658
    5489     RMSD4_NNK1.pdb #6/G PHE 114 O    RMSD4_NNK1.pdb #6/H TYR 38 HE2    -0.033    2.513
    5490     RMSD4_NNK1.pdb #6/G ASP 115 OD1  RMSD4_NNK1.pdb #6/H TYR 51 OH     -0.033    2.613
    5491     RMSD4_NNK1.pdb #6/G PHE 114 N    RMSD4_NNK1.pdb #6/H TYR 38 OH     -0.042    2.767
    5492     RMSD4_NNK1.pdb #6/G TRP 117 CD2  RMSD4_NNK1.pdb #6/H PRO 46 1HG    -0.046    2.746
    5493     RMSD4_NNK1.pdb #6/G ASP 115 CG   RMSD4_NNK1.pdb #6/H TYR 51 HH     -0.065    2.765
    5494     RMSD4_NNK1.pdb #6/G PHE 114 CE1  RMSD4_NNK1.pdb #6/H PHE 101 HZ    -0.082    2.782
    5495     RMSD4_NNK1.pdb #6/G TYR 105 CE2  RMSD4_NNK1.pdb #6/A LEU 36 1HD2   -0.083    2.783
    5496     RMSD4_NNK1.pdb #6/G TYR 111 HH   RMSD4_NNK1.pdb #6/A VAL 77 3HG1   -0.085    2.085
    5497     RMSD4_NNK1.pdb #6/G PHE 114 HE1  RMSD4_NNK1.pdb #6/H PHE 101 HZ    -0.093    2.093
    5498     RMSD4_NNK1.pdb #6/G ASP 107 H    RMSD4_NNK1.pdb #6/A GLU 79 CD     -0.093    2.793
    5499     RMSD4_NNK1.pdb #6/G TRP 117 CE3  RMSD4_NNK1.pdb #6/H PRO 46 1HG    -0.104    2.804
    5500     RMSD4_NNK1.pdb #6/G ASP 107 N    RMSD4_NNK1.pdb #6/A GLU 79 OE1    -0.107    2.812
    5501     RMSD4_NNK1.pdb #6/G TYR 105 OH   RMSD4_NNK1.pdb #6/A VAL 41 3HG1   -0.112    2.612
    5502     RMSD4_NNK1.pdb #6/G TYR 105 HE2  RMSD4_NNK1.pdb #6/A LEU 36 1HD2   -0.122    2.122
    5503     RMSD4_NNK1.pdb #6/G PHE 114 N    RMSD4_NNK1.pdb #6/H LEU 48 CD1    -0.134    3.459
    5504     RMSD4_NNK1.pdb #6/G TYR 105 HE2  RMSD4_NNK1.pdb #6/A VAL 41 2HG2   -0.140    2.140
    5505     RMSD4_NNK1.pdb #6/G TYR 111 CZ   RMSD4_NNK1.pdb #6/H LEU 34 1HD2   -0.146    2.846
    5506     RMSD4_NNK1.pdb #6/G GLY 110 CA   RMSD4_NNK1.pdb #6/H TYR 93 CD1    -0.152    3.552
    5507     RMSD4_NNK1.pdb #6/G GLY 110 C    RMSD4_NNK1.pdb #6/H LEU 34 3HD1   -0.156    2.856
    5508     RMSD4_NNK1.pdb #6/G PHE 114 HD1  RMSD4_NNK1.pdb #6/H TYR 38 CZ     -0.169    2.869
    5509     RMSD4_NNK1.pdb #6/G TRP 117 CZ3  RMSD4_NNK1.pdb #6/H PRO 46 2HG    -0.173    2.873
    5510     RMSD4_NNK1.pdb #6/G TRP 117 CE2  RMSD4_NNK1.pdb #6/H PRO 46 1HG    -0.174    2.874
    5511     RMSD4_NNK1.pdb #6/G TYR 105 CE2  RMSD4_NNK1.pdb #6/A LEU 36 CD2    -0.174    3.574
    5512     RMSD4_NNK1.pdb #6/G GLY 110 O    RMSD4_NNK1.pdb #6/H TYR 93 CB     -0.182    3.362
    5513     RMSD4_NNK1.pdb #6/G TYR 111 OH   RMSD4_NNK1.pdb #6/A VAL 77 CG1    -0.191    3.391
    5514     RMSD4_NNK1.pdb #6/G TYR 105 CD1  RMSD4_NNK1.pdb #6/A MET 49 CE     -0.196    3.596
    5515     RMSD4_NNK1.pdb #6/G PRO 112 1HG  RMSD4_NNK1.pdb #6/H SER 36 HG     -0.205    2.205
    5516     RMSD4_NNK1.pdb #6/G PRO 112 O    RMSD4_NNK1.pdb #6/H TYR 38 OH     -0.208    2.788
    5517     RMSD4_NNK1.pdb #6/G ASN 113 OD1  RMSD4_NNK1.pdb #6/H TYR 51 CE1    -0.209    3.389
    5518     RMSD4_NNK1.pdb #6/G ASP 115 OD1  RMSD4_NNK1.pdb #6/H LEU 48 CD1    -0.215    3.395
    5519     RMSD4_NNK1.pdb #6/G GLY 110 2HA  RMSD4_NNK1.pdb #6/H TYR 93 CE1    -0.217    2.917
    5520     RMSD4_NNK1.pdb #6/G TRP 117 CH2  RMSD4_NNK1.pdb #6/H PRO 46 CG     -0.221    3.621
    5521     RMSD4_NNK1.pdb #6/G PRO 112 C    RMSD4_NNK1.pdb #6/H TYR 38 HH     -0.222    2.922
    5522     RMSD4_NNK1.pdb #6/G TYR 106 1HB  RMSD4_NNK1.pdb #6/A GLU 79 OE1    -0.235    2.715
    5523     RMSD4_NNK1.pdb #6/G TYR 106 OH   RMSD4_NNK1.pdb #6/A TYR 72 CD2    -0.240    3.440
    5524     RMSD4_NNK1.pdb #6/G PRO 112 1HG  RMSD4_NNK1.pdb #6/H SER 36 OG     -0.249    2.749
    5525     RMSD4_NNK1.pdb #6/G GLY 110 2HA  RMSD4_NNK1.pdb #6/H TYR 93 CD1    -0.250    2.950
    5526     RMSD4_NNK1.pdb #6/G TYR 105 CE1  RMSD4_NNK1.pdb #6/A MET 49 SD     -0.251    3.733
    5527     RMSD4_NNK1.pdb #6/G TYR 105 OH   RMSD4_NNK1.pdb #6/A VAL 41 HA     -0.257    2.757
    5528     RMSD4_NNK1.pdb #6/G PHE 114 CB   RMSD4_NNK1.pdb #6/H TYR 38 OH     -0.259    3.459
    5529     RMSD4_NNK1.pdb #6/G TRP 117 CZ3  RMSD4_NNK1.pdb #6/H PRO 46 1HG    -0.276    2.976
    5530     RMSD4_NNK1.pdb #6/G ASP 107 CB   RMSD4_NNK1.pdb #6/A GLU 79 OE1    -0.280    3.460
    5531     RMSD4_NNK1.pdb #6/G GLY 110 CA   RMSD4_NNK1.pdb #6/H TYR 93 CE1    -0.281    3.681
    5532     RMSD4_NNK1.pdb #6/G TYR 111 CE2  RMSD4_NNK1.pdb #6/H LEU 34 2HD2   -0.282    2.982
    5533     RMSD4_NNK1.pdb #6/G ASN 113 HA   RMSD4_NNK1.pdb #6/H LEU 48 CD1    -0.284    2.984
    5534     RMSD4_NNK1.pdb #6/G TRP 117 CD2  RMSD4_NNK1.pdb #6/H PRO 46 CG     -0.287    3.687
    5535     RMSD4_NNK1.pdb #6/G TYR 111 HH   RMSD4_NNK1.pdb #6/A VAL 77 CG1    -0.297    2.997
    5536     RMSD4_NNK1.pdb #6/G PHE 114 H    RMSD4_NNK1.pdb #6/H TYR 38 HH     -0.321    2.321
    5537     RMSD4_NNK1.pdb #6/G TYR 111 CZ   RMSD4_NNK1.pdb #6/H LEU 34 CD2    -0.328    3.728
    5538     RMSD4_NNK1.pdb #6/G TYR 106 OH   RMSD4_NNK1.pdb #6/A TYR 72 CE2    -0.329    3.529
    5539     RMSD4_NNK1.pdb #6/G TYR 106 CG   RMSD4_NNK1.pdb #6/A LEU 70 1HD2   -0.332    3.032
    5540     RMSD4_NNK1.pdb #6/G TYR 105 CD1  RMSD4_NNK1.pdb #6/A MET 49 3HE    -0.332    3.032
    5541     RMSD4_NNK1.pdb #6/G TYR 105 CG   RMSD4_NNK1.pdb #6/A MET 49 CE     -0.332    3.732
    5542     RMSD4_NNK1.pdb #6/G TRP 117 CE3  RMSD4_NNK1.pdb #6/H PRO 46 CD     -0.334    3.734
    5543     RMSD4_NNK1.pdb #6/G PRO 112 O    RMSD4_NNK1.pdb #6/H SER 36 HG     -0.334    2.414
    5544     RMSD4_NNK1.pdb #6/G PHE 114 1HB  RMSD4_NNK1.pdb #6/H TYR 38 OH     -0.339    2.839
    5545     RMSD4_NNK1.pdb #6/G ASP 107 2HB  RMSD4_NNK1.pdb #6/A GLU 79 OE1    -0.340    2.820
    5546     RMSD4_NNK1.pdb #6/G ASN 113 HA   RMSD4_NNK1.pdb #6/H LEU 48 1HD1   -0.341    2.341
    5547     RMSD4_NNK1.pdb #6/G PHE 114 HE1  RMSD4_NNK1.pdb #6/H PHE 101 CZ    -0.343    3.043
    5548     RMSD4_NNK1.pdb #6/G GLY 110 O    RMSD4_NNK1.pdb #6/H TYR 93 CG     -0.343    3.523
    5549     RMSD4_NNK1.pdb #6/G PHE 114 1HB  RMSD4_NNK1.pdb #6/H TYR 38 CE2    -0.347    3.047
    5550     RMSD4_NNK1.pdb #6/G TYR 105 CE2  RMSD4_NNK1.pdb #6/A PHE 40 HE1    -0.349    3.049
    5551     RMSD4_NNK1.pdb #6/G TRP 117 HZ2  RMSD4_NNK1.pdb #6/H TYR 38 CE2    -0.360    3.060
    5552     RMSD4_NNK1.pdb #6/G TYR 105 HE2  RMSD4_NNK1.pdb #6/A LEU 36 CD2    -0.366    3.066
    5553     RMSD4_NNK1.pdb #6/G TRP 117 CE3  RMSD4_NNK1.pdb #6/H PRO 46 1HD    -0.367    3.067
    5554     RMSD4_NNK1.pdb #6/G PHE 114 CA   RMSD4_NNK1.pdb #6/H TYR 38 OH     -0.368    3.568
    5555     RMSD4_NNK1.pdb #6/G TRP 117 CZ2  RMSD4_NNK1.pdb #6/H PRO 46 1HG    -0.371    3.071
    5556     RMSD4_NNK1.pdb #6/G ASN 113 OD1  RMSD4_NNK1.pdb #6/H TYR 51 CD1    -0.372    3.552
    5557     RMSD4_NNK1.pdb #6/G PHE 114 H    RMSD4_NNK1.pdb #6/H TYR 38 CZ     -0.373    3.073
    5558     RMSD4_NNK1.pdb #6/G TYR 106 CE2  RMSD4_NNK1.pdb #6/A LEU 70 1HD2   -0.376    3.076
    5559     RMSD4_NNK1.pdb #6/G GLY 110 O    RMSD4_NNK1.pdb #6/H TYR 93 CD1    -0.380    3.560
    5560     RMSD4_NNK1.pdb #6/G TYR 105 CZ   RMSD4_NNK1.pdb #6/A MET 49 SD     -0.388    3.870
    5561     RMSD4_NNK1.pdb #6/G TRP 117 CH2  RMSD4_NNK1.pdb #6/H PRO 46 2HG    -0.391    3.091
    5562     RMSD4_NNK1.pdb #6/G GLY 110 C    RMSD4_NNK1.pdb #6/H LEU 34 CD1    -0.398    3.798
    5563     RMSD4_NNK1.pdb #6/G TRP 117 CH2  RMSD4_NNK1.pdb #6/H PRO 46 1HG    -0.399    3.099
    5564    
    5565 
    5566  
    5567 98 contacts 
    5568 
    5569 > undo
    5570 
    5571 > hide sel atoms
    5572 
    5573 > select up
    5574 
    5575 310 atoms, 302 bonds, 17 residues, 1 model selected 
    5576 
    5577 > hide sel atoms
    5578 
    5579 > select add #6/G:111
    5580 
    5581 331 atoms, 323 bonds, 18 residues, 1 model selected 
    5582 
    5583 > select up
    5584 
    5585 1781 atoms, 1810 bonds, 112 residues, 1 model selected 
    5586 
    5587 > hide sel atoms
    5588 
    5589 > select clear
    5590 
    5591 > select #6/A:71
    5592 
    5593 20 atoms, 20 bonds, 1 residue, 1 model selected 
    5594 
    5595 > select up
    5596 
    5597 152 atoms, 154 bonds, 9 residues, 1 model selected 
    5598 
    5599 > select up
    5600 
    5601 2815 atoms, 2853 bonds, 174 residues, 1 model selected 
    5602 
    5603 > contacts ignoreHiddenModels true color #ff2600
    5604 
    5605 4408 contacts 
    5606 
    5607 > undo
    5608 
    5609 > select #6/A:70
    5610 
    5611 19 atoms, 18 bonds, 1 residue, 1 model selected 
    5612 
    5613 > select up
    5614 
    5615 152 atoms, 154 bonds, 9 residues, 1 model selected 
    5616 
    5617 > select up
    5618 
    5619 2815 atoms, 2853 bonds, 174 residues, 1 model selected 
    5620 
    5621 > contacts sel restrict cross ignoreHiddenModels true color #ff2600
    5622 
    5623 57 contacts 
    5624 
    5625 > contacts sel restrict cross interModel false intraMol false
    5626 > ignoreHiddenModels true select true color #ff2600 reveal true
    5627 
    5628 57 contacts 
    5629 
    5630 > select up
    5631 
    5632 400 atoms, 387 bonds, 24 residues, 1 model selected 
    5633 
    5634 > color sel byhetero
    5635 
    5636 > show #!1 models
    5637 
    5638 > show #7 models
    5639 
    5640 > hide #7 models
    5641 
    5642 > select #6/A:71
    5643 
    5644 20 atoms, 20 bonds, 1 residue, 1 model selected 
    5645 
    5646 > select up
    5647 
    5648 152 atoms, 154 bonds, 9 residues, 1 model selected 
    5649 
    5650 > select up
    5651 
    5652 2815 atoms, 2853 bonds, 174 residues, 1 model selected 
    5653 
    5654 > matchmaker #!1 to #6 & sel
    5655 
    5656 Parameters 
    5657 --- 
    5658 Chain pairing | bb 
    5659 Alignment algorithm | Needleman-Wunsch 
    5660 Similarity matrix | BLOSUM-62 
    5661 SS fraction | 0.3 
    5662 Gap open (HH/SS/other) | 18/18/6 
    5663 Gap extend | 1 
    5664 SS matrix |  |  | H | S | O 
    5665 ---|---|---|--- 
    5666 H | 6 | -9 | -6 
    5667 S |  | 6 | -6 
    5668 O |  |  | 4 
    5669 Iteration cutoff | 2 
    5670  
    5671 Matchmaker RMSD4_NNK1.pdb, chain A (#6) with
    5672 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1), sequence alignment
    5673 score = 692.2 
    5674 RMSD between 150 pruned atom pairs is 0.641 angstroms; (across all 164 pairs:
    5675 1.442) 
    5676  
    5677 
    5678 > show #7 models
    5679 
    5680 > hide #!6 models
    5681 
    5682 > show #!6 models
    5683 
    5684 > hide #7 models
    5685 
    5686 > select clear
    5687 
    5688 > hide #!1 models
    5689 
    5690 > show #!1 models
    5691 
    5692 > hide #!1 models
    5693 
    5694 > hide #!6 models
    5695 
    5696 > show #7 models
    5697 
    5698 > select #7/A:70
    5699 
    5700 24 atoms, 23 bonds, 1 residue, 1 model selected 
    5701 
    5702 > select up
    5703 
    5704 155 atoms, 156 bonds, 9 residues, 1 model selected 
    5705 
    5706 > select up
    5707 
    5708 2806 atoms, 2845 bonds, 174 residues, 1 model selected 
    5709 
    5710 > contacts sel restrict cross interModel false intraMol false
    5711 > ignoreHiddenModels true select true color #ff2600 name contacts_RMSD6 reveal
    5712 > true
    5713 
    5714 63 contacts 
    5715 
    5716 > select up
    5717 
    5718 344 atoms, 338 bonds, 20 residues, 1 model selected 
    5719 
    5720 > color sel byhetero
    5721 
    5722 > select clear
    5723 
    5724 > hide #8 models
    5725 
    5726 > hide #!7 models
    5727 
    5728 > show #!1 models
    5729 
    5730 > select #1/E:79
    5731 
    5732 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5733 
    5734 > select up
    5735 
    5736 78 atoms, 80 bonds, 9 residues, 1 model selected 
    5737 
    5738 > select up
    5739 
    5740 709 atoms, 728 bonds, 90 residues, 1 model selected 
    5741 
    5742 > select up
    5743 
    5744 727 atoms, 746 bonds, 92 residues, 1 model selected 
    5745 
    5746 > select up
    5747 
    5748 1313 atoms, 1346 bonds, 164 residues, 1 model selected 
    5749 
    5750 > select up
    5751 
    5752 4647 atoms, 4757 bonds, 608 residues, 1 model selected 
    5753 
    5754 > select down
    5755 
    5756 1313 atoms, 1346 bonds, 164 residues, 1 model selected 
    5757 
    5758 > contacts sel restrict cross interModel false intraMol false
    5759 > ignoreHiddenModels true select true color #ff2600 name contacts_poly310
    5760 > reveal true
    5761 
    5762 64 contacts 
    5763 
    5764 > select up
    5765 
    5766 237 atoms, 233 bonds, 27 residues, 1 model selected 
    5767 
    5768 > color sel byhetero
    5769 
    5770 > hide #!1 models
    5771 
    5772 > show #!1 models
    5773 
    5774 > select clear
    5775 
    5776 > select #1/H:126
    5777 
    5778 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5779 
    5780 > select up
    5781 
    5782 36 atoms, 35 bonds, 5 residues, 1 model selected 
    5783 
    5784 > select up
    5785 
    5786 1725 atoms, 1772 bonds, 228 residues, 1 model selected 
    5787 
    5788 > color sel pale goldenrod
    5789 
    5790 > select #1/L:105
    5791 
    5792 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5793 
    5794 > select up
    5795 
    5796 67 atoms, 69 bonds, 8 residues, 1 model selected 
    5797 
    5798 > select up
    5799 
    5800 1609 atoms, 1639 bonds, 216 residues, 1 model selected 
    5801 
    5802 > color sel light yellow
    5803 
    5804 > select clear
    5805 
    5806 [Repeated 2 time(s)]
    5807 
    5808 > select #1/H:111C
    5809 
    5810 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5811 
    5812 > select up
    5813 
    5814 181 atoms, 190 bonds, 22 residues, 1 model selected 
    5815 
    5816 > select subtract #1/H:119
    5817 
    5818 177 atoms, 185 bonds, 21 residues, 1 model selected 
    5819 
    5820 > select subtract #1/H:120
    5821 
    5822 168 atoms, 176 bonds, 20 residues, 1 model selected 
    5823 
    5824 > select subtract #1/H:121
    5825 
    5826 164 atoms, 173 bonds, 19 residues, 1 model selected 
    5827 
    5828 > select subtract #1/H:118
    5829 
    5830 150 atoms, 157 bonds, 18 residues, 1 model selected 
    5831 
    5832 > select subtract #1/H:117
    5833 
    5834 138 atoms, 144 bonds, 17 residues, 1 model selected 
    5835 
    5836 > color sel sky blue
    5837 
    5838 > select add #1
    5839 
    5840 4647 atoms, 4757 bonds, 71 pseudobonds, 608 residues, 4 models selected 
    5841 
    5842 > color sel byhetero
    5843 
    5844 > select clear
    5845 
    5846 > hide #!1 models
    5847 
    5848 > show #!6 models
    5849 
    5850 > select add #6
    5851 
    5852 6309 atoms, 6390 bonds, 114 pseudobonds, 410 residues, 3 models selected 
    5853 
    5854 > select add #7
    5855 
    5856 12609 atoms, 12772 bonds, 177 pseudobonds, 820 residues, 5 models selected 
    5857 
    5858 > show #!7 models
    5859 
    5860 > select H
    5861 
    5862 12439 atoms, 19 pseudobonds, 1640 residues, 7 models selected 
    5863 
    5864 > select clear
    5865 
    5866 > select add #6
    5867 
    5868 6309 atoms, 6390 bonds, 114 pseudobonds, 410 residues, 3 models selected 
    5869 
    5870 > select add #7
    5871 
    5872 12609 atoms, 12772 bonds, 177 pseudobonds, 820 residues, 5 models selected 
    5873 
    5874 > select H
    5875 
    5876 12439 atoms, 19 pseudobonds, 1640 residues, 7 models selected 
    5877 
    5878 > delete atoms (#!6-7 & sel)
    5879 
    5880 > delete bonds (#!6-7 & sel)
    5881 
    5882 > hide #!6 models
    5883 
    5884 > show #!6 models
    5885 
    5886 > hide #!7 models
    5887 
    5888 > show #!7 models
    5889 
    5890 > show #!1 models
    5891 
    5892 > show #2 models
    5893 
    5894 > hide #2 models
    5895 
    5896 > hide #!1 models
    5897 
    5898 > select clear
    5899 
    5900 > hide #!7 models
    5901 
    5902 > show #!1 models
    5903 
    5904 > hide #!6 models
    5905 
    5906 > show #4 models
    5907 
    5908 > hide #4 models
    5909 
    5910 > show #!6 models
    5911 
    5912 > hide #6.1 models
    5913 
    5914 > hide #!6 models
    5915 
    5916 > show #!7 models
    5917 
    5918 > hide #!7 models
    5919 
    5920 > select #1/E:33
    5921 
    5922 7 atoms, 6 bonds, 1 residue, 1 model selected 
    5923 
    5924 > select up
    5925 
    5926 74 atoms, 76 bonds, 10 residues, 1 model selected 
    5927 
    5928 > select up
    5929 
    5930 709 atoms, 728 bonds, 90 residues, 1 model selected 
    5931 
    5932 > select up
    5933 
    5934 727 atoms, 746 bonds, 92 residues, 1 model selected 
    5935 
    5936 > select up
    5937 
    5938 1313 atoms, 1346 bonds, 164 residues, 1 model selected 
    5939 
    5940 > show #5 models
    5941 
    5942 > hide #5 models
    5943 
    5944 > show #!6 models
    5945 
    5946 > select clear
    5947 
    5948 > show #!7 models
    5949 
    5950 > hide #!7 models
    5951 
    5952 > select #6/A:131
    5953 
    5954 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5955 
    5956 > select up
    5957 
    5958 88 atoms, 91 bonds, 10 residues, 1 model selected 
    5959 
    5960 > select up
    5961 
    5962 1416 atoms, 1454 bonds, 174 residues, 1 model selected 
    5963 
    5964 > show #8 models
    5965 
    5966 > matchmaker #4 to #6 & sel
    5967 
    5968 Parameters 
    5969 --- 
    5970 Chain pairing | bb 
    5971 Alignment algorithm | Needleman-Wunsch 
    5972 Similarity matrix | BLOSUM-62 
    5973 SS fraction | 0.3 
    5974 Gap open (HH/SS/other) | 18/18/6 
    5975 Gap extend | 1 
    5976 SS matrix |  |  | H | S | O 
    5977 ---|---|---|--- 
    5978 H | 6 | -9 | -6 
    5979 S |  | 6 | -6 
    5980 O |  |  | 4 
    5981 Iteration cutoff | 2 
    5982  
    5983 Matchmaker RMSD4_NNK1.pdb, chain A (#6) with Cluster2c_lib1.pdb, chain A (#4),
    5984 sequence alignment score = 808.5 
    5985 RMSD between 174 pruned atom pairs is 0.223 angstroms; (across all 174 pairs:
    5986 0.223) 
    5987  
    5988 
    5989 > hide #!6 models
    5990 
    5991 > show #4 models
    5992 
    5993 > hide #4 models
    5994 
    5995 > hide #1.3 models
    5996 
    5997 > hide #1.1 models
    5998 
    5999 > show #1.3 models
    6000 
    6001 > select #1/E:43
    6002 
    6003 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6004 
    6005 > select up
    6006 
    6007 113 atoms, 114 bonds, 14 residues, 1 model selected 
    6008 
    6009 > select subtract #1/E:52
    6010 
    6011 102 atoms, 102 bonds, 13 residues, 1 model selected 
    6012 
    6013 > select subtract #1/E:50
    6014 
    6015 93 atoms, 92 bonds, 12 residues, 1 model selected 
    6016 
    6017 > select subtract #1/E:51
    6018 
    6019 85 atoms, 85 bonds, 11 residues, 1 model selected 
    6020 
    6021 > select subtract #1/E:49
    6022 
    6023 80 atoms, 80 bonds, 10 residues, 1 model selected 
    6024 
    6025 > show sel atoms
    6026 
    6027 > hide sel atoms
    6028 
    6029 > select #1/E:37
    6030 
    6031 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6032 
    6033 > select add #1/E:133
    6034 
    6035 16 atoms, 15 bonds, 2 residues, 1 model selected 
    6036 
    6037 > select add #1/E:134
    6038 
    6039 24 atoms, 22 bonds, 3 residues, 1 model selected 
    6040 
    6041 > select add #1/E:38
    6042 
    6043 28 atoms, 25 bonds, 4 residues, 1 model selected 
    6044 
    6045 > select add #1/E:135
    6046 
    6047 36 atoms, 32 bonds, 5 residues, 1 model selected 
    6048 
    6049 > show sel atoms
    6050 
    6051 > color sel byhetero
    6052 
    6053 > select clear
    6054 
    6055 > hide #!1 models
    6056 
    6057 > show #!6 models
    6058 
    6059 > show #!7 models
    6060 
    6061 > hide #!6 models
    6062 
    6063 > show #!6 models
    6064 
    6065 > hide #!7 models
    6066 
    6067 > show #!7 models
    6068 
    6069 > hide #!6 models
    6070 
    6071 > hide #!7 models
    6072 
    6073 > show #6.1 models
    6074 
    6075 > show #!7 models
    6076 
    6077 > hide #!6 models
    6078 
    6079 > show #!6 models
    6080 
    6081 > hide #!6 models
    6082 
    6083 > show #!6 models
    6084 
    6085 > hide #!7 models
    6086 
    6087 > show #!7 models
    6088 
    6089 > hide #!6 models
    6090 
    6091 > hide #!7 models
    6092 
    6093 > show #!6 models
    6094 
    6095 > hide #!6 models
    6096 
    6097 > show #!7 models
    6098 
    6099 > show #!6 models
    6100 
    6101 > hide #!7 models
    6102 
    6103 > show #!7 models
    6104 
    6105 > hide #!7 models
    6106 
    6107 > show #!7 models
    6108 
    6109 > hide #!6 models
    6110 
    6111 > show #!6 models
    6112 
    6113 > hide #!7 models
    6114 
    6115 > show #!7 models
    6116 
    6117 > hide #!6 models
    6118 
    6119 > hide #!7 models
    6120 
    6121 > show #!6 models
    6122 
    6123 > show #!7 models
    6124 
    6125 > hide #!7 models
    6126 
    6127 > show #!7 models
    6128 
    6129 > hide #!6 models
    6130 
    6131 > show #!6 models
    6132 
    6133 > hide #!7 models
    6134 
    6135 > hide #6.1 models
    6136 
    6137 > show #6.1 models
    6138 
    6139 > hide #6.1 models
    6140 
    6141 > hide #8 models
    6142 
    6143 > show #8 models
    6144 
    6145 > select add #8
    6146 
    6147 21 pseudobonds, 1 model selected 
    6148 
    6149 > select add #6.1
    6150 
    6151 42 pseudobonds, 2 models selected 
    6152 
    6153 > hide #!6 cartoons
    6154 
    6155 > show #!6 cartoons
    6156 
    6157 > hide #!6 atoms
    6158 
    6159 > select clear
    6160 
    6161 > hide #8 models
    6162 
    6163 > show #!7 models
    6164 
    6165 > select add #7
    6166 
    6167 3204 atoms, 3286 bonds, 20 pseudobonds, 410 residues, 2 models selected 
    6168 
    6169 > hide sel atoms
    6170 
    6171 > select clear
    6172 
    6173 > hide #1.3 models
    6174 
    6175 > hide #1.2 models
    6176 
    6177 > hide #!6 models
    6178 
    6179 > hide #7.1 models
    6180 
    6181 > show #!6 models
    6182 
    6183 > hide #!6 models
    6184 
    6185 > show #!6 models
    6186 
    6187 > hide #!7 models
    6188 
    6189 > show #!7 models
    6190 
    6191 > hide #!7 models
    6192 
    6193 > show #!7 models
    6194 
    6195 > hide #!6 models
    6196 
    6197 > show #!6 models
    6198 
    6199 > lighting soft
    6200 
    6201 > hide #!6 models
    6202 
    6203 > lighting gentle
    6204 
    6205 > graphics silhouettes false
    6206 
    6207 > graphics silhouettes true
    6208 
    6209 > graphics silhouettes false
    6210 
    6211 > graphics silhouettes true
    6212 
    6213 > lighting shadows true intensity 0.5
    6214 
    6215 > lighting shadows false
    6216 
    6217 > save view init_design
    6218 
    6219 Cannot determine format for 'view' 
    6220 
    6221 > view name init_design
    6222 
    6223 > view list
    6224 
    6225 Named views: init_design, session-start 
    6226 
    6227 > show #!6 models
    6228 
    6229 > hide #!7 models
    6230 
    6231 > select #6/A:68
    6232 
    6233 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6234 
    6235 > select up
    6236 
    6237 78 atoms, 80 bonds, 9 residues, 1 model selected 
    6238 
    6239 > select up
    6240 
    6241 1416 atoms, 1454 bonds, 174 residues, 1 model selected 
    6242 
    6243 > color sel pink
    6244 
    6245 [Repeated 1 time(s)]
    6246 
    6247 > color sel pale violet red
    6248 
    6249 > color sel dark sea green
    6250 
    6251 > color sel salmon
    6252 
    6253 [Repeated 1 time(s)]
    6254 
    6255 > color sel dark salmon
    6256 
    6257 > color sel coral
    6258 
    6259 > color sel pale violet red
    6260 
    6261 > select clear
    6262 
    6263 > select #6/H:20
    6264 
    6265 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6266 
    6267 > select up
    6268 
    6269 42 atoms, 41 bonds, 6 residues, 1 model selected 
    6270 
    6271 > select up
    6272 
    6273 797 atoms, 812 bonds, 110 residues, 1 model selected 
    6274 
    6275 > color sel pale goldenrod
    6276 
    6277 > select #6/G:4
    6278 
    6279 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6280 
    6281 > select up
    6282 
    6283 33 atoms, 32 bonds, 4 residues, 1 model selected 
    6284 
    6285 > select up
    6286 
    6287 990 atoms, 1018 bonds, 126 residues, 1 model selected 
    6288 
    6289 > color sel burly wood
    6290 
    6291 > color sel goldenrod
    6292 
    6293 > color sel dark goldenrod
    6294 
    6295 > select clear
    6296 
    6297 [Repeated 1 time(s)]
    6298 
    6299 > select #6/G:4
    6300 
    6301 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6302 
    6303 > select #6/G:107
    6304 
    6305 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6306 
    6307 > select up
    6308 
    6309 181 atoms, 190 bonds, 22 residues, 1 model selected 
    6310 
    6311 > select subtract #6/G:115
    6312 
    6313 173 atoms, 181 bonds, 21 residues, 1 model selected 
    6314 
    6315 > select add #6/G:97
    6316 
    6317 178 atoms, 185 bonds, 22 residues, 1 model selected 
    6318 
    6319 > select subtract #6/G:97
    6320 
    6321 173 atoms, 181 bonds, 21 residues, 1 model selected 
    6322 
    6323 > select subtract #6/G:116
    6324 
    6325 161 atoms, 168 bonds, 20 residues, 1 model selected 
    6326 
    6327 > select subtract #6/G:117
    6328 
    6329 147 atoms, 152 bonds, 19 residues, 1 model selected 
    6330 
    6331 > select subtract #6/G:118
    6332 
    6333 143 atoms, 148 bonds, 18 residues, 1 model selected 
    6334 
    6335 > select subtract #6/G:119
    6336 
    6337 134 atoms, 139 bonds, 17 residues, 1 model selected 
    6338 
    6339 > select subtract #6/G:120
    6340 
    6341 130 atoms, 136 bonds, 16 residues, 1 model selected 
    6342 
    6343 > color sel navy
    6344 
    6345 > color sel steel blue
    6346 
    6347 > color sel teal
    6348 
    6349 > color sel dark cyan
    6350 
    6351 > select clear
    6352 
    6353 > show #!7 models
    6354 
    6355 > hide #!6 models
    6356 
    6357 > select #7/H:48
    6358 
    6359 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6360 
    6361 > select up
    6362 
    6363 33 atoms, 32 bonds, 4 residues, 1 model selected 
    6364 
    6365 > select up
    6366 
    6367 797 atoms, 812 bonds, 110 residues, 1 model selected 
    6368 
    6369 > color sel pale goldenrod
    6370 
    6371 > select #7/G:122
    6372 
    6373 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6374 
    6375 > select up
    6376 
    6377 36 atoms, 35 bonds, 5 residues, 1 model selected 
    6378 
    6379 > select up
    6380 
    6381 990 atoms, 1018 bonds, 126 residues, 1 model selected 
    6382 
    6383 > select up
    6384 
    6385 3204 atoms, 3286 bonds, 410 residues, 1 model selected 
    6386 
    6387 > select down
    6388 
    6389 990 atoms, 1018 bonds, 126 residues, 1 model selected 
    6390 
    6391 > color sel goldenrod
    6392 
    6393 > select clear
    6394 
    6395 [Repeated 1 time(s)]
    6396 
    6397 > select #7/G:101
    6398 
    6399 14 atoms, 15 bonds, 1 residue, 1 model selected 
    6400 
    6401 > select up
    6402 
    6403 181 atoms, 190 bonds, 22 residues, 1 model selected 
    6404 
    6405 > select add #7/G:98
    6406 
    6407 192 atoms, 200 bonds, 23 residues, 1 model selected 
    6408 
    6409 > select subtract #7/G:116
    6410 
    6411 180 atoms, 186 bonds, 22 residues, 1 model selected 
    6412 
    6413 > select subtract #7/G:117
    6414 
    6415 166 atoms, 170 bonds, 21 residues, 1 model selected 
    6416 
    6417 > select subtract #7/G:118
    6418 
    6419 162 atoms, 166 bonds, 20 residues, 1 model selected 
    6420 
    6421 > select subtract #7/G:119
    6422 
    6423 153 atoms, 157 bonds, 19 residues, 1 model selected 
    6424 
    6425 > select subtract #7/G:120
    6426 
    6427 149 atoms, 154 bonds, 18 residues, 1 model selected 
    6428 
    6429 > color sel dark cyan
    6430 
    6431 > select clear
    6432 
    6433 > view list
    6434 
    6435 Named views: init_design, session-start 
    6436 
    6437 > view init_design
    6438 
    6439 > show #!6 models
    6440 
    6441 > hide #!7 models
    6442 
    6443 > show #!7 models
    6444 
    6445 > hide #!6 models
    6446 
    6447 > select #7/A:68
    6448 
    6449 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6450 
    6451 > select up
    6452 
    6453 77 atoms, 78 bonds, 9 residues, 1 model selected 
    6454 
    6455 > select up
    6456 
    6457 1417 atoms, 1456 bonds, 174 residues, 1 model selected 
    6458 
    6459 > color sel olive drab
    6460 
    6461 > color sel dark khaki
    6462 
    6463 > color sel dark sea green
    6464 
    6465 > color sel light green
    6466 
    6467 > color sel pale green
    6468 
    6469 > color sel green yellow
    6470 
    6471 > color sel forest green
    6472 
    6473 [Repeated 1 time(s)]
    6474 
    6475 > color sel green
    6476 
    6477 > color sel lime
    6478 
    6479 > color sel lawn green
    6480 
    6481 > color sel blue
    6482 
    6483 > color sel medium blue
    6484 
    6485 > color sel dark blue
    6486 
    6487 > color sel medium sea green
    6488 
    6489 > color sel sea green
    6490 
    6491 > color sel olive drab
    6492 
    6493 > color sel green
    6494 
    6495 > color sel dark blue
    6496 
    6497 > color sel navy
    6498 
    6499 > color sel indigo
    6500 
    6501 > color sel navy
    6502 
    6503 > color sel dark blue
    6504 
    6505 > color sel navy
    6506 
    6507 > color sel medium blue
    6508 
    6509 > select clear
    6510 
    6511 > select #7/A:80
    6512 
    6513 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6514 
    6515 > select up
    6516 
    6517 90 atoms, 92 bonds, 11 residues, 1 model selected 
    6518 
    6519 > select up
    6520 
    6521 1417 atoms, 1456 bonds, 174 residues, 1 model selected 
    6522 
    6523 > color sel dark blue
    6524 
    6525 > select clear
    6526 
    6527 > show #!6 models
    6528 
    6529 > hide #!7 models
    6530 
    6531 > select #6/A:80
    6532 
    6533 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6534 
    6535 > select up
    6536 
    6537 90 atoms, 92 bonds, 11 residues, 1 model selected 
    6538 
    6539 > select up
    6540 
    6541 1416 atoms, 1454 bonds, 174 residues, 1 model selected 
    6542 
    6543 > show sel surfaces
    6544 
    6545 > transparency sel 50
    6546 
    6547 > transparency sel 70
    6548 
    6549 > select clear
    6550 
    6551 > show #!7 models
    6552 
    6553 > hide #!6 models
    6554 
    6555 > select #7/A:36
    6556 
    6557 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6558 
    6559 > select up
    6560 
    6561 74 atoms, 76 bonds, 10 residues, 1 model selected 
    6562 
    6563 > select up
    6564 
    6565 1417 atoms, 1456 bonds, 174 residues, 1 model selected 
    6566 
    6567 > volume style surface
    6568 
    6569 No volumes specified 
    6570 
    6571 > select clear
    6572 
    6573 > select #7/A:81
    6574 
    6575 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6576 
    6577 > select up
    6578 
    6579 90 atoms, 92 bonds, 11 residues, 1 model selected 
    6580 
    6581 > select up
    6582 
    6583 1417 atoms, 1456 bonds, 174 residues, 1 model selected 
    6584 
    6585 > show sel surfaces
    6586 
    6587 > transparency sel 50
    6588 
    6589 > transparency sel 70
    6590 
    6591 > select clear
    6592 
    6593 > show #!6 models
    6594 
    6595 > hide #6.2 models
    6596 
    6597 > show #6.2 models
    6598 
    6599 > hide #6.2 models
    6600 
    6601 > hide #!7 models
    6602 
    6603 > show #!7 models
    6604 
    6605 > show #6.2 models
    6606 
    6607 > hide #!7 models
    6608 
    6609 > hide #6.2 models
    6610 
    6611 > show #6.2 models
    6612 
    6613 > hide #!6 models
    6614 
    6615 > show #!7 models
    6616 
    6617 > show #!6 models
    6618 
    6619 > hide #!7 models
    6620 
    6621 > show #!7 models
    6622 
    6623 > hide #!6 models
    6624 
    6625 > show #!6 models
    6626 
    6627 > hide #!6 models
    6628 
    6629 > show #!6 models
    6630 
    6631 > hide #!7 models
    6632 
    6633 > show #!7 models
    6634 
    6635 > hide #!6 models
    6636 
    6637 > preset cartoons/nucleotides licorice/ovals
    6638 
    6639 Using preset: Cartoons/Nucleotides / Licorice/Ovals 
    6640 Changed 0 atom styles 
    6641 Preset expands to these ChimeraX commands:
    6642 
    6643    
    6644    
    6645     show nucleic
    6646     hide protein|solvent|H
    6647     surf hide
    6648     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    6649     ~worm
    6650     cartoon
    6651     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    6652     cartoon style ~(nucleic|strand) x round
    6653     cartoon style (nucleic|strand) x rect
    6654     cartoon style protein modeh default arrows f x round width 1 thick 1
    6655     cartoon style nucleic x round width 1.6 thick 1.6
    6656     nucleotides tube/slab shape ellipsoid
    6657 
    6658  
    6659 
    6660 > select #7/A:108
    6661 
    6662 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6663 
    6664 > select up
    6665 
    6666 67 atoms, 67 bonds, 8 residues, 2 models selected 
    6667 
    6668 > select up
    6669 
    6670 1417 atoms, 1456 bonds, 174 residues, 2 models selected 
    6671 
    6672 > show sel surfaces
    6673 
    6674 > show #!6 models
    6675 
    6676 > hide #!7 models
    6677 
    6678 > select #6/A:168
    6679 
    6680 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6681 
    6682 > select up
    6683 
    6684 99 atoms, 101 bonds, 13 residues, 2 models selected 
    6685 
    6686 > select up
    6687 
    6688 1416 atoms, 1454 bonds, 174 residues, 2 models selected 
    6689 
    6690 > show sel surfaces
    6691 
    6692 > select clear
    6693 
    6694 > show #!7 models
    6695 
    6696 > hide #!6 models
    6697 
    6698 > select #7/A:45@CG
    6699 
    6700 1 atom, 1 residue, 1 model selected 
    6701 
    6702 > select up
    6703 
    6704 8 atoms, 7 bonds, 1 residue, 2 models selected 
    6705 
    6706 > select up
    6707 
    6708 129 atoms, 133 bonds, 14 residues, 2 models selected 
    6709 
    6710 > select up
    6711 
    6712 1417 atoms, 1456 bonds, 174 residues, 2 models selected 
    6713 
    6714 > hide sel surfaces
    6715 
    6716 > color sel slate gray
    6717 
    6718 > color sel dim gray
    6719 
    6720 > show #!6 models
    6721 
    6722 > hide #!6 models
    6723 
    6724 > show #!6 models
    6725 
    6726 > hide #!6 models
    6727 
    6728 > hide #!7 models
    6729 
    6730 > show #!7 models
    6731 
    6732 > color sel dark orange
    6733 
    6734 > color sel chocolate
    6735 
    6736 > color sel dark red
    6737 
    6738 > color sel maroon
    6739 
    6740 > show sel surfaces
    6741 
    6742 > transparency sel 70
    6743 
    6744 > select clear
    6745 
    6746 > show #!6 models
    6747 
    6748 > hide #!7 models
    6749 
    6750 > show #5 models
    6751 
    6752 > hide #5 models
    6753 
    6754 > show #!7 models
    6755 
    6756 > hide #!6 models
    6757 
    6758 > select #7/A:46@CA
    6759 
    6760 1 atom, 1 residue, 1 model selected 
    6761 
    6762 > select up
    6763 
    6764 8 atoms, 7 bonds, 1 residue, 2 models selected 
    6765 
    6766 > select up
    6767 
    6768 129 atoms, 133 bonds, 14 residues, 2 models selected 
    6769 
    6770 > select up
    6771 
    6772 1417 atoms, 1456 bonds, 174 residues, 2 models selected 
    6773 
    6774 > color sel medium aquamarine
    6775 
    6776 > transparency sel 70
    6777 
    6778 > select clear
    6779 
    6780 > select #7/G:98
    6781 
    6782 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6783 
    6784 > select up
    6785 
    6786 58 atoms, 59 bonds, 7 residues, 1 model selected 
    6787 
    6788 > select up
    6789 
    6790 990 atoms, 1018 bonds, 126 residues, 1 model selected 
    6791 
    6792 > select down
    6793 
    6794 58 atoms, 59 bonds, 7 residues, 1 model selected 
    6795 
    6796 > select #7/G:101
    6797 
    6798 14 atoms, 15 bonds, 1 residue, 1 model selected 
    6799 
    6800 > select up
    6801 
    6802 181 atoms, 190 bonds, 22 residues, 1 model selected 
    6803 
    6804 > select subtract #7/G:116
    6805 
    6806 169 atoms, 176 bonds, 21 residues, 1 model selected 
    6807 
    6808 > select subtract #7/G:117
    6809 
    6810 155 atoms, 160 bonds, 20 residues, 1 model selected 
    6811 
    6812 > select subtract #7/G:118
    6813 
    6814 151 atoms, 156 bonds, 19 residues, 1 model selected 
    6815 
    6816 > select subtract #7/G:119
    6817 
    6818 142 atoms, 147 bonds, 18 residues, 1 model selected 
    6819 
    6820 > select subtract #7/G:120
    6821 
    6822 138 atoms, 144 bonds, 17 residues, 1 model selected 
    6823 
    6824 > select add #7/G:98
    6825 
    6826 149 atoms, 154 bonds, 18 residues, 1 model selected 
    6827 
    6828 > color sel navy
    6829 
    6830 > color sel dark blue
    6831 
    6832 > color sel medium aquamarine
    6833 
    6834 > color sel blue
    6835 
    6836 > color sel medium blue
    6837 
    6838 > color sel dark blue
    6839 
    6840 > color sel navy
    6841 
    6842 > color sel indigo
    6843 
    6844 > color sel midnight blue
    6845 
    6846 > show #!6 models
    6847 
    6848 > hide #!7 models
    6849 
    6850 > hide #!6 models
    6851 
    6852 > show #!7 models
    6853 
    6854 > show #!6 models
    6855 
    6856 > hide #!7 models
    6857 
    6858 > show #!7 models
    6859 
    6860 > hide #!6 models
    6861 
    6862 > hide #!7 models
    6863 
    6864 > show #!6 models
    6865 
    6866 > select #6/G:107
    6867 
    6868 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6869 
    6870 > select up
    6871 
    6872 181 atoms, 190 bonds, 22 residues, 1 model selected 
    6873 
    6874 > select subtract #6/G:120
    6875 
    6876 177 atoms, 186 bonds, 21 residues, 1 model selected 
    6877 
    6878 > select subtract #6/G:119
    6879 
    6880 168 atoms, 177 bonds, 20 residues, 1 model selected 
    6881 
    6882 > select subtract #6/G:118
    6883 
    6884 164 atoms, 173 bonds, 19 residues, 1 model selected 
    6885 
    6886 > select subtract #6/G:117
    6887 
    6888 150 atoms, 157 bonds, 18 residues, 1 model selected 
    6889 
    6890 > select subtract #6/G:115
    6891 
    6892 142 atoms, 148 bonds, 17 residues, 1 model selected 
    6893 
    6894 > select subtract #6/G:116
    6895 
    6896 130 atoms, 136 bonds, 16 residues, 1 model selected 
    6897 
    6898 > color sel midnight blue
    6899 
    6900 > show #!7 models
    6901 
    6902 > hide #!7 models
    6903 
    6904 > select clear
    6905 
    6906 > show #!7 models
    6907 
    6908 > hide #!6 models
    6909 
    6910 > select #7/G:108
    6911 
    6912 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6913 
    6914 > select #7/G:109
    6915 
    6916 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6917 
    6918 > select #7/G:110
    6919 
    6920 4 atoms, 3 bonds, 1 residue, 1 model selected 
    6921 
    6922 > select add #7/G:111
    6923 
    6924 16 atoms, 15 bonds, 2 residues, 1 model selected 
    6925 
    6926 > select add #7/G:112
    6927 
    6928 23 atoms, 22 bonds, 3 residues, 1 model selected 
    6929 
    6930 > select add #7/G:113
    6931 
    6932 31 atoms, 29 bonds, 4 residues, 1 model selected 
    6933 
    6934 > select add #7/G:114
    6935 
    6936 42 atoms, 40 bonds, 5 residues, 1 model selected 
    6937 
    6938 > select add #7/G:115
    6939 
    6940 50 atoms, 47 bonds, 6 residues, 1 model selected 
    6941 
    6942 > select add #7/G:98
    6943 
    6944 61 atoms, 57 bonds, 7 residues, 1 model selected 
    6945 
    6946 > select add #7/G:99
    6947 
    6948 65 atoms, 60 bonds, 8 residues, 1 model selected 
    6949 
    6950 > select add #7/G:100
    6951 
    6952 69 atoms, 63 bonds, 9 residues, 1 model selected 
    6953 
    6954 > select add #7/G:101
    6955 
    6956 83 atoms, 78 bonds, 10 residues, 1 model selected 
    6957 
    6958 > select add #7/G:102
    6959 
    6960 91 atoms, 85 bonds, 11 residues, 1 model selected 
    6961 
    6962 > select add #7/G:103
    6963 
    6964 97 atoms, 90 bonds, 12 residues, 1 model selected 
    6965 
    6966 > select add #7/G:104
    6967 
    6968 105 atoms, 97 bonds, 13 residues, 1 model selected 
    6969 
    6970 > color sel goldenrod
    6971 
    6972 > select clear
    6973 
    6974 > show #!6 models
    6975 
    6976 > hide #!7 models
    6977 
    6978 > name view init_des2
    6979 
    6980 "init_des2": invalid atom specifier 
    6981 
    6982 > view name init_des2
    6983 
    6984 > show #!7 models
    6985 
    6986 > hide #!7 models
    6987 
    6988 > select add #6/G:114
    6989 
    6990 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6991 
    6992 > select add #6/G:99
    6993 
    6994 15 atoms, 14 bonds, 2 residues, 1 model selected 
    6995 
    6996 > select add #6/G:100
    6997 
    6998 19 atoms, 17 bonds, 3 residues, 1 model selected 
    6999 
    7000 > select add #6/G:101
    7001 
    7002 33 atoms, 32 bonds, 4 residues, 1 model selected 
    7003 
    7004 > select add #6/G:102
    7005 
    7006 41 atoms, 39 bonds, 5 residues, 1 model selected 
    7007 
    7008 > select add #6/G:105
    7009 
    7010 53 atoms, 51 bonds, 6 residues, 1 model selected 
    7011 
    7012 > select subtract #6/G:105
    7013 
    7014 41 atoms, 39 bonds, 5 residues, 1 model selected 
    7015 Drag select of RMSD4_NNK1.pdb_A SES surface, 12 of 169006 triangles, 1
    7016 residues 
    7017 
    7018 > select add #6/G:104
    7019 
    7020 55 atoms, 46 bonds, 7 residues, 1 model selected 
    7021 
    7022 > select add #6/G:110
    7023 
    7024 59 atoms, 49 bonds, 8 residues, 1 model selected 
    7025 
    7026 > select add #6/G:111
    7027 
    7028 71 atoms, 61 bonds, 9 residues, 1 model selected 
    7029 
    7030 > select add #6/G:112
    7031 
    7032 78 atoms, 68 bonds, 10 residues, 1 model selected 
    7033 
    7034 > select add #6/G:113
    7035 
    7036 86 atoms, 75 bonds, 11 residues, 1 model selected 
    7037 
    7038 > color sel goldenrod
    7039 
    7040 > select clear
    7041 
    7042 [Repeated 1 time(s)]
    7043 
    7044 > select #6/G:98
    7045 
    7046 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7047 
    7048 > select up
    7049 
    7050 58 atoms, 59 bonds, 7 residues, 1 model selected 
    7051 
    7052 > select up
    7053 
    7054 990 atoms, 1018 bonds, 126 residues, 1 model selected 
    7055 
    7056 > select subtract #6/G:109
    7057 
    7058 984 atoms, 1011 bonds, 125 residues, 1 model selected 
    7059 
    7060 > select subtract #6/G:108
    7061 
    7062 978 atoms, 1005 bonds, 124 residues, 1 model selected 
    7063 
    7064 > select subtract #6/G:107
    7065 
    7066 970 atoms, 997 bonds, 123 residues, 1 model selected 
    7067 
    7068 > select subtract #6/G:105
    7069 
    7070 958 atoms, 983 bonds, 122 residues, 1 model selected 
    7071 
    7072 > select subtract #6/G:106
    7073 
    7074 946 atoms, 971 bonds, 121 residues, 1 model selected 
    7075 
    7076 > color sel goldenrod
    7077 
    7078 > select clear
    7079 
    7080 > view init_des2
    7081 
    7082 > show #!7 models
    7083 
    7084 > hide #!6 models
    7085 
    7086 > show #!6 models
    7087 
    7088 > hide #!7 models
    7089 
    7090 > show #!7 models
    7091 
    7092 > view init_des2
    7093 
    7094 > hide #!6 models
    7095 
    7096 > select clear
    7097 
    7098 > show #!6 models
    7099 
    7100 > hide #!7 models
    7101 
    7102 > save /Users/oswanson/Desktop/Primocalins/Structures/initial_models.cxs
    7103 
    7104 Desktop color scheme is dark 
    7105 Desktop color scheme is light 
    7106 Desktop color scheme is dark 
    7107 Desktop color scheme is light 
    7108 Desktop color scheme is dark 
    7109 Desktop color scheme is light 
    7110 
    7111 > show #!1 models
    7112 
    7113 > hide #!6 models
    7114 
    7115 > show #!3 models
    7116 
    7117 > hide #!3 models
    7118 
    7119 > show #1.2 models
    7120 
    7121 > show #1.3 models
    7122 
    7123 > select add #1.3
    7124 
    7125 64 pseudobonds, 1 model selected 
    7126 
    7127 > show #!1 atoms
    7128 
    7129 > select up
    7130 
    7131 71 pseudobonds, 3 models selected 
    7132 
    7133 > select #1/E:36@CA
    7134 
    7135 1 atom, 1 residue, 1 model selected 
    7136 
    7137 > select #1/E:36
    7138 
    7139 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7140 
    7141 > select add #1/H:111B
    7142 
    7143 20 atoms, 19 bonds, 2 residues, 1 model selected 
    7144 
    7145 > select add #1/E:50
    7146 
    7147 29 atoms, 27 bonds, 1 pseudobond, 3 residues, 2 models selected 
    7148 
    7149 > select add #1/E:49
    7150 
    7151 34 atoms, 31 bonds, 1 pseudobond, 4 residues, 2 models selected 
    7152 
    7153 > select add #1/H:111C
    7154 
    7155 46 atoms, 43 bonds, 1 pseudobond, 5 residues, 2 models selected 
    7156 
    7157 > select add #1/H:109
    7158 
    7159 60 atoms, 58 bonds, 1 pseudobond, 6 residues, 2 models selected 
    7160 
    7161 > select add #1/E:128
    7162 
    7163 68 atoms, 65 bonds, 1 pseudobond, 7 residues, 2 models selected 
    7164 
    7165 > select add #1/E:68
    7166 
    7167 76 atoms, 72 bonds, 1 pseudobond, 8 residues, 2 models selected 
    7168 
    7169 > select add #1/H:59
    7170 
    7171 84 atoms, 79 bonds, 1 pseudobond, 9 residues, 2 models selected 
    7172 
    7173 > select add #1/H:62
    7174 
    7175 90 atoms, 84 bonds, 1 pseudobond, 10 residues, 2 models selected 
    7176 
    7177 > select add #1/H:110
    7178 
    7179 98 atoms, 91 bonds, 1 pseudobond, 11 residues, 2 models selected 
    7180 
    7181 > select add #1/E:72
    7182 
    7183 105 atoms, 98 bonds, 1 pseudobond, 12 residues, 2 models selected 
    7184 
    7185 > select add #1/H:66
    7186 
    7187 113 atoms, 105 bonds, 1 pseudobond, 13 residues, 2 models selected 
    7188 
    7189 > select add #1/E:74
    7190 
    7191 122 atoms, 113 bonds, 1 pseudobond, 14 residues, 2 models selected 
    7192 
    7193 > select add #1/H:112D
    7194 
    7195 130 atoms, 120 bonds, 1 pseudobond, 15 residues, 2 models selected 
    7196 
    7197 > select add #1/E:52
    7198 
    7199 141 atoms, 131 bonds, 1 pseudobond, 16 residues, 2 models selected 
    7200 
    7201 > select add #1/H:111A
    7202 
    7203 149 atoms, 138 bonds, 1 pseudobond, 17 residues, 2 models selected 
    7204 
    7205 > select ~sel & ##selected
    7206 
    7207 4498 atoms, 4613 bonds, 41 pseudobonds, 591 residues, 4 models selected 
    7208 
    7209 > hide sel atoms
    7210 
    7211 > undo
    7212 
    7213 > redo
    7214 
    7215 > select clear
    7216 
    7217 > select #1/H:111C
    7218 
    7219 12 atoms, 12 bonds, 1 residue, 1 model selected 
    7220 
    7221 > hide sel atoms
    7222 
    7223 > select clear
    7224 
    7225 > select add #1.3
    7226 
    7227 64 pseudobonds, 1 model selected 
    7228 
    7229 > select add #1.2
    7230 
    7231 70 pseudobonds, 2 models selected 
    7232 
    7233 > view orient
    7234 
    7235 > select subtract #1.3
    7236 
    7237 6 pseudobonds, 1 model selected 
    7238 
    7239 > select subtract #1.2
    7240 
    7241 Nothing selected 
    7242 
    7243 > select #1/H:111C
    7244 
    7245 12 atoms, 12 bonds, 1 residue, 1 model selected 
    7246 
    7247 > select up
    7248 
    7249 181 atoms, 190 bonds, 22 residues, 1 model selected 
    7250 
    7251 > select up
    7252 
    7253 1725 atoms, 1772 bonds, 228 residues, 1 model selected 
    7254 
    7255 > select up
    7256 
    7257 4647 atoms, 4757 bonds, 608 residues, 1 model selected 
    7258 
    7259 > select down
    7260 
    7261 1725 atoms, 1772 bonds, 228 residues, 1 model selected 
    7262 
    7263 > style sel sphere
    7264 
    7265 Changed 1725 atom styles 
    7266 
    7267 > select up
    7268 
    7269 4647 atoms, 4757 bonds, 608 residues, 1 model selected 
    7270 
    7271 > style sel sphere
    7272 
    7273 Changed 4647 atom styles 
    7274 
    7275 > style sel ball
    7276 
    7277 Changed 4647 atom styles 
    7278 
    7279 > nucleotides sel atoms
    7280 
    7281 > style nucleic & sel stick
    7282 
    7283 Changed 0 atom styles 
    7284 
    7285 > nucleotides sel atoms
    7286 
    7287 > style nucleic & sel stick
    7288 
    7289 Changed 0 atom styles 
    7290 
    7291 > style sel stick
    7292 
    7293 Changed 4647 atom styles 
    7294 
    7295 > hide #1.3 models
    7296 
    7297 > open
    7298 > /Users/oswanson/Desktop/Primocalins/Structures/folds_2025_11_03_22_26/y513_gspy_uca3_notags/fold_y513_gspy_uca3_notags_full_data_0.json
    7299 
    7300 Failed opening file
    7301 /Users/oswanson/Desktop/Primocalins/Structures/folds_2025_11_03_22_26/y513_gspy_uca3_notags/fold_y513_gspy_uca3_notags_full_data_0.json: 
    7302 Opening an AlphaFold PAE file requires first opening the predicted atomic
    7303 model. Did not find an open atomic model from the same directory. If the
    7304 atomic model is already open choose it using menu 
    7305  
    7306 Tools / Structure Prediction / AlphaFold Error Plot 
    7307  
    7308 or use the open command structure option, for example 
    7309  
    7310 open
    7311 /Users/oswanson/Desktop/Primocalins/Structures/folds_2025_11_03_22_26/y513_gspy_uca3_notags/fold_y513_gspy_uca3_notags_full_data_0.json
    7312 structure #1 
    7313  
    7314 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    7315 need to specify the specific JSON format such as 
    7316  
    7317 open mole_channels.json format mole 
    7318 
    7319 > open
    7320 > /Users/oswanson/Desktop/Primocalins/Structures/folds_2025_11_03_22_26/y513_gspy_uca3_notags/fold_y513_gspy_uca3_notags_model_0.cif
    7321 
    7322 Chain information for fold_y513_gspy_uca3_notags_model_0.cif #9 
    7323 --- 
    7324 Chain | Description 
    7325 A | . 
    7326 B | . 
    7327 C | . 
    7328  
    7329 Computing secondary structure 
    7330 
    7331 > open
    7332 > /Users/oswanson/Desktop/Primocalins/Structures/folds_2025_11_03_22_26/poly310_uca3/fold_poly310_uca3_model_0.cif
    7333 
    7334 Chain information for fold_poly310_uca3_model_0.cif #10 
    7335 --- 
    7336 Chain | Description 
    7337 A | . 
    7338 B | . 
    7339 C | . 
    7340  
    7341 Computing secondary structure 
    7342 
    7343 > open
    7344 > /Users/oswanson/Desktop/Primocalins/Structures/folds_2025_11_03_22_26/poly28_uca3/fold_poly28_uca3_model_0.cif
    7345 
    7346 Chain information for fold_poly28_uca3_model_0.cif #11 
    7347 --- 
    7348 Chain | Description 
    7349 A | . 
    7350 B | . 
    7351 C | . 
    7352  
    7353 Computing secondary structure 
    7354 
    7355 > ui tool show Matchmaker
    7356 
    7357 > select #1/E:132
    7358 
    7359 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7360 
    7361 > select up
    7362 
    7363 63 atoms, 63 bonds, 8 residues, 1 model selected 
    7364 
    7365 > select up
    7366 
    7367 604 atoms, 618 bonds, 74 residues, 1 model selected 
    7368 
    7369 > select up
    7370 
    7371 616 atoms, 629 bonds, 76 residues, 1 model selected 
    7372 
    7373 > select up
    7374 
    7375 1313 atoms, 1346 bonds, 164 residues, 1 model selected 
    7376 
    7377 > matchmaker #9-11 to #1 & sel
    7378 
    7379 Parameters 
    7380 --- 
    7381 Chain pairing | bb 
    7382 Alignment algorithm | Needleman-Wunsch 
    7383 Similarity matrix | BLOSUM-62 
    7384 SS fraction | 0.3 
    7385 Gap open (HH/SS/other) | 18/18/6 
    7386 Gap extend | 1 
    7387 SS matrix |  |  | H | S | O 
    7388 ---|---|---|--- 
    7389 H | 6 | -9 | -6 
    7390 S |  | 6 | -6 
    7391 O |  |  | 4 
    7392 Iteration cutoff | 2 
    7393  
    7394 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
    7395 fold_y513_gspy_uca3_notags_model_0.cif, chain A (#9), sequence alignment score
    7396 = 675.4 
    7397 RMSD between 152 pruned atom pairs is 0.658 angstroms; (across all 164 pairs:
    7398 1.656) 
    7399  
    7400 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
    7401 fold_poly310_uca3_model_0.cif, chain A (#10), sequence alignment score = 803.4 
    7402 RMSD between 153 pruned atom pairs is 0.635 angstroms; (across all 164 pairs:
    7403 1.380) 
    7404  
    7405 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
    7406 fold_poly28_uca3_model_0.cif, chain A (#11), sequence alignment score = 766 
    7407 RMSD between 157 pruned atom pairs is 0.633 angstroms; (across all 164 pairs:
    7408 1.406) 
    7409  
    7410 
    7411 > hide #9 models
    7412 
    7413 > hide #11 models
    7414 
    7415 > show #11 models
    7416 
    7417 > hide #10 models
    7418 
    7419 > show #!6 models
    7420 
    7421 > hide #!6 models
    7422 
    7423 > show #5 models
    7424 
    7425 > hide #5 models
    7426 
    7427 > show #4 models
    7428 
    7429 > hide #4 models
    7430 
    7431 > show #4 models
    7432 
    7433 > hide #4 models
    7434 
    7435 > show #4 models
    7436 
    7437 > hide #4 models
    7438 
    7439 > show #9 models
    7440 
    7441 > hide #11 models
    7442 
    7443 > show #2 models
    7444 
    7445 > matchmaker #2 to #1 & sel
    7446 
    7447 Parameters 
    7448 --- 
    7449 Chain pairing | bb 
    7450 Alignment algorithm | Needleman-Wunsch 
    7451 Similarity matrix | BLOSUM-62 
    7452 SS fraction | 0.3 
    7453 Gap open (HH/SS/other) | 18/18/6 
    7454 Gap extend | 1 
    7455 SS matrix |  |  | H | S | O 
    7456 ---|---|---|--- 
    7457 H | 6 | -9 | -6 
    7458 S |  | 6 | -6 
    7459 O |  |  | 4 
    7460 Iteration cutoff | 2 
    7461  
    7462 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
    7463 Y513apo_refine_31.pdb, chain B (#2), sequence alignment score = 692 
    7464 RMSD between 154 pruned atom pairs is 0.689 angstroms; (across all 164 pairs:
    7465 1.591) 
    7466  
    7467 
    7468 > matchmaker #5 to #1 & sel
    7469 
    7470 Parameters 
    7471 --- 
    7472 Chain pairing | bb 
    7473 Alignment algorithm | Needleman-Wunsch 
    7474 Similarity matrix | BLOSUM-62 
    7475 SS fraction | 0.3 
    7476 Gap open (HH/SS/other) | 18/18/6 
    7477 Gap extend | 1 
    7478 SS matrix |  |  | H | S | O 
    7479 ---|---|---|--- 
    7480 H | 6 | -9 | -6 
    7481 S |  | 6 | -6 
    7482 O |  |  | 4 
    7483 Iteration cutoff | 2 
    7484  
    7485 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
    7486 design_start.pdb, chain A (#5), sequence alignment score = 709.7 
    7487 RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 164 pairs:
    7488 1.402) 
    7489  
    7490 
    7491 > show #5 models
    7492 
    7493 > hide #2 models
    7494 
    7495 > hide #9 models
    7496 
    7497 > hide #5 models
    7498 
    7499 > show #5 models
    7500 
    7501 > hide #5 models
    7502 
    7503 > show #5 models
    7504 
    7505 > hide #!1 models
    7506 
    7507 > show #11 models
    7508 
    7509 > hide #11 models
    7510 
    7511 > show #9 models
    7512 
    7513 > hide #9 models
    7514 
    7515 > show #!1 models
    7516 
    7517 > show #2 models
    7518 
    7519 > hide #!1 models
    7520 
    7521 > hide #5 models
    7522 
    7523 > show #9 models
    7524 
    7525 > hide #1.2 models
    7526 
    7527 > hide #2 models
    7528 
    7529 > show #2 models
    7530 
    7531 > hide #2 models
    7532 
    7533 > show #2 models
    7534 
    7535 > hide #2 models
    7536 
    7537 > show #2 models
    7538 
    7539 > hide #2 models
    7540 
    7541 > select #9/A:85
    7542 
    7543 10 atoms, 10 bonds, 1 residue, 1 model selected 
    7544 
    7545 > select up
    7546 
    7547 93 atoms, 96 bonds, 11 residues, 1 model selected 
    7548 
    7549 > select up
    7550 
    7551 1449 atoms, 1487 bonds, 184 residues, 1 model selected 
    7552 
    7553 > color bfactor sel
    7554 
    7555 1449 atoms, 184 residues, atom bfactor range 15.7 to 97.6 
    7556 
    7557 > select clear
    7558 
    7559 [Repeated 1 time(s)]
    7560 
    7561 > select #9/A:3
    7562 
    7563 11 atoms, 11 bonds, 1 residue, 1 model selected 
    7564 
    7565 > select up
    7566 
    7567 129 atoms, 134 bonds, 18 residues, 1 model selected 
    7568 
    7569 > select subtract #9/A:18
    7570 
    7571 122 atoms, 126 bonds, 17 residues, 1 model selected 
    7572 
    7573 > select subtract #9/A:17
    7574 
    7575 115 atoms, 118 bonds, 16 residues, 1 model selected 
    7576 
    7577 > select subtract #9/A:16
    7578 
    7579 110 atoms, 113 bonds, 15 residues, 1 model selected 
    7580 
    7581 > select subtract #9/A:15
    7582 
    7583 103 atoms, 105 bonds, 14 residues, 1 model selected 
    7584 
    7585 > select subtract #9/A:14
    7586 
    7587 95 atoms, 97 bonds, 13 residues, 1 model selected 
    7588 
    7589 > select subtract #9/A:13
    7590 
    7591 90 atoms, 92 bonds, 12 residues, 1 model selected 
    7592 
    7593 > hide sel cartoons
    7594 
    7595 > select #9/A:86
    7596 
    7597 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7598 
    7599 > select up
    7600 
    7601 93 atoms, 96 bonds, 11 residues, 1 model selected 
    7602 
    7603 > select up
    7604 
    7605 1449 atoms, 1487 bonds, 184 residues, 1 model selected 
    7606 
    7607 > ui tool show Contacts
    7608 
    7609 > contacts sel restrict cross interModel false intraMol false
    7610 > ignoreHiddenModels true select true color #ff2600 name contacts_AF3_Y513
    7611 > reveal true log true
    7612    
    7613    
    7614     Allowed overlap: -0.4
    7615     H-bond overlap reduction: 0.4
    7616     Ignore contacts between atoms separated by 4 bonds or less
    7617     Detect intra-residue contacts: False
    7618     Detect intra-molecule contacts: False
    7619    
    7620     116 contacts
    7621                              atom1                                                    atom2                           overlap  distance
    7622     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CG2    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 O     1.315    1.985
    7623     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 O    fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CD1   0.992    2.188
    7624     fold_y513_gspy_uca3_notags_model_0.cif #9/A MET 131 SD   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CB    0.884    2.766
    7625     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASN 135 ND2  fold_y513_gspy_uca3_notags_model_0.cif #9/B ASN 113 ND2   0.667    2.613
    7626     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CB     fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CA    0.633    3.127
    7627     fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CE2  fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CE2   0.606    2.914
    7628     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CG2    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 C     0.598    2.892
    7629     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLY 108 CA   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 32 OH     0.541    2.799
    7630     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CB     fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 O     0.531    2.769
    7631     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 O     0.504    2.156
    7632     fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CZ   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CE2   0.481    3.039
    7633     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CE     fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 50 CH2    0.470    3.170
    7634     fold_y513_gspy_uca3_notags_model_0.cif #9/A TRP 7 CH2    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CD1   0.459    3.061
    7635     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 NE2   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 OH    0.413    2.287
    7636     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 OG1    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CA    0.412    2.928
    7637     fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CE2  fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CD2   0.393    3.127
    7638     fold_y513_gspy_uca3_notags_model_0.cif #9/A TRP 7 CH2    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CE1   0.383    3.137
    7639     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 O    fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 NE1   0.355    2.305
    7640     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CE    fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 93 CE1    0.313    3.327
    7641     fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 NH2  fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CE2   0.258    3.142
    7642     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CG     fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 50 CH2    0.199    3.441
    7643     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CE    fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 93 CZ     0.198    3.292
    7644     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 CG   fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 OG1    0.193    3.147
    7645     fold_y513_gspy_uca3_notags_model_0.cif #9/A MET 74 SD    fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD2   0.177    3.473
    7646     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CB     fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 C     0.135    3.355
    7647     fold_y513_gspy_uca3_notags_model_0.cif #9/A HIS 85 CG    fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD1   0.116    3.374
    7648     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 NE2   fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD2   0.112    3.408
    7649     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 NE2   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CZ    0.093    3.157
    7650     fold_y513_gspy_uca3_notags_model_0.cif #9/A VAL 4 CG1    fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 CG    0.089    3.671
    7651     fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CZ   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CZ    0.084    3.286
    7652     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 133 OD2  fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 OH    0.078    2.402
    7653     fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 109 CB   fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CZ2   0.067    3.573
    7654     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CG2    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CA    0.063    3.697
    7655     fold_y513_gspy_uca3_notags_model_0.cif #9/A HIS 85 ND1   fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD1   0.055    3.465
    7656     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CD     fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 50 CH2    0.053    3.587
    7657     fold_y513_gspy_uca3_notags_model_0.cif #9/A TRP 7 CZ2    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CD1   0.052    3.468
    7658     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 CG   fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 CB     0.044    3.716
    7659     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CE    fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 O     0.040    3.260
    7660     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 CD    fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD2   0.039    3.451
    7661     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 C     0.037    3.213
    7662     fold_y513_gspy_uca3_notags_model_0.cif #9/A MET 131 SD   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CG    0.035    3.345
    7663     fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 CZ   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CE2   0.033    3.337
    7664     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 133 CG   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 OH    0.022    3.318
    7665     fold_y513_gspy_uca3_notags_model_0.cif #9/A HIS 85 CB    fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD1   0.008    3.752
    7666     fold_y513_gspy_uca3_notags_model_0.cif #9/A VAL 4 CG1    fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 OD2   -0.019    3.319
    7667     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CB    fold_y513_gspy_uca3_notags_model_0.cif #9/C LEU 34 CD1    -0.022    3.782
    7668     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 C    fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CD1   -0.034    3.404
    7669     fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 109 CD2  fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CH2   -0.048    3.688
    7670     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CG2    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CA    -0.055    3.815
    7671     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CB     fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 N     -0.060    3.580
    7672     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CE     fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 50 CZ3    -0.069    3.709
    7673     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CE    fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 93 OH     -0.088    3.428
    7674     fold_y513_gspy_uca3_notags_model_0.cif #9/A HIS 85 CD2   fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD1   -0.089    3.729
    7675     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 NE2   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CE2   -0.090    3.490
    7676     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CG    fold_y513_gspy_uca3_notags_model_0.cif #9/C LEU 34 CD1    -0.107    3.867
    7677     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CE     fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 33 OH     -0.120    3.460
    7678     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 CB   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 27 CA     -0.128    3.888
    7679     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 OG1    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 C     -0.128    3.198
    7680     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 N     -0.140    3.420
    7681     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CG2    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 N     -0.140    3.660
    7682     fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 89 CZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 OH    -0.142    3.362
    7683     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 CG   fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 OG1    -0.147    3.487
    7684     fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 NE   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CE2   -0.147    3.547
    7685     fold_y513_gspy_uca3_notags_model_0.cif #9/A TRP 7 CZ2    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CE1   -0.149    3.669
    7686     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 OE1   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CE2   -0.154    3.334
    7687     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CG     fold_y513_gspy_uca3_notags_model_0.cif #9/B GLY 57 CA     -0.158    3.918
    7688     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CG    fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 93 CE2    -0.161    3.801
    7689     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CG     fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 50 CZ3    -0.165    3.805
    7690     fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CZ   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CD2   -0.167    3.687
    7691     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASN 135 CG   fold_y513_gspy_uca3_notags_model_0.cif #9/B ASN 113 ND2   -0.180    3.430
    7692     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CD    fold_y513_gspy_uca3_notags_model_0.cif #9/C LEU 34 CD1    -0.183    3.943
    7693     fold_y513_gspy_uca3_notags_model_0.cif #9/A ALA 13 CB    fold_y513_gspy_uca3_notags_model_0.cif #9/C ASN 33 ND2    -0.184    3.704
    7694     fold_y513_gspy_uca3_notags_model_0.cif #9/A MET 131 CE   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CB    -0.186    3.946
    7695     fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 CB   fold_y513_gspy_uca3_notags_model_0.cif #9/C GLU 52 OE2    -0.194    3.494
    7696     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CB     fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CB    -0.200    3.960
    7697     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 CG   fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 N      -0.204    3.724
    7698     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CD    fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 O     -0.208    3.508
    7699     fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 NH2  fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 108 CB    -0.210    3.730
    7700     fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 109 CD2  fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CZ2   -0.214    3.854
    7701     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 C    fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 NE1   -0.215    3.465
    7702     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 NZ     fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 33 OH     -0.218    2.918
    7703     fold_y513_gspy_uca3_notags_model_0.cif #9/A HIS 85 CE1   fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD1   -0.219    3.859
    7704     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CB     fold_y513_gspy_uca3_notags_model_0.cif #9/B GLY 57 CA     -0.234    3.994
    7705     fold_y513_gspy_uca3_notags_model_0.cif #9/A MET 131 SD   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CD2   -0.237    3.767
    7706     fold_y513_gspy_uca3_notags_model_0.cif #9/A VAL 4 CG1    fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 CB    -0.243    4.003
    7707     fold_y513_gspy_uca3_notags_model_0.cif #9/A ALA 5 CB     fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 O     -0.254    3.554
    7708     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CE     fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 33 CE1    -0.255    3.895
    7709     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 108 CA    -0.257    3.777
    7710     fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 NH1  fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 111 CE2   -0.262    3.662
    7711     fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CZ   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 OH    -0.269    3.489
    7712     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 108 C     -0.270    3.520
    7713     fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 9 O      fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 O     -0.271    3.111
    7714     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CE    fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 93 CE2    -0.272    3.912
    7715     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 OE1   fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD2   -0.274    3.574
    7716     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 CD    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 OH    -0.286    3.356
    7717     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASN 135 CA   fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 51 CE2    -0.290    3.930
    7718     fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CE2  fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CZ    -0.296    3.666
    7719     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLY 108 N    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 32 OH     -0.298    2.998
    7720     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 CG   fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 CG2    -0.300    4.060
    7721     fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 109 CD1  fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CH2   -0.301    3.941
    7722     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 O      fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 CB    -0.304    3.604
    7723     fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 109 CB   fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CH2   -0.308    3.948
    7724     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 O    fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CG    -0.310    3.340
    7725     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 C    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 32 OH     -0.314    3.384
    7726     fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 NH1  fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 111 CD2   -0.323    3.723
    7727     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 NZ     fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 CB    -0.334    3.854
    7728     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASN 135 CB   fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 51 CE2    -0.336    3.976
    7729     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CE    fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 93 CD1    -0.339    3.979
    7730     fold_y513_gspy_uca3_notags_model_0.cif #9/A HIS 85 CB    fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD2   -0.347    4.107
    7731     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 OG1    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 C     -0.368    3.438
    7732     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 CA    -0.375    3.895
    7733     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLY 108 CA   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 32 CZ     -0.383    3.873
    7734     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 133 CB   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 OH    -0.384    3.724
    7735     fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 89 CE1   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 OH    -0.393    3.613
    7736     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 133 OD2  fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CZ    -0.396    3.426
    7737     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 O    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 32 CE1    -0.400    3.580
    7738    
    7739 
    7740  
    7741 116 contacts 
    7742 
    7743 > select up
    7744 
    7745 373 atoms, 366 bonds, 41 residues, 1 model selected 
    7746 
    7747 > show sel cartoons
    7748 
    7749 > select clear
    7750 
    7751 > select #9/A:9
    7752 
    7753 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7754 
    7755 > select up
    7756 
    7757 129 atoms, 134 bonds, 18 residues, 1 model selected 
    7758 
    7759 > select subtract #9/A:13
    7760 
    7761 124 atoms, 128 bonds, 17 residues, 1 model selected 
    7762 
    7763 > select subtract #9/A:14
    7764 
    7765 116 atoms, 120 bonds, 16 residues, 1 model selected 
    7766 
    7767 > select subtract #9/A:15
    7768 
    7769 109 atoms, 112 bonds, 15 residues, 1 model selected 
    7770 
    7771 > select subtract #9/A:16
    7772 
    7773 104 atoms, 107 bonds, 14 residues, 1 model selected 
    7774 
    7775 > select subtract #9/A:17
    7776 
    7777 97 atoms, 99 bonds, 13 residues, 1 model selected 
    7778 
    7779 > select subtract #9/A:18
    7780 
    7781 90 atoms, 92 bonds, 12 residues, 1 model selected 
    7782 
    7783 > hide sel atoms
    7784 
    7785 > hide sel cartoons
    7786 
    7787 > select #9/A:77
    7788 
    7789 11 atoms, 11 bonds, 1 residue, 1 model selected 
    7790 
    7791 > select up
    7792 
    7793 73 atoms, 74 bonds, 9 residues, 1 model selected 
    7794 
    7795 > select up
    7796 
    7797 1449 atoms, 1487 bonds, 184 residues, 1 model selected 
    7798 
    7799 > ui tool show H-Bonds
    7800 
    7801 > hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8
    7802 > intraMol false intraRes false select true reveal true log true
    7803    
    7804    
    7805     Finding intramodel H-bonds
    7806     Constraints relaxed by 0.8 angstroms and 20 degrees
    7807     Models used:
    7808         9 fold_y513_gspy_uca3_notags_model_0.cif
    7809    
    7810     12 H-bonds
    7811     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    7812     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 NZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 33 OH    no hydrogen  2.918  N/A
    7813     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 NZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 OD1  no hydrogen  3.757  N/A
    7814     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 NZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 OG   no hydrogen  3.788  N/A
    7815     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ   fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 O    no hydrogen  3.089  N/A
    7816     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ   fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 O    no hydrogen  2.156  N/A
    7817     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 NE2  fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 OH   no hydrogen  2.287  N/A
    7818     fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 N    fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 O    no hydrogen  3.544  N/A
    7819     fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 OG1  fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 OD1  no hydrogen  2.990  N/A
    7820     fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 OG1  fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 OD2  no hydrogen  2.993  N/A
    7821     fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 OH  fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 133 OD2  no hydrogen  2.402  N/A
    7822     fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 N   fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 9 O      no hydrogen  3.520  N/A
    7823     fold_y513_gspy_uca3_notags_model_0.cif #9/C LYS 55 NZ   fold_y513_gspy_uca3_notags_model_0.cif #9/A ASN 135 O    no hydrogen  3.388  N/A
    7824    
    7825 
    7826  
    7827 12 hydrogen bonds found 
    7828 
    7829 > hide #9.1 models
    7830 
    7831 > select up
    7832 
    7833 6 atoms, 3 bonds, 3 residues, 1 model selected 
    7834 
    7835 > select up
    7836 
    7837 26 atoms, 24 bonds, 3 residues, 1 model selected 
    7838 
    7839 > hide sel atoms
    7840 
    7841 > show #2 models
    7842 
    7843 > select #2/B:100
    7844 
    7845 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7846 
    7847 > select up
    7848 
    7849 150 atoms, 152 bonds, 21 residues, 1 model selected 
    7850 
    7851 > show sel atoms
    7852 
    7853 > select clear
    7854 
    7855 > hide #2 models
    7856 
    7857 > hide #!9 models
    7858 
    7859 > show #10 models
    7860 
    7861 > select #10/A:74
    7862 
    7863 12 atoms, 12 bonds, 1 residue, 1 model selected 
    7864 
    7865 > select up
    7866 
    7867 70 atoms, 71 bonds, 8 residues, 1 model selected 
    7868 
    7869 > select up
    7870 
    7871 1533 atoms, 1572 bonds, 191 residues, 1 model selected 
    7872 
    7873 > color bfactor sel
    7874 
    7875 1533 atoms, 191 residues, atom bfactor range 23 to 97.7 
    7876 
    7877 > select clear
    7878 
    7879 > select #10/A:33
    7880 
    7881 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7882 
    7883 > select up
    7884 
    7885 74 atoms, 76 bonds, 10 residues, 1 model selected 
    7886 
    7887 > select up
    7888 
    7889 1533 atoms, 1572 bonds, 191 residues, 1 model selected 
    7890 
    7891 > hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8
    7892 > intraMol false intraRes false select true reveal true log true
    7893    
    7894    
    7895     Finding intramodel H-bonds
    7896     Constraints relaxed by 0.8 angstroms and 20 degrees
    7897     Models used:
    7898         10 fold_poly310_uca3_model_0.cif
    7899    
    7900     27 H-bonds
    7901     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    7902     fold_poly310_uca3_model_0.cif #10/A HIS 1 NE2    fold_poly310_uca3_model_0.cif #10/B ASN 54 O     no hydrogen  3.290  N/A
    7903     fold_poly310_uca3_model_0.cif #10/A LYS 42 NZ    fold_poly310_uca3_model_0.cif #10/B THR 74 O     no hydrogen  2.445  N/A
    7904     fold_poly310_uca3_model_0.cif #10/A THR 50 OG1   fold_poly310_uca3_model_0.cif #10/B TYR 105 OH   no hydrogen  3.816  N/A
    7905     fold_poly310_uca3_model_0.cif #10/A LYS 70 NZ    fold_poly310_uca3_model_0.cif #10/B TYR 116 OH   no hydrogen  3.243  N/A
    7906     fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ    fold_poly310_uca3_model_0.cif #10/B ASP 107 OD1  no hydrogen  2.708  N/A
    7907     fold_poly310_uca3_model_0.cif #10/A ARG 123 NH1  fold_poly310_uca3_model_0.cif #10/B GLY 103 O    no hydrogen  1.975  N/A
    7908     fold_poly310_uca3_model_0.cif #10/A ARG 123 NH1  fold_poly310_uca3_model_0.cif #10/B TYR 106 O    no hydrogen  3.125  N/A
    7909     fold_poly310_uca3_model_0.cif #10/A ASN 125 ND2  fold_poly310_uca3_model_0.cif #10/B THR 58 O     no hydrogen  3.150  N/A
    7910     fold_poly310_uca3_model_0.cif #10/A GLU 189 N    fold_poly310_uca3_model_0.cif #10/C GLU 52 OE1   no hydrogen  3.690  N/A
    7911     fold_poly310_uca3_model_0.cif #10/B THR 28 OG1   fold_poly310_uca3_model_0.cif #10/A ASP 43 OD1   no hydrogen  3.445  N/A
    7912     fold_poly310_uca3_model_0.cif #10/B THR 28 OG1   fold_poly310_uca3_model_0.cif #10/A ASP 43 OD2   no hydrogen  2.892  N/A
    7913     fold_poly310_uca3_model_0.cif #10/B THR 30 OG1   fold_poly310_uca3_model_0.cif #10/A GLU 40 OE1   no hydrogen  2.847  N/A
    7914     fold_poly310_uca3_model_0.cif #10/B THR 30 OG1   fold_poly310_uca3_model_0.cif #10/A GLU 40 OE2   no hydrogen  3.309  N/A
    7915     fold_poly310_uca3_model_0.cif #10/B TYR 33 OH    fold_poly310_uca3_model_0.cif #10/A ASP 124 OD1  no hydrogen  2.574  N/A
    7916     fold_poly310_uca3_model_0.cif #10/B TYR 33 OH    fold_poly310_uca3_model_0.cif #10/A ASP 124 OD2  no hydrogen  3.482  N/A
    7917     fold_poly310_uca3_model_0.cif #10/B ASN 52 ND2   fold_poly310_uca3_model_0.cif #10/A ASP 124 OD2  no hydrogen  2.754  N/A
    7918     fold_poly310_uca3_model_0.cif #10/B ASN 54 ND2   fold_poly310_uca3_model_0.cif #10/A ALA 36 O     no hydrogen  2.530  N/A
    7919     fold_poly310_uca3_model_0.cif #10/B SER 55 OG    fold_poly310_uca3_model_0.cif #10/A ASP 124 OD2  no hydrogen  3.777  N/A
    7920     fold_poly310_uca3_model_0.cif #10/B ARG 72 NH2   fold_poly310_uca3_model_0.cif #10/A HIS 1 NE2    no hydrogen  3.406  N/A
    7921     fold_poly310_uca3_model_0.cif #10/B ARG 98 NH1   fold_poly310_uca3_model_0.cif #10/A ASP 69 OD2   no hydrogen  2.768  N/A
    7922     fold_poly310_uca3_model_0.cif #10/B ARG 98 NH2   fold_poly310_uca3_model_0.cif #10/A ASP 69 OD2   no hydrogen  3.151  N/A
    7923     fold_poly310_uca3_model_0.cif #10/B TYR 105 OH   fold_poly310_uca3_model_0.cif #10/A THR 50 OG1   no hydrogen  3.816  N/A
    7924     fold_poly310_uca3_model_0.cif #10/B TYR 105 OH   fold_poly310_uca3_model_0.cif #10/A ASP 64 OD1   no hydrogen  3.083  N/A
    7925     fold_poly310_uca3_model_0.cif #10/B TYR 105 OH   fold_poly310_uca3_model_0.cif #10/A ASP 64 OD2   no hydrogen  3.375  N/A
    7926     fold_poly310_uca3_model_0.cif #10/C LYS 55 NZ    fold_poly310_uca3_model_0.cif #10/A TRP 187 O    no hydrogen  3.072  N/A
    7927     fold_poly310_uca3_model_0.cif #10/C TYR 93 OH    fold_poly310_uca3_model_0.cif #10/A ASP 96 OD2   no hydrogen  1.879  N/A
    7928     fold_poly310_uca3_model_0.cif #10/C SER 97 N     fold_poly310_uca3_model_0.cif #10/A ASP 96 OD2   no hydrogen  3.403  N/A
    7929    
    7930 
    7931  
    7932 27 hydrogen bonds found 
    7933 
    7934 > show #!1 models
    7935 
    7936 > show #1.2 models
    7937 
    7938 > hide #1.2 models
    7939 
    7940 > hide #!1 models
    7941 
    7942 > select #10/A:119
    7943 
    7944 11 atoms, 11 bonds, 1 residue, 1 model selected 
    7945 
    7946 > select up
    7947 
    7948 72 atoms, 74 bonds, 9 residues, 1 model selected 
    7949 
    7950 > select up
    7951 
    7952 1533 atoms, 1572 bonds, 191 residues, 1 model selected 
    7953 
    7954 > contacts sel restrict cross interModel false intraMol false
    7955 > ignoreHiddenModels true select true color #ff2600 name contacts_AF3_Y513
    7956 > reveal true log true
    7957    
    7958    
    7959     Allowed overlap: -0.4
    7960     H-bond overlap reduction: 0.4
    7961     Ignore contacts between atoms separated by 4 bonds or less
    7962     Detect intra-residue contacts: False
    7963     Detect intra-molecule contacts: False
    7964    
    7965     149 contacts
    7966                          atom1                                            atom2                       overlap  distance
    7967     fold_poly310_uca3_model_0.cif #10/A LEU 190 CD2  fold_poly310_uca3_model_0.cif #10/B TYR 111 OH    1.410    1.930
    7968     fold_poly310_uca3_model_0.cif #10/A ARG 77 NH2   fold_poly310_uca3_model_0.cif #10/B TYR 105 CE1   0.724    2.676
    7969     fold_poly310_uca3_model_0.cif #10/A LEU 32 CD2   fold_poly310_uca3_model_0.cif #10/B LEU 104 CD1   0.708    3.052
    7970     fold_poly310_uca3_model_0.cif #10/A ARG 123 NH1  fold_poly310_uca3_model_0.cif #10/B GLY 103 O     0.685    1.975
    7971     fold_poly310_uca3_model_0.cif #10/A ARG 77 NH1   fold_poly310_uca3_model_0.cif #10/B TYR 105 CD1   0.681    2.719
    7972     fold_poly310_uca3_model_0.cif #10/A MET 73 SD    fold_poly310_uca3_model_0.cif #10/B TRP 101 CE3   0.672    2.858
    7973     fold_poly310_uca3_model_0.cif #10/A ASP 96 OD2   fold_poly310_uca3_model_0.cif #10/C TYR 93 OH     0.601    1.879
    7974     fold_poly310_uca3_model_0.cif #10/A ARG 123 CD   fold_poly310_uca3_model_0.cif #10/B TYR 106 O     0.432    2.868
    7975     fold_poly310_uca3_model_0.cif #10/A LEU 32 CD1   fold_poly310_uca3_model_0.cif #10/B LEU 104 CD1   0.425    3.335
    7976     fold_poly310_uca3_model_0.cif #10/A LEU 190 CD1  fold_poly310_uca3_model_0.cif #10/B TYR 106 CD1   0.423    3.217
    7977     fold_poly310_uca3_model_0.cif #10/A ASP 96 CG    fold_poly310_uca3_model_0.cif #10/C TYR 93 OH     0.406    2.934
    7978     fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ    fold_poly310_uca3_model_0.cif #10/B ASP 107 CG    0.401    3.119
    7979     fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ    fold_poly310_uca3_model_0.cif #10/B GLY 110 N     0.359    2.921
    7980     fold_poly310_uca3_model_0.cif #10/A GLU 186 CG   fold_poly310_uca3_model_0.cif #10/C TYR 51 OH     0.353    2.987
    7981     fold_poly310_uca3_model_0.cif #10/A ARG 77 NH1   fold_poly310_uca3_model_0.cif #10/B TYR 105 CE1   0.336    3.064
    7982     fold_poly310_uca3_model_0.cif #10/A LEU 130 CD2  fold_poly310_uca3_model_0.cif #10/B LEU 104 CB    0.324    3.436
    7983     fold_poly310_uca3_model_0.cif #10/A PHE 48 CZ    fold_poly310_uca3_model_0.cif #10/B LEU 104 CD1   0.314    3.326
    7984     fold_poly310_uca3_model_0.cif #10/A LEU 90 CD2   fold_poly310_uca3_model_0.cif #10/B TYR 105 O     0.283    3.017
    7985     fold_poly310_uca3_model_0.cif #10/A LEU 130 CD2  fold_poly310_uca3_model_0.cif #10/B TYR 105 CD2   0.271    3.369
    7986     fold_poly310_uca3_model_0.cif #10/A PHE 48 CE1   fold_poly310_uca3_model_0.cif #10/B LEU 104 CD1   0.262    3.378
    7987     fold_poly310_uca3_model_0.cif #10/A ASP 96 CG    fold_poly310_uca3_model_0.cif #10/C SER 96 N      0.249    3.271
    7988     fold_poly310_uca3_model_0.cif #10/A LYS 94 CB    fold_poly310_uca3_model_0.cif #10/C TYR 93 CE2    0.241    3.399
    7989     fold_poly310_uca3_model_0.cif #10/A LEU 190 CD2  fold_poly310_uca3_model_0.cif #10/B TYR 111 CZ    0.239    3.251
    7990     fold_poly310_uca3_model_0.cif #10/A ASP 43 OD2   fold_poly310_uca3_model_0.cif #10/B THR 28 CA     0.220    3.080
    7991     fold_poly310_uca3_model_0.cif #10/A LYS 42 NZ    fold_poly310_uca3_model_0.cif #10/B THR 74 O      0.215    2.445
    7992     fold_poly310_uca3_model_0.cif #10/A LYS 94 CD    fold_poly310_uca3_model_0.cif #10/C TYR 93 CZ     0.147    3.343
    7993     fold_poly310_uca3_model_0.cif #10/A ASP 43 OD2   fold_poly310_uca3_model_0.cif #10/B THR 28 CG2    0.144    3.156
    7994     fold_poly310_uca3_model_0.cif #10/A ALA 36 O     fold_poly310_uca3_model_0.cif #10/B ASN 54 ND2    0.130    2.530
    7995     fold_poly310_uca3_model_0.cif #10/A ARG 77 CZ    fold_poly310_uca3_model_0.cif #10/B TYR 105 CE1   0.120    3.250
    7996     fold_poly310_uca3_model_0.cif #10/A ASP 43 OD2   fold_poly310_uca3_model_0.cif #10/B THR 28 CB     0.119    3.181
    7997     fold_poly310_uca3_model_0.cif #10/A ARG 123 NH1  fold_poly310_uca3_model_0.cif #10/B GLY 103 C     0.107    3.143
    7998     fold_poly310_uca3_model_0.cif #10/A HIS 188 ND1  fold_poly310_uca3_model_0.cif #10/C GLU 52 OE2    0.102    2.558
    7999     fold_poly310_uca3_model_0.cif #10/A ARG 77 NH1   fold_poly310_uca3_model_0.cif #10/B TYR 106 CB    0.100    3.420
    8000     fold_poly310_uca3_model_0.cif #10/A MET 73 SD    fold_poly310_uca3_model_0.cif #10/B TRP 101 CB    0.095    3.555
    8001     fold_poly310_uca3_model_0.cif #10/A LYS 94 CD    fold_poly310_uca3_model_0.cif #10/C TYR 93 OH     0.094    3.246
    8002     fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ    fold_poly310_uca3_model_0.cif #10/B SER 109 OG    0.092    2.608
    8003     fold_poly310_uca3_model_0.cif #10/A LEU 190 CD1  fold_poly310_uca3_model_0.cif #10/B TYR 106 CB    0.058    3.702
    8004     fold_poly310_uca3_model_0.cif #10/A PRO 68 CG    fold_poly310_uca3_model_0.cif #10/B TYR 32 OH     0.044    3.296
    8005     fold_poly310_uca3_model_0.cif #10/A ASN 92 OD1   fold_poly310_uca3_model_0.cif #10/B ASP 107 CB    0.034    3.266
    8006     fold_poly310_uca3_model_0.cif #10/A ARG 123 CG   fold_poly310_uca3_model_0.cif #10/B ASP 107 CG    0.031    3.729
    8007     fold_poly310_uca3_model_0.cif #10/A ARG 123 CZ   fold_poly310_uca3_model_0.cif #10/B GLY 103 O     0.025    3.005
    8008     fold_poly310_uca3_model_0.cif #10/A ARG 77 NH2   fold_poly310_uca3_model_0.cif #10/B TYR 105 CD1   0.014    3.386
    8009     fold_poly310_uca3_model_0.cif #10/A ARG 123 CD   fold_poly310_uca3_model_0.cif #10/B ASP 107 CA    0.014    3.746
    8010     fold_poly310_uca3_model_0.cif #10/A LYS 94 CD    fold_poly310_uca3_model_0.cif #10/C TYR 93 CE1    0.012    3.628
    8011     fold_poly310_uca3_model_0.cif #10/A ARG 123 CG   fold_poly310_uca3_model_0.cif #10/B ASP 107 CB    -0.004    3.764
    8012     fold_poly310_uca3_model_0.cif #10/A LYS 94 CE    fold_poly310_uca3_model_0.cif #10/B ASP 107 CG    -0.012    3.772
    8013     fold_poly310_uca3_model_0.cif #10/A LEU 32 CG    fold_poly310_uca3_model_0.cif #10/B LEU 104 CD1   -0.028    3.788
    8014     fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ    fold_poly310_uca3_model_0.cif #10/B SER 109 N     -0.035    3.315
    8015     fold_poly310_uca3_model_0.cif #10/A ARG 123 O    fold_poly310_uca3_model_0.cif #10/B ASP 107 OD2   -0.042    2.882
    8016     fold_poly310_uca3_model_0.cif #10/A LEU 190 CD1  fold_poly310_uca3_model_0.cif #10/B TYR 106 CG    -0.044    3.534
    8017     fold_poly310_uca3_model_0.cif #10/A PHE 119 CD2  fold_poly310_uca3_model_0.cif #10/B TYR 105 CB    -0.044    3.684
    8018     fold_poly310_uca3_model_0.cif #10/A LYS 94 CE    fold_poly310_uca3_model_0.cif #10/B GLY 110 N     -0.046    3.566
    8019     fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ    fold_poly310_uca3_model_0.cif #10/B ASP 107 OD1   -0.048    2.708
    8020     fold_poly310_uca3_model_0.cif #10/A LEU 190 CG   fold_poly310_uca3_model_0.cif #10/B TYR 111 OH    -0.059    3.399
    8021     fold_poly310_uca3_model_0.cif #10/A ARG 77 CZ    fold_poly310_uca3_model_0.cif #10/B TYR 105 CD1   -0.059    3.429
    8022     fold_poly310_uca3_model_0.cif #10/A LYS 42 NZ    fold_poly310_uca3_model_0.cif #10/B SER 75 CA     -0.066    3.586
    8023     fold_poly310_uca3_model_0.cif #10/A ASP 96 OD2   fold_poly310_uca3_model_0.cif #10/C TYR 93 CZ     -0.069    3.099
    8024     fold_poly310_uca3_model_0.cif #10/A ASP 124 CG   fold_poly310_uca3_model_0.cif #10/B TYR 33 OH     -0.070    3.410
    8025     fold_poly310_uca3_model_0.cif #10/A GLU 40 CD    fold_poly310_uca3_model_0.cif #10/B THR 30 OG1    -0.076    3.416
    8026     fold_poly310_uca3_model_0.cif #10/A PRO 68 CB    fold_poly310_uca3_model_0.cif #10/B TYR 32 OH     -0.077    3.417
    8027     fold_poly310_uca3_model_0.cif #10/A ASP 69 OD2   fold_poly310_uca3_model_0.cif #10/B VAL 2 CG2     -0.078    3.378
    8028     fold_poly310_uca3_model_0.cif #10/A MET 73 SD    fold_poly310_uca3_model_0.cif #10/B TRP 101 CD2   -0.082    3.462
    8029     fold_poly310_uca3_model_0.cif #10/A ARG 123 CG   fold_poly310_uca3_model_0.cif #10/B ASP 107 CA    -0.083    3.843
    8030     fold_poly310_uca3_model_0.cif #10/A ASP 124 OD2  fold_poly310_uca3_model_0.cif #10/B ASN 52 ND2    -0.094    2.754
    8031     fold_poly310_uca3_model_0.cif #10/A ASP 124 OD1  fold_poly310_uca3_model_0.cif #10/B TYR 33 OH     -0.094    2.574
    8032     fold_poly310_uca3_model_0.cif #10/A LEU 99 CD2   fold_poly310_uca3_model_0.cif #10/B ASP 107 OD2   -0.107    3.407
    8033     fold_poly310_uca3_model_0.cif #10/A ASP 69 OD2   fold_poly310_uca3_model_0.cif #10/B ARG 98 NH1    -0.108    2.768
    8034     fold_poly310_uca3_model_0.cif #10/A HIS 188 ND1  fold_poly310_uca3_model_0.cif #10/B TYR 111 CE2   -0.110    3.510
    8035     fold_poly310_uca3_model_0.cif #10/A HIS 188 CE1  fold_poly310_uca3_model_0.cif #10/C GLU 52 OE2    -0.121    3.301
    8036     fold_poly310_uca3_model_0.cif #10/A ARG 123 CD   fold_poly310_uca3_model_0.cif #10/B TYR 106 C     -0.122    3.612
    8037     fold_poly310_uca3_model_0.cif #10/A HIS 1 NE2    fold_poly310_uca3_model_0.cif #10/B ARG 72 NH2    -0.126    3.406
    8038     fold_poly310_uca3_model_0.cif #10/A ARG 77 CD    fold_poly310_uca3_model_0.cif #10/B TYR 106 CB    -0.136    3.896
    8039     fold_poly310_uca3_model_0.cif #10/A GLU 40 OE2   fold_poly310_uca3_model_0.cif #10/B THR 30 CG2    -0.141    3.441
    8040     fold_poly310_uca3_model_0.cif #10/A ASP 64 OD2   fold_poly310_uca3_model_0.cif #10/B TYR 105 CE1   -0.143    3.323
    8041     fold_poly310_uca3_model_0.cif #10/A ARG 77 NH1   fold_poly310_uca3_model_0.cif #10/B TYR 106 CD2   -0.145    3.545
    8042     fold_poly310_uca3_model_0.cif #10/A LYS 94 CB    fold_poly310_uca3_model_0.cif #10/C TYR 93 CZ     -0.146    3.636
    8043     fold_poly310_uca3_model_0.cif #10/A LYS 94 CG    fold_poly310_uca3_model_0.cif #10/C TYR 93 CE2    -0.154    3.794
    8044     fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ    fold_poly310_uca3_model_0.cif #10/B SER 109 CB    -0.164    3.684
    8045     fold_poly310_uca3_model_0.cif #10/A MET 73 CE    fold_poly310_uca3_model_0.cif #10/B TRP 101 CB    -0.167    3.927
    8046     fold_poly310_uca3_model_0.cif #10/A MET 73 SD    fold_poly310_uca3_model_0.cif #10/B TRP 101 CZ3   -0.172    3.702
    8047     fold_poly310_uca3_model_0.cif #10/A ASP 43 CG    fold_poly310_uca3_model_0.cif #10/B THR 28 OG1    -0.172    3.512
    8048     fold_poly310_uca3_model_0.cif #10/A ASP 64 CG    fold_poly310_uca3_model_0.cif #10/B TYR 105 OH    -0.181    3.521
    8049     fold_poly310_uca3_model_0.cif #10/A ASP 96 OD2   fold_poly310_uca3_model_0.cif #10/C SER 96 CA     -0.184    3.484
    8050     fold_poly310_uca3_model_0.cif #10/A MET 73 CG    fold_poly310_uca3_model_0.cif #10/B TRP 101 CE3   -0.188    3.828
    8051     fold_poly310_uca3_model_0.cif #10/A ASP 69 CB    fold_poly310_uca3_model_0.cif #10/B TYR 32 OH     -0.189    3.529
    8052     fold_poly310_uca3_model_0.cif #10/A ASP 69 CG    fold_poly310_uca3_model_0.cif #10/B VAL 2 CG2     -0.190    3.950
    8053     fold_poly310_uca3_model_0.cif #10/A LYS 70 CE    fold_poly310_uca3_model_0.cif #10/B TYR 116 OH    -0.194    3.534
    8054     fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ    fold_poly310_uca3_model_0.cif #10/B SER 109 CA    -0.198    3.718
    8055     fold_poly310_uca3_model_0.cif #10/A HIS 188 CE1  fold_poly310_uca3_model_0.cif #10/B ASN 113 ND2   -0.198    3.598
    8056     fold_poly310_uca3_model_0.cif #10/A ASP 96 OD2   fold_poly310_uca3_model_0.cif #10/C SER 96 N      -0.207    2.867
    8057     fold_poly310_uca3_model_0.cif #10/A ASP 69 CG    fold_poly310_uca3_model_0.cif #10/B ARG 98 NH1    -0.208    3.728
    8058     fold_poly310_uca3_model_0.cif #10/A VAL 75 CG2   fold_poly310_uca3_model_0.cif #10/B TYR 106 OH    -0.210    3.550
    8059     fold_poly310_uca3_model_0.cif #10/A ARG 123 NH1  fold_poly310_uca3_model_0.cif #10/B ILE 102 CG2   -0.212    3.732
    8060     fold_poly310_uca3_model_0.cif #10/A ILE 93 CG2   fold_poly310_uca3_model_0.cif #10/B TYR 111 OH    -0.216    3.556
    8061     fold_poly310_uca3_model_0.cif #10/A ARG 123 O    fold_poly310_uca3_model_0.cif #10/B ASP 107 CG    -0.221    3.521
    8062     fold_poly310_uca3_model_0.cif #10/A LYS 94 CB    fold_poly310_uca3_model_0.cif #10/C TYR 93 OH     -0.227    3.567
    8063     fold_poly310_uca3_model_0.cif #10/A TRP 187 C    fold_poly310_uca3_model_0.cif #10/C LYS 55 NZ     -0.229    3.479
    8064     fold_poly310_uca3_model_0.cif #10/A TYR 102 CE2  fold_poly310_uca3_model_0.cif #10/B TYR 105 C     -0.234    3.604
    8065     fold_poly310_uca3_model_0.cif #10/A LEU 190 CD1  fold_poly310_uca3_model_0.cif #10/B TYR 106 CE1   -0.237    3.877
    8066     fold_poly310_uca3_model_0.cif #10/A LEU 99 CD1   fold_poly310_uca3_model_0.cif #10/B ASP 107 OD2   -0.238    3.538
    8067     fold_poly310_uca3_model_0.cif #10/A SER 95 N     fold_poly310_uca3_model_0.cif #10/C TYR 32 CE1    -0.239    3.639
    8068     fold_poly310_uca3_model_0.cif #10/A GLU 189 CG   fold_poly310_uca3_model_0.cif #10/C LYS 55 NZ     -0.242    3.762
    8069     fold_poly310_uca3_model_0.cif #10/A ASP 96 OD1   fold_poly310_uca3_model_0.cif #10/C GLY 95 CA     -0.242    3.542
    8070     fold_poly310_uca3_model_0.cif #10/A LEU 130 CD2  fold_poly310_uca3_model_0.cif #10/B LEU 104 O     -0.244    3.544
    8071     fold_poly310_uca3_model_0.cif #10/A VAL 75 CG2   fold_poly310_uca3_model_0.cif #10/B TRP 101 CZ3   -0.245    3.885
    8072     fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ    fold_poly310_uca3_model_0.cif #10/B GLY 110 CA    -0.247    3.767
    8073     fold_poly310_uca3_model_0.cif #10/A PHE 119 CE2  fold_poly310_uca3_model_0.cif #10/B TYR 105 CD1   -0.250    3.770
    8074     fold_poly310_uca3_model_0.cif #10/A LYS 42 NZ    fold_poly310_uca3_model_0.cif #10/B THR 74 C      -0.254    3.504
    8075     fold_poly310_uca3_model_0.cif #10/A VAL 75 CG2   fold_poly310_uca3_model_0.cif #10/B TYR 106 CZ    -0.257    3.747
    8076     fold_poly310_uca3_model_0.cif #10/A HIS 1 CD2    fold_poly310_uca3_model_0.cif #10/B ARG 72 NH2    -0.261    3.661
    8077     fold_poly310_uca3_model_0.cif #10/A LYS 94 CG    fold_poly310_uca3_model_0.cif #10/C TYR 93 CZ     -0.264    3.754
    8078     fold_poly310_uca3_model_0.cif #10/A VAL 75 CG2   fold_poly310_uca3_model_0.cif #10/B TYR 106 CE2   -0.266    3.906
    8079     fold_poly310_uca3_model_0.cif #10/A HIS 188 ND1  fold_poly310_uca3_model_0.cif #10/C GLU 52 CD     -0.267    3.787
    8080     fold_poly310_uca3_model_0.cif #10/A ASP 43 CG    fold_poly310_uca3_model_0.cif #10/B THR 28 CG2    -0.271    4.031
    8081     fold_poly310_uca3_model_0.cif #10/A ASP 96 CG    fold_poly310_uca3_model_0.cif #10/C GLY 95 CA     -0.279    4.039
    8082     fold_poly310_uca3_model_0.cif #10/A ARG 77 NH1   fold_poly310_uca3_model_0.cif #10/B TYR 105 C     -0.281    3.531
    8083     fold_poly310_uca3_model_0.cif #10/A ASP 124 CG   fold_poly310_uca3_model_0.cif #10/B TRP 50 CH2    -0.282    3.922
    8084     fold_poly310_uca3_model_0.cif #10/A TRP 187 O    fold_poly310_uca3_model_0.cif #10/C LYS 55 CD     -0.284    3.584
    8085     fold_poly310_uca3_model_0.cif #10/A PRO 68 CB    fold_poly310_uca3_model_0.cif #10/B TRP 101 NE1   -0.286    3.806
    8086     fold_poly310_uca3_model_0.cif #10/A LYS 94 CD    fold_poly310_uca3_model_0.cif #10/C TYR 93 CE2    -0.293    3.933
    8087     fold_poly310_uca3_model_0.cif #10/A LYS 94 CE    fold_poly310_uca3_model_0.cif #10/B ASP 107 O     -0.297    3.597
    8088     fold_poly310_uca3_model_0.cif #10/A ILE 93 CG2   fold_poly310_uca3_model_0.cif #10/B TYR 111 CE1   -0.297    3.937
    8089     fold_poly310_uca3_model_0.cif #10/A ASP 96 CG    fold_poly310_uca3_model_0.cif #10/C SER 96 CA     -0.298    4.058
    8090     fold_poly310_uca3_model_0.cif #10/A LYS 94 CA    fold_poly310_uca3_model_0.cif #10/C TYR 32 CE1    -0.310    3.950
    8091     fold_poly310_uca3_model_0.cif #10/A PHE 119 CE2  fold_poly310_uca3_model_0.cif #10/B TYR 105 CG    -0.310    3.680
    8092     fold_poly310_uca3_model_0.cif #10/A LYS 94 CE    fold_poly310_uca3_model_0.cif #10/B GLY 110 CA    -0.322    4.082
    8093     fold_poly310_uca3_model_0.cif #10/A TRP 187 CB   fold_poly310_uca3_model_0.cif #10/C LYS 55 NZ     -0.333    3.853
    8094     fold_poly310_uca3_model_0.cif #10/A LYS 94 CE    fold_poly310_uca3_model_0.cif #10/B ASP 107 OD1   -0.334    3.634
    8095     fold_poly310_uca3_model_0.cif #10/A LYS 42 NZ    fold_poly310_uca3_model_0.cif #10/B SER 75 C      -0.350    3.600
    8096     fold_poly310_uca3_model_0.cif #10/A ASP 69 OD2   fold_poly310_uca3_model_0.cif #10/B ARG 98 CZ     -0.354    3.384
    8097     fold_poly310_uca3_model_0.cif #10/A GLU 186 CG   fold_poly310_uca3_model_0.cif #10/C TYR 51 CZ     -0.355    3.845
    8098     fold_poly310_uca3_model_0.cif #10/A LEU 190 CD2  fold_poly310_uca3_model_0.cif #10/B TYR 111 CE2   -0.365    4.005
    8099     fold_poly310_uca3_model_0.cif #10/A ASP 124 CG   fold_poly310_uca3_model_0.cif #10/B ASN 52 ND2    -0.366    3.886
    8100     fold_poly310_uca3_model_0.cif #10/A ASP 124 OD1  fold_poly310_uca3_model_0.cif #10/B TYR 33 CE1    -0.366    3.546
    8101     fold_poly310_uca3_model_0.cif #10/A HIS 188 CA   fold_poly310_uca3_model_0.cif #10/C GLU 52 OE2    -0.367    3.667
    8102     fold_poly310_uca3_model_0.cif #10/A GLU 40 OE1   fold_poly310_uca3_model_0.cif #10/B THR 30 OG1    -0.367    2.847
    8103     fold_poly310_uca3_model_0.cif #10/A LYS 42 CE    fold_poly310_uca3_model_0.cif #10/B THR 74 O      -0.369    3.669
    8104     fold_poly310_uca3_model_0.cif #10/A HIS 188 CA   fold_poly310_uca3_model_0.cif #10/C LYS 55 NZ     -0.371    3.891
    8105     fold_poly310_uca3_model_0.cif #10/A PHE 119 CZ   fold_poly310_uca3_model_0.cif #10/B TYR 105 CD2   -0.375    3.895
    8106     fold_poly310_uca3_model_0.cif #10/A ASP 69 OD1   fold_poly310_uca3_model_0.cif #10/B VAL 2 CG2     -0.375    3.675
    8107     fold_poly310_uca3_model_0.cif #10/A ASP 43 CG    fold_poly310_uca3_model_0.cif #10/B THR 28 CB     -0.379    4.139
    8108     fold_poly310_uca3_model_0.cif #10/A TYR 102 CE2  fold_poly310_uca3_model_0.cif #10/B TYR 105 O     -0.381    3.561
    8109     fold_poly310_uca3_model_0.cif #10/A ARG 77 NH1   fold_poly310_uca3_model_0.cif #10/B TYR 105 O     -0.381    3.041
    8110     fold_poly310_uca3_model_0.cif #10/A ASP 124 CB   fold_poly310_uca3_model_0.cif #10/B TRP 50 CH2    -0.382    4.022
    8111     fold_poly310_uca3_model_0.cif #10/A PHE 119 CZ   fold_poly310_uca3_model_0.cif #10/B TYR 105 CE2   -0.384    3.904
    8112     fold_poly310_uca3_model_0.cif #10/A ASP 124 OD2  fold_poly310_uca3_model_0.cif #10/B ASN 52 CB     -0.386    3.686
    8113     fold_poly310_uca3_model_0.cif #10/A VAL 75 CG1   fold_poly310_uca3_model_0.cif #10/B TYR 106 CE2   -0.393    4.033
    8114     fold_poly310_uca3_model_0.cif #10/A ARG 123 NH1  fold_poly310_uca3_model_0.cif #10/B GLY 103 N     -0.393    3.673
    8115     fold_poly310_uca3_model_0.cif #10/A PHE 119 CD2  fold_poly310_uca3_model_0.cif #10/B TYR 105 CG    -0.399    3.769
    8116    
    8117 
    8118  
    8119 149 contacts 
    8120 
    8121 > hide #10.2 models
    8122 
    8123 > hide #!10 models
    8124 
    8125 > select add #10
    8126 
    8127 3324 atoms, 3406 bonds, 176 pseudobonds, 428 residues, 3 models selected 
    8128 
    8129 > select subtract #10
    8130 
    8131 Nothing selected 
    8132 
    8133 > show #11 models
    8134 
    8135 > select #11/A:35
    8136 
    8137 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8138 
    8139 > select up
    8140 
    8141 74 atoms, 76 bonds, 10 residues, 1 model selected 
    8142 
    8143 > select up
    8144 
    8145 1590 atoms, 1630 bonds, 197 residues, 1 model selected 
    8146 
    8147 > color bfactor sel
    8148 
    8149 1590 atoms, 197 residues, atom bfactor range 14.1 to 97.5 
    8150 
    8151 > hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8
    8152 > intraMol false intraRes false select true reveal true log true
    8153    
    8154    
    8155     Finding intramodel H-bonds
    8156     Constraints relaxed by 0.8 angstroms and 20 degrees
    8157     Models used:
    8158         11 fold_poly28_uca3_model_0.cif
    8159    
    8160     8 H-bonds
    8161     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    8162     fold_poly28_uca3_model_0.cif #11/A SER 7 OG    fold_poly28_uca3_model_0.cif #11/C ASN 33 OD1  no hydrogen  3.348  N/A
    8163     fold_poly28_uca3_model_0.cif #11/B THR 28 OG1  fold_poly28_uca3_model_0.cif #11/A SER 101 O   no hydrogen  3.603  N/A
    8164     fold_poly28_uca3_model_0.cif #11/B ASN 54 ND2  fold_poly28_uca3_model_0.cif #11/A TYR 80 O    no hydrogen  3.294  N/A
    8165     fold_poly28_uca3_model_0.cif #11/B LEU 104 N   fold_poly28_uca3_model_0.cif #11/A GLU 81 OE2  no hydrogen  3.487  N/A
    8166     fold_poly28_uca3_model_0.cif #11/C TYR 32 OH   fold_poly28_uca3_model_0.cif #11/A GLU 46 OE1  no hydrogen  2.872  N/A
    8167     fold_poly28_uca3_model_0.cif #11/C TYR 51 OH   fold_poly28_uca3_model_0.cif #11/A ASN 131 O   no hydrogen  2.250  N/A
    8168     fold_poly28_uca3_model_0.cif #11/C SER 54 OG   fold_poly28_uca3_model_0.cif #11/A ASP 8 OD1   no hydrogen  2.636  N/A
    8169     fold_poly28_uca3_model_0.cif #11/C SER 96 N    fold_poly28_uca3_model_0.cif #11/A GLU 46 OE2  no hydrogen  3.304  N/A
    8170    
    8171 
    8172  
    8173 8 hydrogen bonds found 
    8174 
    8175 > select #11/A:138
    8176 
    8177 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8178 
    8179 > select up
    8180 
    8181 76 atoms, 77 bonds, 9 residues, 1 model selected 
    8182 
    8183 > select up
    8184 
    8185 1590 atoms, 1630 bonds, 197 residues, 1 model selected 
    8186 
    8187 > contacts sel restrict cross interModel false intraMol false
    8188 > ignoreHiddenModels true select true color #ff2600 name contacts_AF3_Y513
    8189 > reveal true log true
    8190    
    8191    
    8192     Allowed overlap: -0.4
    8193     H-bond overlap reduction: 0.4
    8194     Ignore contacts between atoms separated by 4 bonds or less
    8195     Detect intra-residue contacts: False
    8196     Detect intra-molecule contacts: False
    8197    
    8198     97 contacts
    8199                         atom1                                           atom2                       overlap  distance
    8200     fold_poly28_uca3_model_0.cif #11/A LEU 136 CD2  fold_poly28_uca3_model_0.cif #11/B TYR 105 CB    0.972    2.788
    8201     fold_poly28_uca3_model_0.cif #11/A ASN 131 CB   fold_poly28_uca3_model_0.cif #11/C TYR 51 OH     0.818    2.522
    8202     fold_poly28_uca3_model_0.cif #11/A ARG 83 NH1   fold_poly28_uca3_model_0.cif #11/B TYR 105 CE2   0.767    2.633
    8203     fold_poly28_uca3_model_0.cif #11/A SER 70 CB    fold_poly28_uca3_model_0.cif #11/B LEU 104 CD1   0.592    3.168
    8204     fold_poly28_uca3_model_0.cif #11/A LEU 196 CD1  fold_poly28_uca3_model_0.cif #11/B ARG 72 NH2    0.548    2.972
    8205     fold_poly28_uca3_model_0.cif #11/A LEU 196 CD2  fold_poly28_uca3_model_0.cif #11/B ARG 72 NH1    0.481    3.039
    8206     fold_poly28_uca3_model_0.cif #11/A MET 79 CE    fold_poly28_uca3_model_0.cif #11/B LEU 104 CD2   0.440    3.320
    8207     fold_poly28_uca3_model_0.cif #11/A LEU 136 CD2  fold_poly28_uca3_model_0.cif #11/B TYR 105 CG    0.367    3.123
    8208     fold_poly28_uca3_model_0.cif #11/A GLU 81 CB    fold_poly28_uca3_model_0.cif #11/B LEU 104 CD1   0.341    3.419
    8209     fold_poly28_uca3_model_0.cif #11/A GLU 134 OE1  fold_poly28_uca3_model_0.cif #11/B TYR 106 CE1   0.329    2.851
    8210     fold_poly28_uca3_model_0.cif #11/A ARG 132 NH1  fold_poly28_uca3_model_0.cif #11/B TYR 111 CE2   0.304    3.096
    8211     fold_poly28_uca3_model_0.cif #11/A LEU 9 CB     fold_poly28_uca3_model_0.cif #11/C LYS 55 NZ     0.273    3.247
    8212     fold_poly28_uca3_model_0.cif #11/A ASN 131 O    fold_poly28_uca3_model_0.cif #11/C TYR 51 OH     0.230    2.250
    8213     fold_poly28_uca3_model_0.cif #11/A LEU 44 CD1   fold_poly28_uca3_model_0.cif #11/C TYR 32 CD1    0.219    3.421
    8214     fold_poly28_uca3_model_0.cif #11/A MET 79 SD    fold_poly28_uca3_model_0.cif #11/B ILE 102 CG2   0.197    3.453
    8215     fold_poly28_uca3_model_0.cif #11/A ARG 83 NH2   fold_poly28_uca3_model_0.cif #11/B TYR 105 CE2   0.197    3.203
    8216     fold_poly28_uca3_model_0.cif #11/A GLU 46 OE1   fold_poly28_uca3_model_0.cif #11/C TYR 93 CE1    0.186    2.994
    8217     fold_poly28_uca3_model_0.cif #11/A ASN 131 CA   fold_poly28_uca3_model_0.cif #11/C TYR 51 OH     0.181    3.159
    8218     fold_poly28_uca3_model_0.cif #11/A ARG 132 CZ   fold_poly28_uca3_model_0.cif #11/C GLU 52 OE1    0.177    2.853
    8219     fold_poly28_uca3_model_0.cif #11/A LEU 136 CD2  fold_poly28_uca3_model_0.cif #11/B TYR 105 CD1   0.170    3.470
    8220     fold_poly28_uca3_model_0.cif #11/A ARG 83 NH2   fold_poly28_uca3_model_0.cif #11/B TYR 105 CZ    0.124    3.126
    8221     fold_poly28_uca3_model_0.cif #11/A GLU 134 OE1  fold_poly28_uca3_model_0.cif #11/B TYR 106 CD1   0.120    3.060
    8222     fold_poly28_uca3_model_0.cif #11/A ASN 131 C    fold_poly28_uca3_model_0.cif #11/C TYR 51 OH     0.117    2.953
    8223     fold_poly28_uca3_model_0.cif #11/A ASN 131 CB   fold_poly28_uca3_model_0.cif #11/C TYR 51 CZ     0.113    3.377
    8224     fold_poly28_uca3_model_0.cif #11/A ARG 132 CD   fold_poly28_uca3_model_0.cif #11/C GLU 52 OE1    0.108    3.192
    8225     fold_poly28_uca3_model_0.cif #11/A LEU 44 CD1   fold_poly28_uca3_model_0.cif #11/C LEU 34 CD1    0.106    3.654
    8226     fold_poly28_uca3_model_0.cif #11/A GLU 46 OE1   fold_poly28_uca3_model_0.cif #11/C TYR 32 CE1    0.102    3.078
    8227     fold_poly28_uca3_model_0.cif #11/A ASP 75 CG    fold_poly28_uca3_model_0.cif #11/B TRP 50 CH2    0.098    3.542
    8228     fold_poly28_uca3_model_0.cif #11/A ARG 83 CZ    fold_poly28_uca3_model_0.cif #11/B TYR 105 CE2   0.062    3.308
    8229     fold_poly28_uca3_model_0.cif #11/A MET 79 CE    fold_poly28_uca3_model_0.cif #11/B LEU 104 CG    0.045    3.715
    8230     fold_poly28_uca3_model_0.cif #11/A GLU 46 CD    fold_poly28_uca3_model_0.cif #11/C TYR 93 OH     0.032    3.308
    8231     fold_poly28_uca3_model_0.cif #11/A GLU 134 CD   fold_poly28_uca3_model_0.cif #11/B TYR 106 CE1   -0.011    3.651
    8232     fold_poly28_uca3_model_0.cif #11/A PHE 54 CZ    fold_poly28_uca3_model_0.cif #11/B LEU 104 O     -0.023    3.203
    8233     fold_poly28_uca3_model_0.cif #11/A SER 70 C     fold_poly28_uca3_model_0.cif #11/B LEU 104 CD1   -0.039    3.529
    8234     fold_poly28_uca3_model_0.cif #11/A SER 70 O     fold_poly28_uca3_model_0.cif #11/B LEU 104 CD1   -0.043    3.343
    8235     fold_poly28_uca3_model_0.cif #11/A ASP 75 OD2   fold_poly28_uca3_model_0.cif #11/B TRP 50 CH2    -0.062    3.242
    8236     fold_poly28_uca3_model_0.cif #11/A ARG 83 NH1   fold_poly28_uca3_model_0.cif #11/B TYR 105 CD2   -0.064    3.464
    8237     fold_poly28_uca3_model_0.cif #11/A GLU 46 CD    fold_poly28_uca3_model_0.cif #11/C TYR 32 OH     -0.077    3.417
    8238     fold_poly28_uca3_model_0.cif #11/A LEU 9 CD2    fold_poly28_uca3_model_0.cif #11/C LYS 55 NZ     -0.080    3.600
    8239     fold_poly28_uca3_model_0.cif #11/A LEU 9 CD1    fold_poly28_uca3_model_0.cif #11/C GLU 52 OE2    -0.089    3.389
    8240     fold_poly28_uca3_model_0.cif #11/A MET 79 CG    fold_poly28_uca3_model_0.cif #11/B ASN 54 ND2    -0.098    3.618
    8241     fold_poly28_uca3_model_0.cif #11/A TYR 108 OH   fold_poly28_uca3_model_0.cif #11/B TYR 105 CE2   -0.101    3.321
    8242     fold_poly28_uca3_model_0.cif #11/A SER 7 CB     fold_poly28_uca3_model_0.cif #11/C ASN 33 OD1    -0.104    3.404
    8243     fold_poly28_uca3_model_0.cif #11/A ARG 83 NH2   fold_poly28_uca3_model_0.cif #11/B TYR 105 OH    -0.121    2.821
    8244     fold_poly28_uca3_model_0.cif #11/A LEU 9 CB     fold_poly28_uca3_model_0.cif #11/C LYS 55 CE     -0.127    3.887
    8245     fold_poly28_uca3_model_0.cif #11/A PHE 125 CE1  fold_poly28_uca3_model_0.cif #11/B TYR 105 OH    -0.143    3.363
    8246     fold_poly28_uca3_model_0.cif #11/A PHE 54 CE1   fold_poly28_uca3_model_0.cif #11/B LEU 104 O     -0.144    3.324
    8247     fold_poly28_uca3_model_0.cif #11/A ALA 42 CB    fold_poly28_uca3_model_0.cif #11/B TYR 111 OH    -0.148    3.488
    8248     fold_poly28_uca3_model_0.cif #11/A ASP 8 OD1    fold_poly28_uca3_model_0.cif #11/C SER 54 OG     -0.156    2.636
    8249     fold_poly28_uca3_model_0.cif #11/A SER 70 CA    fold_poly28_uca3_model_0.cif #11/B LEU 104 CD1   -0.170    3.930
    8250     fold_poly28_uca3_model_0.cif #11/A ARG 132 NE   fold_poly28_uca3_model_0.cif #11/C GLU 52 CD     -0.177    3.697
    8251     fold_poly28_uca3_model_0.cif #11/A GLU 46 OE1   fold_poly28_uca3_model_0.cif #11/C TYR 32 CZ     -0.182    3.212
    8252     fold_poly28_uca3_model_0.cif #11/A MET 79 SD    fold_poly28_uca3_model_0.cif #11/B ASN 52 ND2    -0.184    3.194
    8253     fold_poly28_uca3_model_0.cif #11/A ARG 132 CZ   fold_poly28_uca3_model_0.cif #11/C GLU 52 CD     -0.186    3.676
    8254     fold_poly28_uca3_model_0.cif #11/A ALA 42 O     fold_poly28_uca3_model_0.cif #11/B TYR 111 OH    -0.188    2.668
    8255     fold_poly28_uca3_model_0.cif #11/A LEU 9 CD1    fold_poly28_uca3_model_0.cif #11/C GLU 52 CD     -0.198    3.958
    8256     fold_poly28_uca3_model_0.cif #11/A LEU 136 CD2  fold_poly28_uca3_model_0.cif #11/B TYR 105 CA    -0.200    3.960
    8257     fold_poly28_uca3_model_0.cif #11/A LEU 196 CD2  fold_poly28_uca3_model_0.cif #11/B ARG 72 NH2    -0.206    3.726
    8258     fold_poly28_uca3_model_0.cif #11/A GLU 46 OE2   fold_poly28_uca3_model_0.cif #11/C GLY 95 CA     -0.224    3.524
    8259     fold_poly28_uca3_model_0.cif #11/A ARG 83 NH1   fold_poly28_uca3_model_0.cif #11/B TYR 105 CZ    -0.226    3.476
    8260     fold_poly28_uca3_model_0.cif #11/A PHE 125 CZ   fold_poly28_uca3_model_0.cif #11/B TYR 105 OH    -0.235    3.455
    8261     fold_poly28_uca3_model_0.cif #11/A SER 7 OG     fold_poly28_uca3_model_0.cif #11/C VAL 53 CG1    -0.238    3.578
    8262     fold_poly28_uca3_model_0.cif #11/A LEU 38 CD2   fold_poly28_uca3_model_0.cif #11/B TYR 105 O     -0.243    3.543
    8263     fold_poly28_uca3_model_0.cif #11/A PRO 103 O    fold_poly28_uca3_model_0.cif #11/B TYR 32 OH     -0.244    2.724
    8264     fold_poly28_uca3_model_0.cif #11/A SER 7 CB     fold_poly28_uca3_model_0.cif #11/C ASN 33 ND2    -0.246    3.766
    8265     fold_poly28_uca3_model_0.cif #11/A GLU 46 CD    fold_poly28_uca3_model_0.cif #11/C TYR 93 CE1    -0.250    3.890
    8266     fold_poly28_uca3_model_0.cif #11/A ASP 75 CB    fold_poly28_uca3_model_0.cif #11/B GLY 57 CA     -0.259    4.019
    8267     fold_poly28_uca3_model_0.cif #11/A SER 7 CB     fold_poly28_uca3_model_0.cif #11/C ASN 33 CG     -0.259    3.749
    8268     fold_poly28_uca3_model_0.cif #11/A LEU 196 CD2  fold_poly28_uca3_model_0.cif #11/B ARG 72 CZ     -0.259    3.749
    8269     fold_poly28_uca3_model_0.cif #11/A LEU 136 CD2  fold_poly28_uca3_model_0.cif #11/B TYR 105 CD2   -0.263    3.903
    8270     fold_poly28_uca3_model_0.cif #11/A ARG 132 CD   fold_poly28_uca3_model_0.cif #11/C GLU 52 CD     -0.269    4.029
    8271     fold_poly28_uca3_model_0.cif #11/A GLU 81 N     fold_poly28_uca3_model_0.cif #11/B LEU 104 CD1   -0.276    3.796
    8272     fold_poly28_uca3_model_0.cif #11/A ALA 77 CB    fold_poly28_uca3_model_0.cif #11/B SER 55 O      -0.282    3.582
    8273     fold_poly28_uca3_model_0.cif #11/A ASP 75 OD1   fold_poly28_uca3_model_0.cif #11/B TRP 50 CH2    -0.283    3.463
    8274     fold_poly28_uca3_model_0.cif #11/A THR 138 CG2  fold_poly28_uca3_model_0.cif #11/B TYR 105 CD1   -0.286    3.926
    8275     fold_poly28_uca3_model_0.cif #11/A GLU 46 CD    fold_poly28_uca3_model_0.cif #11/C GLY 95 CA     -0.289    4.049
    8276     fold_poly28_uca3_model_0.cif #11/A PHE 54 CZ    fold_poly28_uca3_model_0.cif #11/B TYR 105 CA    -0.291    3.931
    8277     fold_poly28_uca3_model_0.cif #11/A ARG 132 NH1  fold_poly28_uca3_model_0.cif #11/C GLU 52 OE1    -0.302    2.962
    8278     fold_poly28_uca3_model_0.cif #11/A LEU 196 CD1  fold_poly28_uca3_model_0.cif #11/B ARG 72 CZ     -0.303    3.793
    8279     fold_poly28_uca3_model_0.cif #11/A SER 7 OG     fold_poly28_uca3_model_0.cif #11/C VAL 53 CG2    -0.304    3.644
    8280     fold_poly28_uca3_model_0.cif #11/A LEU 9 CG     fold_poly28_uca3_model_0.cif #11/C LYS 55 NZ     -0.320    3.840
    8281     fold_poly28_uca3_model_0.cif #11/A ARG 132 NE   fold_poly28_uca3_model_0.cif #11/C GLU 52 OE1    -0.324    2.984
    8282     fold_poly28_uca3_model_0.cif #11/A ASN 131 CB   fold_poly28_uca3_model_0.cif #11/C TYR 51 CE1    -0.333    3.973
    8283     fold_poly28_uca3_model_0.cif #11/A PRO 103 CB   fold_poly28_uca3_model_0.cif #11/B TYR 32 OH     -0.338    3.678
    8284     fold_poly28_uca3_model_0.cif #11/A ARG 132 CG   fold_poly28_uca3_model_0.cif #11/C LYS 55 NZ     -0.338    3.858
    8285     fold_poly28_uca3_model_0.cif #11/A ARG 132 NH1  fold_poly28_uca3_model_0.cif #11/B TYR 111 CD2   -0.350    3.750
    8286     fold_poly28_uca3_model_0.cif #11/A ASP 8 OD1    fold_poly28_uca3_model_0.cif #11/C SER 54 CB     -0.363    3.663
    8287     fold_poly28_uca3_model_0.cif #11/A MET 79 CE    fold_poly28_uca3_model_0.cif #11/B ILE 102 CG2   -0.367    4.127
    8288     fold_poly28_uca3_model_0.cif #11/A ARG 130 CZ   fold_poly28_uca3_model_0.cif #11/C SER 58 OG     -0.368    3.438
    8289     fold_poly28_uca3_model_0.cif #11/A ARG 83 CZ    fold_poly28_uca3_model_0.cif #11/B TYR 105 OH    -0.369    3.439
    8290     fold_poly28_uca3_model_0.cif #11/A ASN 131 ND2  fold_poly28_uca3_model_0.cif #11/C PRO 57 CA     -0.373    3.893
    8291     fold_poly28_uca3_model_0.cif #11/A ASP 49 CB    fold_poly28_uca3_model_0.cif #11/C SER 96 CA     -0.379    4.139
    8292     fold_poly28_uca3_model_0.cif #11/A GLU 134 CD   fold_poly28_uca3_model_0.cif #11/B TYR 106 CZ    -0.382    3.872
    8293     fold_poly28_uca3_model_0.cif #11/A GLU 46 CG    fold_poly28_uca3_model_0.cif #11/C TYR 93 OH     -0.382    3.722
    8294     fold_poly28_uca3_model_0.cif #11/A LEU 196 CD1  fold_poly28_uca3_model_0.cif #11/B ARG 72 NH1    -0.386    3.906
    8295     fold_poly28_uca3_model_0.cif #11/A PHE 125 CE1  fold_poly28_uca3_model_0.cif #11/B TYR 105 CZ    -0.387    3.757
    8296     fold_poly28_uca3_model_0.cif #11/A GLU 46 OE1   fold_poly28_uca3_model_0.cif #11/C TYR 32 OH     -0.392    2.872
    8297    
    8298 
    8299  
    8300 97 contacts 
    8301 
    8302 > select clear
    8303 
    8304 > select #11/A:194
    8305 
    8306 10 atoms, 10 bonds, 1 residue, 1 model selected 
    8307 
    8308 > select up
    8309 
    8310 133 atoms, 136 bonds, 15 residues, 1 model selected 
    8311 
    8312 > hide sel atoms
    8313 
    8314 > hide sel cartoons
    8315 
    8316 > select clear
    8317 
    8318 [Repeated 2 time(s)]
    8319 
    8320 > select #11/A:197
    8321 
    8322 10 atoms, 9 bonds, 1 residue, 1 model selected 
    8323 
    8324 > hide sel cartoons
    8325 
    8326 > select #11/A:4
    8327 
    8328 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8329 
    8330 > select up
    8331 
    8332 104 atoms, 107 bonds, 14 residues, 1 model selected 
    8333 
    8334 > show #!1 models
    8335 
    8336 > hide #10.1 models
    8337 
    8338 > hide #!11 models
    8339 
    8340 > show #1.2 models
    8341 
    8342 > show #1.3 models
    8343 
    8344 > select #1/E:126
    8345 
    8346 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8347 
    8348 > select up
    8349 
    8350 63 atoms, 63 bonds, 8 residues, 1 model selected 
    8351 
    8352 > select up
    8353 
    8354 604 atoms, 618 bonds, 74 residues, 1 model selected 
    8355 
    8356 > select up
    8357 
    8358 616 atoms, 629 bonds, 76 residues, 1 model selected 
    8359 
    8360 > select up
    8361 
    8362 1313 atoms, 1346 bonds, 164 residues, 1 model selected 
    8363 
    8364 > hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8
    8365 > intraMol false intraRes false select true reveal true log true
    8366    
    8367    
    8368     Finding intramodel H-bonds
    8369     Constraints relaxed by 0.8 angstroms and 20 degrees
    8370     Models used:
    8371         1 231023_poly310-DH270UCA3_refine_001.pdb
    8372    
    8373     6 H-bonds
    8374     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    8375     231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 N    231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B O  no hydrogen  2.874  N/A
    8376     231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ   231023_poly310-DH270UCA3_refine_001.pdb #1/H THR 65 O    no hydrogen  2.993  N/A
    8377     231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ   231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 66 OD1  no hydrogen  3.440  N/A
    8378     231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 OH   231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1  no hydrogen  2.679  N/A
    8379     231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 57 ND2  231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1  no hydrogen  3.050  N/A
    8380     231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 59 ND2  231023_poly310-DH270UCA3_refine_001.pdb #1/E TYR 78 O    no hydrogen  3.339  N/A
    8381    
    8382 
    8383  
    8384 6 hydrogen bonds found 
    8385 
    8386 > hide #1.3 models
    8387 
    8388 > select #1/E:79
    8389 
    8390 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8391 
    8392 > select up
    8393 
    8394 78 atoms, 80 bonds, 9 residues, 1 model selected 
    8395 
    8396 > select up
    8397 
    8398 709 atoms, 728 bonds, 90 residues, 1 model selected 
    8399 
    8400 > select up
    8401 
    8402 727 atoms, 746 bonds, 92 residues, 1 model selected 
    8403 
    8404 > select up
    8405 
    8406 1313 atoms, 1346 bonds, 164 residues, 1 model selected 
    8407 
    8408 > contacts sel restrict cross interModel false intraMol false
    8409 > ignoreHiddenModels true select true color #ff2600 name contacts_AF3_Y513
    8410 > reveal true log true
    8411    
    8412    
    8413     Allowed overlap: -0.4
    8414     H-bond overlap reduction: 0.4
    8415     Ignore contacts between atoms separated by 4 bonds or less
    8416     Detect intra-residue contacts: False
    8417     Detect intra-molecule contacts: False
    8418    
    8419     64 contacts
    8420                              atom1                                                     atom2                            overlap  distance
    8421     231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 68 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD1   0.171    3.589
    8422     231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CG  231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CD1    0.157    3.483
    8423     231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H SER 111 O      0.142    3.158
    8424     231023_poly310-DH270UCA3_refine_001.pdb #1/E ALA 49 CA   231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B O     0.137    3.163
    8425     231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 CE   231023_poly310-DH270UCA3_refine_001.pdb #1/H ILE 110 CG2    0.135    3.625
    8426     231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CA  231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CZ2    0.103    3.537
    8427     231023_poly310-DH270UCA3_refine_001.pdb #1/E LEU 36 CD2  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CE2   0.101    3.539
    8428     231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 O    231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CB    0.095    3.205
    8429     231023_poly310-DH270UCA3_refine_001.pdb #1/E LEU 36 CD2  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CD2   0.080    3.560
    8430     231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 CE   231023_poly310-DH270UCA3_refine_001.pdb #1/H THR 65 O       0.077    3.223
    8431     231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 CG   231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 59 ND2     0.069    3.451
    8432     231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 O    231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CA    0.058    3.242
    8433     231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 CG   231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 55 CH2     0.052    3.588
    8434     231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 CE1     0.052    3.128
    8435     231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CG  231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 NE1    0.046    3.474
    8436     231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 128 CB  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 37 OH      0.028    3.312
    8437     231023_poly310-DH270UCA3_refine_001.pdb #1/E GLY 70 CA   231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2   0.025    3.735
    8438     231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 55 CH2     0.022    3.618
    8439     231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 SD   231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 59 CB      -0.019    3.669
    8440     231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 128 CG  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 37 OH      -0.052    3.392
    8441     231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 O    231023_poly310-DH270UCA3_refine_001.pdb #1/H ASP 112D CG    -0.060    3.360
    8442     231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 CD   231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2   -0.118    3.878
    8443     231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 CE   231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2   -0.120    3.880
    8444     231023_poly310-DH270UCA3_refine_001.pdb #1/E PHE 52 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CB    -0.127    3.887
    8445     231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CA  231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CE2    -0.129    3.619
    8446     231023_poly310-DH270UCA3_refine_001.pdb #1/E CYS 76 O    231023_poly310-DH270UCA3_refine_001.pdb #1/H SER 62 CB      -0.147    3.447
    8447     231023_poly310-DH270UCA3_refine_001.pdb #1/E PHE 52 CD2  231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD1   -0.154    3.794
    8448     231023_poly310-DH270UCA3_refine_001.pdb #1/E ALA 49 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B O     -0.159    3.459
    8449     231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CA  231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CH2    -0.166    3.806
    8450     231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 O    231023_poly310-DH270UCA3_refine_001.pdb #1/H ASP 112D CA    -0.172    3.472
    8451     231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 CG   231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 OH      -0.172    3.512
    8452     231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 O    231023_poly310-DH270UCA3_refine_001.pdb #1/H ASP 112D CB    -0.184    3.484
    8453     231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 OH      -0.199    2.679
    8454     231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H ILE 110 CG2    -0.212    3.972
    8455     231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 N    231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B O     -0.214    2.874
    8456     231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CB  231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CE2    -0.251    3.741
    8457     231023_poly310-DH270UCA3_refine_001.pdb #1/E PHE 52 CG   231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CB    -0.252    3.742
    8458     231023_poly310-DH270UCA3_refine_001.pdb #1/E PHE 52 CD1  231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CB    -0.254    3.894
    8459     231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 CA   231023_poly310-DH270UCA3_refine_001.pdb #1/H ASP 112D CG    -0.259    4.019
    8460     231023_poly310-DH270UCA3_refine_001.pdb #1/E PHE 52 CE1  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CB    -0.259    3.899
    8461     231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CB  231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CD2    -0.263    3.753
    8462     231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 CG   231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 59 CG      -0.267    3.757
    8463     231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 OH      -0.268    3.608
    8464     231023_poly310-DH270UCA3_refine_001.pdb #1/E LEU 36 CD2  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CZ    -0.280    3.770
    8465     231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 CZ      -0.289    3.319
    8466     231023_poly310-DH270UCA3_refine_001.pdb #1/E ALA 49 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CD1   -0.291    3.931
    8467     231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CG  231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CE2    -0.307    3.797
    8468     231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 CE   231023_poly310-DH270UCA3_refine_001.pdb #1/H ILE 110 CB     -0.315    4.075
    8469     231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 CA   231023_poly310-DH270UCA3_refine_001.pdb #1/H SER 111 O      -0.318    3.618
    8470     231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 NZ   231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111C CA    -0.322    3.842
    8471     231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ   231023_poly310-DH270UCA3_refine_001.pdb #1/H THR 65 O       -0.333    2.993
    8472     231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CG  231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CG     -0.334    3.824
    8473     231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 NZ   231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111C C     -0.335    3.585
    8474     231023_poly310-DH270UCA3_refine_001.pdb #1/E LEU 36 CD2  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CG    -0.339    3.829
    8475     231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 NZ   231023_poly310-DH270UCA3_refine_001.pdb #1/H ASP 112D N     -0.340    3.620
    8476     231023_poly310-DH270UCA3_refine_001.pdb #1/E GLY 70 N    231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2   -0.342    3.862
    8477     231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2   -0.361    4.121
    8478     231023_poly310-DH270UCA3_refine_001.pdb #1/E LEU 36 CD2  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CE1   -0.370    4.010
    8479     231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 SD   231023_poly310-DH270UCA3_refine_001.pdb #1/H ILE 110 CG2    -0.372    4.022
    8480     231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 55 CZ2     -0.386    4.026
    8481     231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 CB   231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2   -0.388    4.148
    8482     231023_poly310-DH270UCA3_refine_001.pdb #1/E LEU 36 CD2  231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CD1   -0.388    4.028
    8483     231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1  231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 57 ND2     -0.390    3.050
    8484     231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 CG   231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2   -0.396    4.156
    8485    
    8486 
    8487  
    8488 64 contacts 
    8489 
    8490 > select clear
    8491 
    8492 > hide #1.4 models
    8493 
    8494 > show #1.4 models
    8495 
    8496 > hide #1.4 models
    8497 
    8498 > show #1.3 models
    8499 
    8500 > hide #1.3 models
    8501 
    8502 > show #1.4 models
    8503 
    8504 > show #1.3 models
    8505 
    8506 > hide #1.3 models
    8507 
    8508 > open
    8509 > /Users/oswanson/Downloads/fold_lee_rdrp_trimer_dimer/fold_lee_rdrp_trimer_dimer_model_0.cif
    8510 
    8511 Chain information for fold_lee_rdrp_trimer_dimer_model_0.cif #12 
    8512 --- 
    8513 Chain | Description 
    8514 A B | . 
    8515 C D | . 
    8516 E F | . 
    8517  
    8518 
    8519 > hide #!1 models
    8520 
    8521 > hide #12 atoms
    8522 
    8523 > show #12 cartoons
    8524 
    8525 Computing secondary structure 
    8526 
    8527 > color #12 bychain
    8528 
    8529 > open pdb:6QWL
    8530 
    8531 Summary of feedback from opening 6QWL fetched from pdb 
    8532 --- 
    8533 note | Fetching compressed mmCIF 6qwl from http://files.rcsb.org/download/6qwl.cif 
    8534  
    8535 6qwl title: 
    8536 Influenza B virus (B/Panama/45) polymerase Hetermotrimer in complex with 3'5'
    8537 cRNA promoter [more info...] 
    8538  
    8539 Chain information for 6qwl #13 
    8540 --- 
    8541 Chain | Description | UniProt 
    8542 E | Polymerase acidic protein | PA_INBP9 1-726 
    8543 K | RNA-directed RNA polymerase catalytic subunit | RDRP_INBP9 1-752 
    8544 Q | Polymerase basic protein 2 | PB2_INBP9 1-770 
    8545 T | 3' cRNA |   
    8546 W | 5' cRNA |   
    8547  
    8548 
    8549 > ui tool show Matchmaker
    8550 
    8551 > matchmaker #!13 to #12
    8552 
    8553 Parameters 
    8554 --- 
    8555 Chain pairing | bb 
    8556 Alignment algorithm | Needleman-Wunsch 
    8557 Similarity matrix | BLOSUM-62 
    8558 SS fraction | 0.3 
    8559 Gap open (HH/SS/other) | 18/18/6 
    8560 Gap extend | 1 
    8561 SS matrix |  |  | H | S | O 
    8562 ---|---|---|--- 
    8563 H | 6 | -9 | -6 
    8564 S |  | 6 | -6 
    8565 O |  |  | 4 
    8566 Iteration cutoff | 2 
    8567  
    8568 Matchmaker fold_lee_rdrp_trimer_dimer_model_0.cif, chain C (#12) with 6qwl,
    8569 chain K (#13), sequence alignment score = 3220.4 
    8570 RMSD between 301 pruned atom pairs is 1.204 angstroms; (across all 539 pairs:
    8571 3.053) 
    8572  
    8573 
    8574 > select add #13
    8575 
    8576 10408 atoms, 10668 bonds, 24 pseudobonds, 1270 residues, 3 models selected 
    8577 
    8578 > hide sel atoms
    8579 
    8580 > show sel cartoons
    8581 
    8582 > select clear
    8583 
    8584 > hide #12 models
    8585 
    8586 > nucleotides #!13 atoms
    8587 
    8588 > style nucleic & #!13 stick
    8589 
    8590 Changed 553 atom styles 
    8591 
    8592 > nucleotides #!13 fill
    8593 
    8594 > style nucleic & #!13 stick
    8595 
    8596 Changed 553 atom styles 
    8597 
    8598 > nucleotides #!13 fill
    8599 
    8600 > style nucleic & #!13 stick
    8601 
    8602 Changed 553 atom styles 
    8603 
    8604 > nucleotides #!13 tube/slab shape box
    8605 
    8606 > nucleotides #!13 ladder
    8607 
    8608 > select #13/T:6
    8609 
    8610 20 atoms, 21 bonds, 1 residue, 1 model selected 
    8611 
    8612 > select up
    8613 
    8614 249 atoms, 275 bonds, 12 residues, 1 model selected 
    8615 
    8616 > nucleotides sel ladder
    8617 
    8618 > nucleotides sel tube/slab shape box
    8619 
    8620 [Repeated 2 time(s)]
    8621 
    8622 > nucleotides sel fill
    8623 
    8624 > style nucleic & sel stick
    8625 
    8626 Changed 249 atom styles 
    8627 
    8628 > nucleotides sel atoms
    8629 
    8630 > style nucleic & sel stick
    8631 
    8632 Changed 249 atom styles 
    8633 
    8634 > select add #13
    8635 
    8636 10408 atoms, 10668 bonds, 24 pseudobonds, 1270 residues, 3 models selected 
    8637 
    8638 > color sel bychain
    8639 
    8640 > select clear
    8641 
    8642 > show #12 models
    8643 
    8644 > hide #12 models
    8645 
    8646 > show #12 models
    8647 
    8648 > hide #12 models
    8649 
    8650 > show #12 models
    8651 
    8652 > hide #!13 models
    8653 
    8654 > show #!13 models
    8655 
    8656 > hide #!13 models
    8657 
    8658 > show #!13 models
    8659 
    8660 > hide #12 models
    8661 
    8662 > close #12#13
    8663 
    8664 > show #!1 models
    8665 
    8666 > save /Users/oswanson/Desktop/Primocalins/Structures/initial_models.cxs
    8667 
    8668 > hide #1.4 models
    8669 
    8670 > show #1.3 models
    8671 
    8672 > show #1.4 models
    8673 
    8674 > hide #1.4 models
    8675 
    8676 > show #1.4 models
    8677 
    8678 > hide #1.3 models
    8679 
    8680 > show #1.3 models
    8681 
    8682 > hide #1.4 models
    8683 
    8684 > close #1.4
    8685 
    8686 > color #1.3 #0433ffff models
    8687 
    8688 > color #1.3 #7a81ffff models
    8689 
    8690 > color #1.3 #0433ffff models
    8691 
    8692 > color #1.3 #f3f3f3ff models
    8693 
    8694 > color #1.3 #0433ffff models
    8695 
    8696 > color #1.3 #0b1e97ff models
    8697 
    8698 > color #1.2 #ea99faff models
    8699 
    8700 > hide #1.3 models
    8701 
    8702 > select add #1
    8703 
    8704 4647 atoms, 4757 bonds, 71 pseudobonds, 608 residues, 4 models selected 
    8705 
    8706 > size stickRadius 0.25
    8707 
    8708 Changed 41190 bond radii 
    8709 
    8710 > size stickRadius 0.
    8711 
    8712 Bond radius must be greater than 0. 
    8713 
    8714 > size stickRadius 0.3
    8715 
    8716 Changed 41190 bond radii 
    8717 
    8718 > size stickRadius 0.275
    8719 
    8720 Changed 41190 bond radii 
    8721 
    8722 > size stickRadius 0.25
    8723 
    8724 Changed 41190 bond radii 
    8725 
    8726 > select clear
    8727 
    8728 > ui tool show "Show Sequence Viewer"
    8729 
    8730 > sequence chain #1/H
    8731 
    8732 Alignment identifier is 1/H 
    8733 
    8734 > select #1/H:190
    8735 
    8736 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8737 
    8738 > select #1/H:190
    8739 
    8740 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8741 
    8742 > select #1/H:111A
    8743 
    8744 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8745 
    8746 > select #1/H:111A
    8747 
    8748 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8749 
    8750 > select #1/H:112D
    8751 
    8752 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8753 
    8754 > select #1/H:112D
    8755 
    8756 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8757 
    8758 > select #1/H:111A,112D
    8759 
    8760 16 atoms, 14 bonds, 2 residues, 1 model selected 
    8761 
    8762 > select #1/H:111A,112B,112D
    8763 
    8764 22 atoms, 19 bonds, 3 residues, 1 model selected 
    8765 
    8766 > show sel cartoons
    8767 
    8768 > show sel atoms
    8769 
    8770 > select #1/H:112B
    8771 
    8772 6 atoms, 5 bonds, 1 residue, 1 model selected 
    8773 
    8774 > hide sel atoms
    8775 
    8776 > select #1/H:111B
    8777 
    8778 12 atoms, 12 bonds, 1 residue, 1 model selected 
    8779 
    8780 > select #1/H:111B-111C,112A,112B,112C,112D
    8781 
    8782 48 atoms, 49 bonds, 6 residues, 1 model selected 
    8783 
    8784 > open pdb:8sax
    8785 
    8786 Summary of feedback from opening 8sax fetched from pdb 
    8787 --- 
    8788 notes | Fetching compressed mmCIF 8sax from http://files.rcsb.org/download/8sax.cif 
    8789 Fetching CCD BMA from
    8790 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/BMA/BMA.cif 
    8791 Fetching CCD MAN from
    8792 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MAN/MAN.cif 
    8793  
    8794 8sax title: 
    8795 CryoEM structure of DH270.UCA-CH848.10.17DT [more info...] 
    8796  
    8797 Chain information for 8sax #12 
    8798 --- 
    8799 Chain | Description | UniProt 
    8800 A E I | CH848.10.17.SOSIP gp120 | A0A1W6IPB2_9HIV1 34-511 
    8801 B F J | CH848.10.17.SOSIP gp41 |   
    8802 C G K | DH270.UCA heavy chain |   
    8803 D H L | DH270.UCA light chain |   
    8804  
    8805 Non-standard residues in 8sax #12 
    8806 --- 
    8807 BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) 
    8808 MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) 
    8809 NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
    8810 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
    8811 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) 
    8812  
    8813 
    8814 > select clear
    8815 
    8816 > select #1/H:66
    8817 
    8818 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8819 
    8820 > select add #1/L:109
    8821 
    8822 12 atoms, 10 bonds, 2 residues, 1 model selected 
    8823 
    8824 > select up
    8825 
    8826 55 atoms, 54 bonds, 8 residues, 1 model selected 
    8827 
    8828 > select up
    8829 
    8830 3334 atoms, 3411 bonds, 444 residues, 1 model selected 
    8831 
    8832 > ui tool show Matchmaker
    8833 
    8834 > matchmaker #12 to #1 & sel
    8835 
    8836 Parameters 
    8837 --- 
    8838 Chain pairing | bb 
    8839 Alignment algorithm | Needleman-Wunsch 
    8840 Similarity matrix | BLOSUM-62 
    8841 SS fraction | 0.3 
    8842 Gap open (HH/SS/other) | 18/18/6 
    8843 Gap extend | 1 
    8844 SS matrix |  |  | H | S | O 
    8845 ---|---|---|--- 
    8846 H | 6 | -9 | -6 
    8847 S |  | 6 | -6 
    8848 O |  |  | 4 
    8849 Iteration cutoff | 2 
    8850  
    8851 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1) with 8sax,
    8852 chain C (#12), sequence alignment score = 647.8 
    8853 RMSD between 126 pruned atom pairs is 0.769 angstroms; (across all 127 pairs:
    8854 0.792) 
    8855  
    8856 
    8857 > select add #12
    8858 
    8859 23194 atoms, 23760 bonds, 2991 residues, 2 models selected 
    8860 
    8861 > select #12/G:23@CE
    8862 
    8863 1 atom, 1 residue, 1 model selected 
    8864 
    8865 > select #12/G:23@CE
    8866 
    8867 1 atom, 1 residue, 1 model selected 
    8868 
    8869 > select add #12
    8870 
    8871 19860 atoms, 20349 bonds, 2547 residues, 1 model selected 
    8872 
    8873 > hide sel atoms
    8874 
    8875 > show sel cartoons
    8876 
    8877 > select clear
    8878 
    8879 > hide #!1 models
    8880 
    8881 > ui mousemode right select
    8882 
    8883 Drag select of 29 residues 
    8884 
    8885 > select up
    8886 
    8887 508 atoms, 510 bonds, 67 residues, 1 model selected 
    8888 
    8889 > ui tool show H-Bonds
    8890 
    8891 > hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8
    8892 > intraMol false intraRes false select true reveal true log true
    8893    
    8894    
    8895     Finding intramodel H-bonds
    8896     Constraints relaxed by 0.8 angstroms and 20 degrees
    8897     Models used:
    8898         12 8sax
    8899    
    8900     6 H-bonds
    8901     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    8902     8sax #12/A LYS 327 NZ   8sax #12/C TYR 33 OH    no hydrogen  3.095  N/A
    8903     8sax #12/A THR 415 OG1  8sax #12/N NAG 1 O5     no hydrogen  3.662  N/A
    8904     8sax #12/A THR 415 OG1  8sax #12/N NAG 1 O6     no hydrogen  3.431  N/A
    8905     8sax #12/C TYR 33 OH    8sax #12/A ASP 325 OD2  no hydrogen  2.827  N/A
    8906     8sax #12/N NAG 1 N2     8sax #12/A HIS 330 NE2  no hydrogen  3.281  N/A
    8907     8sax #12/N NAG 1 O6     8sax #12/A THR 415 OG1  no hydrogen  3.431  N/A
    8908    
    8909 
    8910  
    8911 6 hydrogen bonds found 
    8912 
    8913 > select up
    8914 
    8915 60 atoms, 57 bonds, 6 residues, 1 model selected 
    8916 
    8917 > style sel stick
    8918 
    8919 Changed 60 atom styles 
    8920 
    8921 > color sel byhetero
    8922 
    8923 > select clear
    8924 
    8925 > select #12/A:414
    8926 
    8927 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8928 
    8929 > select up
    8930 
    8931 73 atoms, 72 bonds, 9 residues, 1 model selected 
    8932 
    8933 > select up
    8934 
    8935 3582 atoms, 3664 bonds, 462 residues, 1 model selected 
    8936 
    8937 > select down
    8938 
    8939 73 atoms, 72 bonds, 9 residues, 1 model selected 
    8940 
    8941 > select clear
    8942 
    8943 Drag select of 9 atoms, 43 residues, 7 bonds 
    8944 
    8945 > select up
    8946 
    8947 636 atoms, 638 bonds, 84 residues, 1 model selected 
    8948 
    8949 > contacts sel restrict cross interModel false intraMol false
    8950 > ignoreHiddenModels true select true color #ff2600 reveal true log true
    8951    
    8952    
    8953     Allowed overlap: -0.4
    8954     H-bond overlap reduction: 0.4
    8955     Ignore contacts between atoms separated by 4 bonds or less
    8956     Detect intra-residue contacts: False
    8957     Detect intra-molecule contacts: False
    8958    
    8959     31 contacts
    8960              atom1                   atom2           overlap  distance
    8961     8sax #12/A ASN 332 ND2   8sax #12/N NAG 1 C1      1.117    2.403
    8962     8sax #12/A ASN 332 CG    8sax #12/N NAG 1 C1      0.545    2.945
    8963     8sax #12/A ASN 332 OD1   8sax #12/N NAG 1 C1      0.528    2.772
    8964     8sax #12/A ASN 332 ND2   8sax #12/N NAG 1 C2      0.307    3.213
    8965     8sax #12/A HIS 330 NE2   8sax #12/N NAG 1 C8      0.296    3.224
    8966     8sax #12/A HIS 330 CE1   8sax #12/C TYR 105 O     0.162    3.018
    8967     8sax #12/A THR 415 CG2   8sax #12/C TYR 105 CE1   0.118    3.522
    8968     8sax #12/A ASN 332 ND2   8sax #12/N NAG 1 C7      0.059    3.191
    8969     8sax #12/A HIS 330 CB    8sax #12/C TYR 105 CD1   0.051    3.589
    8970     8sax #12/A HIS 330 NE2   8sax #12/N NAG 1 N2      -0.001    3.281
    8971     8sax #12/A PRO 299 CG    8sax #12/C TYR 105 O     -0.063    3.363
    8972     8sax #12/A HIS 330 ND1   8sax #12/C TYR 105 CD1   -0.063    3.463
    8973     8sax #12/A HIS 330 CE1   8sax #12/C TYR 105 CB    -0.079    3.719
    8974     8sax #12/A ASN 332 ND2   8sax #12/N NAG 1 N2      -0.087    3.367
    8975     8sax #12/A THR 138 O     8sax #12/C GLY 57 CA     -0.102    3.402
    8976     8sax #12/A ILE 323c CG2  8sax #12/D SER 96 CB     -0.107    3.867
    8977     8sax #12/A ASN 332 ND2   8sax #12/N NAG 1 O7      -0.136    2.796
    8978     8sax #12/A HIS 330 CG    8sax #12/C TYR 105 CD1   -0.144    3.514
    8979     8sax #12/A THR 138 CG2   8sax #12/C ASN 59 ND2    -0.165    3.685
    8980     8sax #12/A HIS 330 CB    8sax #12/C TYR 105 CE1   -0.182    3.822
    8981     8sax #12/A HIS 330 ND1   8sax #12/C TYR 105 CB    -0.258    3.778
    8982     8sax #12/A THR 297 CG2   8sax #12/N NAG 1 C8      -0.283    4.043
    8983     8sax #12/A LYS 327 CD    8sax #12/C LEU 104 CA    -0.296    4.056
    8984     8sax #12/A THR 413 CG2   8sax #12/N NAG 1 O5      -0.304    3.644
    8985     8sax #12/A LYS 327 CE    8sax #12/C TYR 33 OH     -0.323    3.663
    8986     8sax #12/A ASP 325 OD2   8sax #12/C TYR 33 OH     -0.347    2.827
    8987     8sax #12/A HIS 330 CE1   8sax #12/C TYR 105 C     -0.350    3.720
    8988     8sax #12/A THR 415 CG2   8sax #12/C TYR 105 CZ    -0.354    3.844
    8989     8sax #12/A HIS 330 CE1   8sax #12/C TYR 105 CA    -0.358    3.998
    8990     8sax #12/A ILE 323c CG2  8sax #12/D SER 96 CA     -0.368    4.128
    8991     8sax #12/A LYS 327 NZ    8sax #12/C TYR 33 OH     -0.395    3.095
    8992    
    8993 
    8994  
    8995 31 contacts 
    8996 
    8997 > select add #12
    8998 
    8999 19860 atoms, 20349 bonds, 37 pseudobonds, 2547 residues, 3 models selected 
    9000 
    9001 > style sel stick
    9002 
    9003 Changed 19860 atom styles 
    9004 
    9005 > select clear
    9006 
    9007 > show #!1 models
    9008 
    9009 > hide #!1 models
    9010 
    9011 > select add #12
    9012 
    9013 19860 atoms, 20349 bonds, 37 pseudobonds, 2547 residues, 3 models selected 
    9014 
    9015 > color sel byhetero
    9016 
    9017 > select subtract #12
    9018 
    9019 Nothing selected 
    9020 
    9021 > hide #12.2 models
    9022 
    9023 > show #!1 models
    9024 
    9025 > hide #!12 models
    9026 
    9027 > show #!12 models
    9028 
    9029 > hide #!12 models
    9030 
    9031 > show #!12 models
    9032 
    9033 > hide #!12 models
    9034 
    9035 > show #!12 models
    9036 
    9037 > hide #!12 models
    9038 
    9039 > show #!12 models
    9040 
    9041 > hide #!12 models
    9042 
    9043 > show #!12 models
    9044 
    9045 > hide #!12 models
    9046 
    9047 > show #12.2 models
    9048 
    9049 > hide #!12 models
    9050 
    9051 > show #1.3 models
    9052 
    9053 > hide #1.2 models
    9054 
    9055 > show #!12 models
    9056 
    9057 > hide #!1 models
    9058 
    9059 > show #!1 models
    9060 
    9061 > hide #!1 models
    9062 
    9063 > open pdb:9aug
    9064 
    9065 Summary of feedback from opening 9aug fetched from pdb 
    9066 --- 
    9067 note | Fetching compressed mmCIF 9aug from http://files.rcsb.org/download/9aug.cif 
    9068  
    9069 9aug title: 
    9070 Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3.G57R [more info...] 
    9071  
    9072 Chain information for 9aug #13 
    9073 --- 
    9074 Chain | Description | UniProt 
    9075 A B C | HIV-1 BG505 DS-SOSIP glycoprotein gp120 | Q2N0S6_9HIV1 31-498 
    9076 D E F | HIV-1 BG505 DS-SOSIP glycoprotein gp41 | Q2N0S6_9HIV1 512-664 
    9077 G H I | UCA3.G57R heavy chain |   
    9078 J K L | UCA3.G57R light chain |   
    9079  
    9080 Non-standard residues in 9aug #13 
    9081 --- 
    9082 BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) 
    9083 MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) 
    9084 NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
    9085 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
    9086 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) 
    9087  
    9088 
    9089 > matchmaker #!13 to #1 & sel
    9090 
    9091 No 'to' model specified 
    9092 
    9093 > show #!1 models
    9094 
    9095 > select #1/H:112D
    9096 
    9097 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9098 
    9099 > select up
    9100 
    9101 181 atoms, 190 bonds, 22 residues, 1 model selected 
    9102 
    9103 > select up
    9104 
    9105 1725 atoms, 1772 bonds, 228 residues, 1 model selected 
    9106 
    9107 > select up
    9108 
    9109 4647 atoms, 4757 bonds, 608 residues, 1 model selected 
    9110 
    9111 > select down
    9112 
    9113 1725 atoms, 1772 bonds, 228 residues, 1 model selected 
    9114 
    9115 > select subtract #1/H:74
    9116 
    9117 1721 atoms, 1767 bonds, 227 residues, 1 model selected 
    9118 
    9119 > select up
    9120 
    9121 1725 atoms, 1772 bonds, 228 residues, 1 model selected 
    9122 
    9123 > select add #1/L:56
    9124 
    9125 1734 atoms, 1780 bonds, 229 residues, 1 model selected 
    9126 
    9127 > select up
    9128 
    9129 1828 atoms, 1876 bonds, 241 residues, 1 model selected 
    9130 
    9131 > select up
    9132 
    9133 3334 atoms, 3411 bonds, 444 residues, 1 model selected 
    9134 
    9135 > select up
    9136 
    9137 4647 atoms, 4757 bonds, 608 residues, 1 model selected 
    9138 
    9139 > select down
    9140 
    9141 3334 atoms, 3411 bonds, 444 residues, 1 model selected 
    9142 
    9143 > matchmaker #!13 to #1 & sel
    9144 
    9145 Parameters 
    9146 --- 
    9147 Chain pairing | bb 
    9148 Alignment algorithm | Needleman-Wunsch 
    9149 Similarity matrix | BLOSUM-62 
    9150 SS fraction | 0.3 
    9151 Gap open (HH/SS/other) | 18/18/6 
    9152 Gap extend | 1 
    9153 SS matrix |  |  | H | S | O 
    9154 ---|---|---|--- 
    9155 H | 6 | -9 | -6 
    9156 S |  | 6 | -6 
    9157 O |  |  | 4 
    9158 Iteration cutoff | 2 
    9159  
    9160 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1) with 9aug,
    9161 chain G (#13), sequence alignment score = 999.8 
    9162 RMSD between 125 pruned atom pairs is 0.728 angstroms; (across all 126 pairs:
    9163 0.755) 
    9164  
    9165 
    9166 > hide #!1 models
    9167 
    9168 > select add #1
    9169 
    9170 4647 atoms, 4757 bonds, 71 pseudobonds, 608 residues, 4 models selected 
    9171 
    9172 > select subtract #1
    9173 
    9174 Nothing selected 
    9175 
    9176 > select add #13
    9177 
    9178 20211 atoms, 20745 bonds, 3 pseudobonds, 2544 residues, 2 models selected 
    9179 
    9180 > show sel cartoons
    9181 
    9182 > style sel stick
    9183 
    9184 Changed 20211 atom styles 
    9185 
    9186 > hide sel atoms
    9187 
    9188 > select clear
    9189 
    9190 > hide #!12 models
    9191 
    9192 Drag select of 32 residues 
    9193 
    9194 > select up
    9195 
    9196 392 atoms, 391 bonds, 53 residues, 1 model selected 
    9197 
    9198 > hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8
    9199 > intraMol false intraRes false select true reveal true log true
    9200    
    9201    
    9202     Finding intramodel H-bonds
    9203     Constraints relaxed by 0.8 angstroms and 20 degrees
    9204     Models used:
    9205         13 9aug
    9206    
    9207     12 H-bonds
    9208     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    9209     9aug #13/A SER 136 OG   9aug #13/G THR 58 O     no hydrogen  3.683  N/A
    9210     9aug #13/A SER 136 OG   9aug #13/G THR 58 OG1   no hydrogen  3.145  N/A
    9211     9aug #13/A GLY 138 N    9aug #13/G SER 55 OG    no hydrogen  3.662  N/A
    9212     9aug #13/A ASP 325 N    9aug #13/G ASP 107 OD2  no hydrogen  3.149  N/A
    9213     9aug #13/A LYS 327 NZ   9aug #13/G TYR 33 OH    no hydrogen  3.222  N/A
    9214     9aug #13/A THR 415 OG1  9aug #13/G TYR 105 OH   no hydrogen  3.764  N/A
    9215     9aug #13/G TYR 33 OH    9aug #13/A ASP 325 OD2  no hydrogen  2.362  N/A
    9216     9aug #13/G ASN 52 ND2   9aug #13/A ASP 325 OD1  no hydrogen  3.191  N/A
    9217     9aug #13/G SER 55 OG    9aug #13/A GLY 138 O    no hydrogen  3.500  N/A
    9218     9aug #13/G ARG 57 NH2   9aug #13/A ILE 322 O    no hydrogen  3.168  N/A
    9219     9aug #13/G THR 58 OG1   9aug #13/A SER 136 OG   no hydrogen  3.145  N/A
    9220     9aug #13/G TYR 105 OH   9aug #13/A GLN 417 OE1  no hydrogen  3.170  N/A
    9221    
    9222 
    9223  
    9224 12 hydrogen bonds found 
    9225 
    9226 > select add #13
    9227 
    9228 20211 atoms, 20745 bonds, 15 pseudobonds, 2544 residues, 3 models selected 
    9229 
    9230 > color sel byhetero
    9231 
    9232 > select clear
    9233 
    9234 Drag select of 5 atoms, 15 residues, 3 bonds 
    9235 
    9236 > select up
    9237 
    9238 113 atoms, 105 bonds, 17 residues, 1 model selected 
    9239 
    9240 > select up
    9241 
    9242 128 atoms, 121 bonds, 17 residues, 1 model selected 
    9243 
    9244 > select down
    9245 
    9246 113 atoms, 105 bonds, 17 residues, 1 model selected 
    9247 
    9248 > select #13/G:57
    9249 
    9250 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9251 
    9252 > select #13/G:57
    9253 
    9254 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9255 
    9256 > select clear
    9257 
    9258 Drag select of 8 atoms, 33 residues, 7 bonds, 2 pseudobonds 
    9259 
    9260 > select subtract #13/G:57
    9261 
    9262 240 atoms, 5 bonds, 1 pseudobond, 33 residues, 2 models selected 
    9263 
    9264 > select up
    9265 
    9266 530 atoms, 533 bonds, 1 pseudobond, 72 residues, 2 models selected 
    9267 
    9268 > contacts sel restrict cross interModel false intraMol false
    9269 > ignoreHiddenModels true select true color #ff2600 reveal true log true
    9270    
    9271    
    9272     Allowed overlap: -0.4
    9273     H-bond overlap reduction: 0.4
    9274     Ignore contacts between atoms separated by 4 bonds or less
    9275     Detect intra-residue contacts: False
    9276     Detect intra-molecule contacts: False
    9277    
    9278     25 contacts
    9279             atom1                   atom2           overlap  distance
    9280     9aug #13/A ASP 325 CG   9aug #13/G ASN 52 ND2    0.265    3.255
    9281     9aug #13/A ASP 325 CG   9aug #13/G TYR 33 OH     0.200    3.140
    9282     9aug #13/A HIS 330 ND1  9aug #13/G TYR 105 CD1   0.133    3.267
    9283     9aug #13/A ILE 326 CG1  9aug #13/G ARG 57 NH1    0.123    3.397
    9284     9aug #13/A ASP 325 OD2  9aug #13/G TYR 33 OH     0.118    2.362
    9285     9aug #13/A ASP 325 OD2  9aug #13/G ASN 52 ND2    0.066    2.594
    9286     9aug #13/A HIS 330 CE1  9aug #13/G TYR 105 CB    0.064    3.576
    9287     9aug #13/A GLN 417 OE1  9aug #13/G TYR 105 CE1   0.062    3.118
    9288     9aug #13/A GLY 324 CA   9aug #13/J SER 97 OG     0.047    3.293
    9289     9aug #13/A ILE 323 CG2  9aug #13/J SER 96 CA     0.041    3.719
    9290     9aug #13/A GLY 137 CA   9aug #13/G ARG 57 CD     0.022    3.738
    9291     9aug #13/A LYS 327 CD   9aug #13/G LEU 104 CA    0.006    3.754
    9292     9aug #13/A HIS 330 CE1  9aug #13/G TYR 105 O     -0.009    3.189
    9293     9aug #13/A ILE 323 CG2  9aug #13/J SER 96 CB     -0.042    3.802
    9294     9aug #13/A HIS 330 CE1  9aug #13/G TYR 105 CD1   -0.045    3.565
    9295     9aug #13/A LYS 327 CE   9aug #13/G TYR 106 O     -0.048    3.348
    9296     9aug #13/A ASP 325 CB   9aug #13/G TYR 33 OH     -0.116    3.456
    9297     9aug #13/A SER 136 CB   9aug #13/G THR 58 OG1    -0.136    3.476
    9298     9aug #13/A ILE 326 CD1  9aug #13/G ARG 57 NH1    -0.178    3.698
    9299     9aug #13/A ILE 323 CG2  9aug #13/J SER 96 O      -0.194    3.494
    9300     9aug #13/A HIS 330 CE1  9aug #13/G TYR 105 CA    -0.208    3.848
    9301     9aug #13/A ILE 323 CG2  9aug #13/J SER 96 C      -0.226    3.716
    9302     9aug #13/A HIS 330 CG   9aug #13/G TYR 105 CD1   -0.287    3.657
    9303     9aug #13/A LYS 327 CE   9aug #13/G LEU 104 CA    -0.364    4.124
    9304     9aug #13/A GLY 324 C    9aug #13/G TRP 50 CH2    -0.385    3.755
    9305    
    9306 
    9307  
    9308 25 contacts 
    9309 
    9310 > select clear
    9311 
    9312 > hide #13.3 models
    9313 
    9314 > hide #13.2 models
    9315 
    9316 > show #13.3 models
    9317 
    9318 > show #13.2 models
    9319 
    9320 > hide #13.3 models
    9321 
    9322 Desktop color scheme is dark 
    9323 Desktop color scheme is light 
    9324 
    9325 > open pdb:6QWL
    9326 
    9327 6qwl title: 
    9328 Influenza B virus (B/Panama/45) polymerase Hetermotrimer in complex with 3'5'
    9329 cRNA promoter [more info...] 
    9330  
    9331 Chain information for 6qwl #14 
    9332 --- 
    9333 Chain | Description | UniProt 
    9334 E | Polymerase acidic protein | PA_INBP9 1-726 
    9335 K | RNA-directed RNA polymerase catalytic subunit | RDRP_INBP9 1-752 
    9336 Q | Polymerase basic protein 2 | PB2_INBP9 1-770 
    9337 T | 3' cRNA |   
    9338 W | 5' cRNA |   
    9339  
    9340 
    9341 > hide #!13 models
    9342 
    9343 > select add #14
    9344 
    9345 10408 atoms, 10668 bonds, 24 pseudobonds, 1270 residues, 3 models selected 
    9346 
    9347 > view orient
    9348 
    9349 > select clear
    9350 
    9351 > select #14/E:549@NH1
    9352 
    9353 1 atom, 1 residue, 1 model selected 
    9354 
    9355 > select add #14/K:331@CD1
    9356 
    9357 2 atoms, 2 residues, 1 model selected 
    9358 
    9359 > ui tool show Distances
    9360 
    9361 > distance #14/E:549@NH1 #14/K:331@CD1
    9362 
    9363 Distance between 6qwl #14/E ARG 549 NH1 and /K ILE 331 CD1: 104.224Å 
    9364 
    9365 > open
    9366 > /Users/oswanson/Downloads/fold_lee_rdrp_trimer_dimer/fold_lee_rdrp_trimer_dimer_model_0.cif
    9367 
    9368 Chain information for fold_lee_rdrp_trimer_dimer_model_0.cif #16 
    9369 --- 
    9370 Chain | Description 
    9371 A B | . 
    9372 C D | . 
    9373 E F | . 
    9374  
    9375 
    9376 > select clear
    9377 
    9378 > select add #16
    9379 
    9380 35830 atoms, 36512 bonds, 4496 residues, 1 model selected 
    9381 
    9382 > select subtract #16
    9383 
    9384 Nothing selected 
    9385 
    9386 > select add #16
    9387 
    9388 35830 atoms, 36512 bonds, 4496 residues, 1 model selected 
    9389 
    9390 > view orient
    9391 
    9392 > hide #!14 models
    9393 
    9394 > view orient
    9395 
    9396 > select clear
    9397 
    9398 [Repeated 1 time(s)]
    9399 
    9400 > select #16/D:196@NH1
    9401 
    9402 1 atom, 1 residue, 1 model selected 
    9403 
    9404 > select add #16/C:196@NH2
    9405 
    9406 2 atoms, 2 residues, 1 model selected 
    9407 
    9408 > distance #16/D:196@NH1 #16/C:196@NH2
    9409 
    9410 Distance between fold_lee_rdrp_trimer_dimer_model_0.cif #16/D ARG 196 NH1 and
    9411 /C ARG 196 NH2: 197.716Å 
    9412 
    9413 > select #16/A:621@OE1
    9414 
    9415 1 atom, 1 residue, 1 model selected 
    9416 
    9417 > select add #16/E:631@ND2
    9418 
    9419 2 atoms, 2 residues, 1 model selected 
    9420 
    9421 > distance #16/A:621@OE1 #16/E:631@ND2
    9422 
    9423 Distance between fold_lee_rdrp_trimer_dimer_model_0.cif #16/A GLU 621 OE1 and
    9424 /E ASN 631 ND2: 126.822Å 
    9425 
    9426 > select clear
    9427 
    9428 > select #16/A:621@OE1
    9429 
    9430 1 atom, 1 residue, 1 model selected 
    9431 
    9432 > select add #16/E:631@CB
    9433 
    9434 2 atoms, 2 residues, 1 model selected 
    9435 
    9436 > distance #16/A:621@OE1 #16/E:631@CB
    9437 
    9438 Distance between fold_lee_rdrp_trimer_dimer_model_0.cif #16/A GLU 621 OE1 and
    9439 /E ASN 631 CB: 128.258Å 
    9440 
    9441 > select #16/B:321@CG
    9442 
    9443 1 atom, 1 residue, 1 model selected 
    9444 
    9445 > select add #16/B:100@O
    9446 
    9447 2 atoms, 2 residues, 1 model selected 
    9448 
    9449 > distance #16/B:321@CG #16/B:100@O
    9450 
    9451 Distance between fold_lee_rdrp_trimer_dimer_model_0.cif #16/B ASP 321 CG and
    9452 GLY 100 O: 131.686Å 
    9453 
    9454 > select #16/D:194@CE
    9455 
    9456 1 atom, 1 residue, 1 model selected 
    9457 
    9458 > select add #16/B:206@OE1
    9459 
    9460 2 atoms, 2 residues, 1 model selected 
    9461 
    9462 > distance #16/D:194@CE #16/B:206@OE1
    9463 
    9464 Distance between fold_lee_rdrp_trimer_dimer_model_0.cif #16/D LYS 194 CE and
    9465 /B GLN 206 OE1: 62.308Å 
    9466 
    9467 > select add #16
    9468 
    9469 35830 atoms, 36512 bonds, 5 pseudobonds, 4496 residues, 2 models selected 
    9470 
    9471 > hide sel atoms
    9472 
    9473 > show sel cartoons
    9474 
    9475 Computing secondary structure 
    9476 
    9477 > select clear
    9478 
    9479 Desktop color scheme is dark 
    9480 
    9481 > molmap #16 4
    9482 
    9483 Opened fold_lee_rdrp_trimer_dimer_model_0.cif map 4 as #17, grid size
    9484 142,148,110, pixel 1.33, shown at level 0.102, step 1, values float32 
    9485 
    9486 > hide #!17 models
    9487 
    9488 > select add #16
    9489 
    9490 35830 atoms, 36512 bonds, 5 pseudobonds, 4496 residues, 2 models selected 
    9491 
    9492 > color sel bychain
    9493 
    9494 > select clear
    9495 
    9496 Desktop color scheme is light 
    9497 
    9498 > show #!17 models
    9499 
    9500 > molmap #16 8
    9501 
    9502 Opened fold_lee_rdrp_trimer_dimer_model_0.cif map 8 as #17, grid size
    9503 80,83,64, pixel 2.67, shown at level 0.0919, step 1, values float32 
    9504 
    9505 > save
    9506 > /Users/oswanson/Desktop/Primocalins/Structures/initial_models_plusRdRp.cxs
    9507 
    9508 ——— End of log from Wed Nov 5 13:19:26 2025 ———
    9509 
    9510 > view name session-start
    9511 
    9512 opened ChimeraX session 
    9513 
    9514 > close #2,4-5,8#1,3,6-7,9-15
    9515 
    9516 > open /Users/oswanson/Downloads/cryosparc_P605_J52_005_volume_map_sharp.mrc
    9517 
    9518 Opened cryosparc_P605_J52_005_volume_map_sharp.mrc as #1, grid size
    9519 256,256,256, pixel 1.45, shown at level 0.0832, step 1, values float32 
    9520 
    9521 > open /Users/oswanson/Downloads/cryosparc_P605_J45_class_00_final_volume.mrc
    9522 
    9523 Opened cryosparc_P605_J45_class_00_final_volume.mrc as #2, grid size
    9524 256,256,256, pixel 1.45, shown at level 0.0414, step 1, values float32 
    9525 
    9526 > open /Users/oswanson/Downloads/cryosparc_P605_J23_class_00_final_volume.mrc
    9527 
    9528 Opened cryosparc_P605_J23_class_00_final_volume.mrc as #3, grid size
    9529 128,128,128, pixel 2.9, shown at level 0.115, step 1, values float32 
    9530 
    9531 > hide #!2 models
    9532 
    9533 > hide #!3 models
    9534 
    9535 > hide #16 models
    9536 
    9537 > hide #!17 models
    9538 
    9539 > volume #1 level 0.1315
    9540 
    9541 Drag select of 1 cryosparc_P605_J52_005_volume_map_sharp.mrc 
    9542 
    9543 > select clear
    9544 
    9545 > volume #1 level 0.1798
    9546 
    9547 > show #16 models
    9548 
    9549 > hide #16 models
    9550 
    9551 > show #16 models
    9552 
    9553 > select add #16
    9554 
    9555 35830 atoms, 36512 bonds, 4496 residues, 1 model selected 
    9556 
    9557 > ui mousemode right "move picked models"
    9558 
    9559 > select clear
    9560 
    9561 > select add #16
    9562 
    9563 35830 atoms, 36512 bonds, 4496 residues, 1 model selected 
    9564 
    9565 > select subtract #16
    9566 
    9567 Nothing selected 
    9568 
    9569 > select add #16
    9570 
    9571 35830 atoms, 36512 bonds, 4496 residues, 1 model selected 
    9572 
    9573 > ui mousemode right "translate selected models"
    9574 
    9575 > view matrix models #16,1,0,0,251.43,0,1,0,74.5,0,0,1,126.23
    9576 
    9577 > ui mousemode right "rotate selected models"
    9578 
    9579 > view matrix models
    9580 > #16,0.56617,0.046792,-0.82296,254.29,0.5826,0.68356,0.43968,72.162,0.58311,-0.72839,0.35975,126.33
    9581 
    9582 > ui mousemode right "translate selected models"
    9583 
    9584 > view matrix models
    9585 > #16,0.56617,0.046792,-0.82296,192.3,0.5826,0.68356,0.43968,179.37,0.58311,-0.72839,0.35975,272.53
    9586 
    9587 > hide #16 models
    9588 
    9589 > show #16 models
    9590 
    9591 > hide #!1 models
    9592 
    9593 > show #!1 models
    9594 
    9595 > ui mousemode right "rotate selected models"
    9596 
    9597 > view matrix models
    9598 > #16,-0.38773,-0.54695,-0.74196,192.02,0.74337,0.29041,-0.60255,181.59,0.54504,-0.78518,0.29398,272.66
    9599 
    9600 > transparency #1.1 50
    9601 
    9602 > ui tool show "Fit in Map"
    9603 
    9604 > fitmap #16 inMap #1
    9605 
    9606 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
    9607 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    9608 average map value = 0.02551, steps = 112 
    9609 shifted from previous position = 5.67 
    9610 rotated from previous position = 6.57 degrees 
    9611 atoms outside contour = 33233, contour level = 0.17978 
    9612  
    9613 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
    9614 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    9615 Matrix rotation and translation 
    9616 -0.39844947 -0.54410540 -0.73836800 190.02273044 
    9617 0.79663890 0.19365023 -0.57259590 186.77602359 
    9618 0.45453767 -0.81636320 0.35629570 271.90745353 
    9619 Axis -0.13459712 -0.65866778 0.74029749 
    9620 Axis point 24.61963021 298.99662788 0.00000000 
    9621 Rotation angle (degrees) 115.10331204 
    9622 Shift along axis 52.69254484 
    9623  
    9624 
    9625 > select up
    9626 
    9627 35830 atoms, 36512 bonds, 4496 residues, 9 models selected 
    9628 
    9629 > select down
    9630 
    9631 35830 atoms, 36512 bonds, 4496 residues, 1 model selected 
    9632 
    9633 > select down
    9634 
    9635 35830 atoms, 36512 bonds, 4496 residues, 1 model selected 
    9636 
    9637 > select down
    9638 
    9639 35830 atoms, 36512 bonds, 4496 residues, 1 model selected 
    9640 
    9641 > select down
    9642 
    9643 35830 atoms, 36512 bonds, 4496 residues, 1 model selected 
    9644 
    9645 > select down
    9646 
    9647 35830 atoms, 36512 bonds, 4496 residues, 1 model selected 
    9648 
    9649 > select down
    9650 
    9651 35830 atoms, 36512 bonds, 4496 residues, 1 model selected 
    9652 
    9653 > select up
    9654 
    9655 35830 atoms, 36512 bonds, 4496 residues, 9 models selected 
    9656 
    9657 > select up
    9658 
    9659 35830 atoms, 36512 bonds, 4496 residues, 9 models selected 
    9660 
    9661 > select up
    9662 
    9663 35830 atoms, 36512 bonds, 4496 residues, 9 models selected 
    9664 
    9665 > select up
    9666 
    9667 35830 atoms, 36512 bonds, 4496 residues, 9 models selected 
    9668 
    9669 > select up
    9670 
    9671 35830 atoms, 36512 bonds, 4496 residues, 9 models selected 
    9672 
    9673 > combine #16
    9674 
    9675 > hide #16 models
    9676 
    9677 > view matrix models
    9678 > #16,-0.4592,-0.20322,-0.86478,161.58,0.79591,0.33825,-0.50211,178.98,0.39455,-0.91885,0.0064224,267.12,#17,0.93206,0.090002,-0.35094,63.084,-0.13043,0.98706,-0.093261,44.764,0.338,0.1327,0.93174,-75.241,#1,0.93206,0.090002,-0.35094,63.084,-0.13043,0.98706,-0.093261,44.764,0.338,0.1327,0.93174,-75.241,#2,0.93206,0.090002,-0.35094,63.084,-0.13043,0.98706,-0.093261,44.764,0.338,0.1327,0.93174,-75.241,#3,0.93206,0.090002,-0.35094,63.084,-0.13043,0.98706,-0.093261,44.764,0.338,0.1327,0.93174,-75.241
    9679 
    9680 > undo
    9681 
    9682 > select subtract #1
    9683 
    9684 35830 atoms, 36512 bonds, 4496 residues, 7 models selected 
    9685 
    9686 > select subtract #2
    9687 
    9688 35830 atoms, 36512 bonds, 4496 residues, 5 models selected 
    9689 
    9690 > select subtract #3
    9691 
    9692 35830 atoms, 36512 bonds, 4496 residues, 3 models selected 
    9693 
    9694 > select subtract #16
    9695 
    9696 2 models selected 
    9697 
    9698 > select subtract #17
    9699 
    9700 Nothing selected 
    9701 
    9702 > show #16 models
    9703 
    9704 > select add #4
    9705 
    9706 35830 atoms, 36512 bonds, 4496 residues, 1 model selected 
    9707 
    9708 > view matrix models
    9709 > #4,0.10637,-0.45445,-0.8844,190.1,-0.8361,-0.52228,0.16781,185.06,-0.53816,0.7216,-0.43552,277.63
    9710 
    9711 > ui mousemode right "translate selected models"
    9712 
    9713 > view matrix models
    9714 > #4,0.10637,-0.45445,-0.8844,203.66,-0.8361,-0.52228,0.16781,179.65,-0.53816,0.7216,-0.43552,96.334
    9715 
    9716 > fitmap #4 inMap #1
    9717 
    9718 Fit molecule copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) to map
    9719 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    9720 average map value = 0.02552, steps = 228 
    9721 shifted from previous position = 16.3 
    9722 rotated from previous position = 6.81 degrees 
    9723 atoms outside contour = 33525, contour level = 0.17978 
    9724  
    9725 Position of copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) relative to
    9726 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    9727 Matrix rotation and translation 
    9728 0.18892573 -0.37307282 -0.90836325 188.74522050 
    9729 -0.81392816 -0.57700782 0.06769757 173.07520212 
    9730 -0.54938881 0.72655259 -0.41266609 94.69324234 
    9731 Axis 0.75710159 -0.41250367 -0.50659442 
    9732 Axis point 0.00000000 121.83472913 138.13230218 
    9733 Rotation angle (degrees) 154.20728304 
    9734 Shift along axis 23.53408244 
    9735  
    9736 
    9737 > hide #!1 models
    9738 
    9739 > show #!1 models
    9740 
    9741 > view matrix models
    9742 > #4,0.18893,-0.37307,-0.90836,198.73,-0.81393,-0.57701,0.067698,180.73,-0.54939,0.72655,-0.41267,94.573
    9743 
    9744 > ui mousemode right "rotate selected models"
    9745 
    9746 > view matrix models
    9747 > #4,0.29527,-0.31847,-0.90077,198.69,-0.79417,-0.60594,-0.046092,180.99,-0.53114,0.72898,-0.43184,94.615
    9748 
    9749 > view matrix models
    9750 > #4,0.9147,0.3554,0.19241,196.04,0.31964,-0.34483,-0.88257,182.75,-0.24732,0.86878,-0.42901,94.559
    9751 
    9752 > view matrix models
    9753 > #4,0.86991,0.46396,0.16731,196.33,0.2363,-0.094317,-0.96709,183.48,-0.43292,0.88082,-0.19168,94.074
    9754 
    9755 > view matrix models
    9756 > #4,0.091797,0.19202,0.97709,194.3,0.91711,0.36596,-0.15808,181.23,-0.38793,0.9106,-0.1425,93.937
    9757 
    9758 > hide #4 models
    9759 
    9760 > hide #!1 models
    9761 
    9762 > show #4 models
    9763 
    9764 > view matrix models
    9765 > #4,0.098519,0.18624,0.97755,194.29,0.91632,0.36617,-0.16211,181.25,-0.38814,0.91172,-0.13459,93.916
    9766 
    9767 > view matrix models
    9768 > #4,0.22392,0.65435,0.72228,195.66,0.97264,-0.10301,-0.20821,180.57,-0.061839,0.74915,-0.65951,94.851
    9769 
    9770 > view matrix models
    9771 > #4,0.11714,0.64063,0.75886,195.63,0.89902,0.25624,-0.3551,181.64,-0.42194,0.72383,-0.54593,94.83
    9772 
    9773 > view matrix models
    9774 > #4,-0.51937,-0.04866,-0.85316,199.78,-0.73329,-0.48726,0.47419,179.62,-0.43879,0.8719,0.21739,92.887
    9775 
    9776 > view matrix models
    9777 > #4,-0.51813,-0.047949,-0.85396,199.78,-0.73652,-0.48258,0.47398,179.63,-0.43483,0.87454,0.21473,92.895
    9778 
    9779 > fitmap #4 inMap #1
    9780 
    9781 Fit molecule copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) to map
    9782 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    9783 average map value = 0.02196, steps = 252 
    9784 shifted from previous position = 21.3 
    9785 rotated from previous position = 15.8 degrees 
    9786 atoms outside contour = 33403, contour level = 0.17978 
    9787  
    9788 Position of copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) relative to
    9789 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    9790 Matrix rotation and translation 
    9791 -0.41550158 -0.11613734 -0.90214776 180.80356337 
    9792 -0.86176437 -0.26711732 0.43128940 180.04918454 
    9793 -0.29106810 0.95664019 0.01090465 102.61544368 
    9794 Axis 0.47850771 -0.55659253 -0.67914294 
    9795 Axis point 155.97061527 -0.61103272 0.00000000 
    9796 Rotation angle (degrees) 146.70519388 
    9797 Shift along axis -83.38868580 
    9798  
    9799 
    9800 > show #!1 models
    9801 
    9802 > hide #16 models
    9803 
    9804 > hide #4 models
    9805 
    9806 > show #4 models
    9807 
    9808 > hide #!1 models
    9809 
    9810 > show sel surfaces
    9811 
    9812 > show #!1 models
    9813 
    9814 > hide #!1 models
    9815 
    9816 > view matrix models
    9817 > #4,0.24231,0.83862,0.48785,177.58,0.86634,0.039325,-0.49791,180.74,-0.43674,0.54329,-0.717,104.17
    9818 
    9819 > show #!1 models
    9820 
    9821 > view matrix models
    9822 > #4,0.29279,0.56852,0.7688,175.81,0.83406,0.24132,-0.49609,181.29,-0.46757,0.78648,-0.40352,103.68
    9823 
    9824 > view matrix models
    9825 > #4,0.28705,0.60074,0.74614,175.97,0.83717,0.22125,-0.5002,181.25,-0.46557,0.76822,-0.43941,103.75
    9826 
    9827 > hide sel atoms
    9828 
    9829 > show sel cartoons
    9830 
    9831 > hide sel surfaces
    9832 
    9833 > fitmap #4 inMap #1
    9834 
    9835 Fit molecule copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) to map
    9836 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    9837 average map value = 0.02541, steps = 116 
    9838 shifted from previous position = 3.44 
    9839 rotated from previous position = 2.75 degrees 
    9840 atoms outside contour = 33396, contour level = 0.17978 
    9841  
    9842 Position of copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) relative to
    9843 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    9844 Matrix rotation and translation 
    9845 0.24909426 0.59258494 0.76602556 178.89606311 
    9846 0.83930792 0.26257111 -0.47604480 179.61164172 
    9847 -0.48323317 0.76151133 -0.43195628 104.75578622 
    9848 Axis 0.69694492 0.70353538 0.13894508 
    9849 Axis point 29.80507567 0.00000000 37.32606388 
    9850 Rotation angle (degrees) 117.39649343 
    9851 Shift along axis 265.59914953 
    9852  
    9853 
    9854 > color #1 #73fdffff models
    9855 
    9856 > color #1 #73fdff7e models
    9857 
    9858 > show #16 models
    9859 
    9860 > volume #1 level 0.1843
    9861 
    9862 > volume #1 level 0.182
    9863 
    9864 > surface dust #1 size 14.5
    9865 
    9866 > ui mousemode right select
    9867 
    9868 Drag select of 1689 residues 
    9869 
    9870 > select up
    9871 
    9872 14802 atoms, 15071 bonds, 1857 residues, 4 models selected 
    9873 
    9874 > select up
    9875 
    9876 17915 atoms, 18256 bonds, 2248 residues, 4 models selected 
    9877 
    9878 > select up
    9879 
    9880 35830 atoms, 36512 bonds, 4496 residues, 4 models selected 
    9881 
    9882 > select down
    9883 
    9884 17915 atoms, 18256 bonds, 2248 residues, 7 models selected 
    9885 
    9886 > delete atoms (#!4 & sel)
    9887 
    9888 > delete bonds (#!4 & sel)
    9889 
    9890 > fitmap #4 inMap #1
    9891 
    9892 Fit molecule copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) to map
    9893 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 17915 atoms 
    9894 average map value = 0.053, steps = 52 
    9895 shifted from previous position = 0.264 
    9896 rotated from previous position = 1.64 degrees 
    9897 atoms outside contour = 15515, contour level = 0.18205 
    9898  
    9899 Position of copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) relative to
    9900 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    9901 Matrix rotation and translation 
    9902 0.26529394 0.57167712 0.77640480 180.26796487 
    9903 0.83656024 0.26387438 -0.48014300 179.40307714 
    9904 -0.47936011 0.77688840 -0.40823808 104.79232831 
    9905 Axis 0.69973038 0.69902538 0.14744800 
    9906 Axis point 0.00000000 -29.51186539 30.17715972 
    9907 Rotation angle (degrees) 116.07420772 
    9908 Shift along axis 266.99769535 
    9909  
    9910 
    9911 > select add #4
    9912 
    9913 17915 atoms, 18256 bonds, 2248 residues, 1 model selected 
    9914 
    9915 > ui mousemode right "rotate selected models"
    9916 
    9917 > view matrix models
    9918 > #4,-0.28105,0.41568,0.865,178.89,0.88896,0.45238,0.07144,180.7,-0.36161,0.78903,-0.49666,104.95
    9919 
    9920 > view matrix models
    9921 > #4,-0.57757,-0.009911,0.81628,187.49,0.33218,-0.91625,0.22391,217.2,0.7457,0.40048,0.53249,143.43
    9922 
    9923 > ui mousemode right "translate selected models"
    9924 
    9925 > view matrix models
    9926 > #4,-0.57757,-0.009911,0.81628,188.27,0.33218,-0.91625,0.22391,216.04,0.7457,0.40048,0.53249,131.46
    9927 
    9928 > ui mousemode right "rotate selected models"
    9929 
    9930 > view matrix models
    9931 > #4,-0.59219,-0.011829,0.80571,188.01,0.29067,-0.93571,0.19991,215.81,0.75154,0.35258,0.55756,133.3
    9932 
    9933 > fitmap #4 inMap #1
    9934 
    9935 Fit molecule copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) to map
    9936 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 17915 atoms 
    9937 average map value = 0.0596, steps = 236 
    9938 shifted from previous position = 23.8 
    9939 rotated from previous position = 32.2 degrees 
    9940 atoms outside contour = 15550, contour level = 0.18205 
    9941  
    9942 Position of copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) relative to
    9943 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    9944 Matrix rotation and translation 
    9945 -0.15230889 0.25759098 0.95417447 180.22911477 
    9946 0.10867085 -0.95521977 0.27521963 220.55572962 
    9947 0.98234041 0.14560933 0.11749582 158.81578038 
    9948 Axis -0.64992799 -0.14123747 -0.74675671 
    9949 Axis point 27.12258547 95.03239742 0.00000000 
    9950 Rotation angle (degrees) 174.27745516 
    9951 Shift along axis -266.88342951 
    9952  
    9953 
    9954 > view matrix models
    9955 > #4,-0.023921,0.11317,0.99329,186.81,-0.91464,-0.40356,0.023952,187.19,0.40356,-0.90793,0.11316,183.51
    9956 
    9957 > view matrix models
    9958 > #4,0.86467,-0.26556,-0.4264,193.69,-0.31079,-0.94969,-0.038764,211.21,-0.39466,0.16604,-0.9037,128.18
    9959 
    9960 > hide #16 models
    9961 
    9962 > show #16 models
    9963 
    9964 > view matrix models
    9965 > #4,0.8809,-0.19269,-0.4323,191.6,-0.22048,-0.97528,-0.014569,213.47,-0.41881,0.10815,-0.90161,129.67
    9966 
    9967 > view matrix models
    9968 > #4,0.81876,-0.1335,-0.5584,187.49,-0.21735,-0.97228,-0.086245,212.59,-0.5314,0.19198,-0.82508,126.49
    9969 
    9970 > view matrix models
    9971 > #4,-0.68377,0.31464,-0.65838,152.75,0.57787,0.78442,-0.22529,167.47,0.44556,-0.5345,-0.71818,162.94
    9972 
    9973 > view matrix models
    9974 > #4,-0.76635,0.52854,0.36518,156.97,0.63368,0.7154,0.29436,176.35,-0.10567,0.45699,-0.88317,123.29
    9975 
    9976 > ui mousemode right "translate selected models"
    9977 
    9978 > view matrix models
    9979 > #4,-0.76635,0.52854,0.36518,150.69,0.63368,0.7154,0.29436,181.66,-0.10567,0.45699,-0.88317,109.99
    9980 
    9981 > ui mousemode right "rotate selected models"
    9982 
    9983 > view matrix models
    9984 > #4,-0.65517,0.61494,0.43885,150.36,0.73556,0.65173,0.1849,183.69,-0.17231,0.44394,-0.87933,109.56
    9985 
    9986 > view matrix models
    9987 > #4,-0.76882,0.5424,0.3387,149.93,0.49591,0.84012,-0.21971,170.04,-0.40372,-0.00095226,-0.91488,119.77
    9988 
    9989 > view matrix models
    9990 > #4,-0.02401,0.47969,0.87711,167.92,0.26947,0.84799,-0.45639,164.07,-0.96271,0.2254,-0.14962,114.33
    9991 
    9992 > ui mousemode right "translate selected models"
    9993 
    9994 > view matrix models
    9995 > #4,-0.02401,0.47969,0.87711,166.32,0.26947,0.84799,-0.45639,148.6,-0.96271,0.2254,-0.14962,121.59
    9996 
    9997 > ui mousemode right "rotate selected models"
    9998 
    9999 > view matrix models
    10000 > #4,0.11936,0.52233,0.84435,166.52,0.65667,0.59632,-0.46172,161.37,-0.74467,0.60957,-0.27182,111.24
    10001 
    10002 > ui mousemode right "translate selected models"
    10003 
    10004 > view matrix models
    10005 > #4,0.11936,0.52233,0.84435,171.68,0.65667,0.59632,-0.46172,184.72,-0.74467,0.60957,-0.27182,110.91
    10006 
    10007 > fitmap #4 inMap #1
    10008 
    10009 Fit molecule copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) to map
    10010 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 17915 atoms 
    10011 average map value = 0.05302, steps = 88 
    10012 shifted from previous position = 7.14 
    10013 rotated from previous position = 5.08 degrees 
    10014 atoms outside contour = 15522, contour level = 0.18205 
    10015  
    10016 Position of copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) relative to
    10017 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    10018 Matrix rotation and translation 
    10019 0.17959804 0.46678727 0.86594119 179.64862220 
    10020 0.67601034 0.58092839 -0.45335658 181.25416971 
    10021 -0.71467093 0.66680716 -0.21121943 107.52467305 
    10022 Axis 0.57486824 0.81117044 0.10737332 
    10023 Axis point 64.51605416 0.00000000 27.49417563 
    10024 Rotation angle (degrees) 103.02325425 
    10025 Shift along axis 261.84759214 
    10026  
    10027 
    10028 > open pdb:6QWL)
    10029 
    10030 PDB identifiers are either 4 or 8 characters long, got "6QWL)" 
    10031 
    10032 > open pdb:6QWL
    10033 
    10034 6qwl title: 
    10035 Influenza B virus (B/Panama/45) polymerase Hetermotrimer in complex with 3'5'
    10036 cRNA promoter [more info...] 
    10037  
    10038 Chain information for 6qwl #5 
    10039 --- 
    10040 Chain | Description | UniProt 
    10041 E | Polymerase acidic protein | PA_INBP9 1-726 
    10042 K | RNA-directed RNA polymerase catalytic subunit | RDRP_INBP9 1-752 
    10043 Q | Polymerase basic protein 2 | PB2_INBP9 1-770 
    10044 T | 3' cRNA |   
    10045 W | 5' cRNA |   
    10046  
    10047 
    10048 > hide #16 models
    10049 
    10050 > hide #!4 models
    10051 
    10052 > select add #5
    10053 
    10054 28323 atoms, 28924 bonds, 24 pseudobonds, 3518 residues, 7 models selected 
    10055 
    10056 > select subtract #4
    10057 
    10058 10408 atoms, 10668 bonds, 24 pseudobonds, 1270 residues, 6 models selected 
    10059 
    10060 > hide sel atoms
    10061 
    10062 > show sel cartoons
    10063 
    10064 > ui mousemode right "rotate selected models"
    10065 
    10066 > view matrix models
    10067 > #5,0.48454,-0.1978,-0.85211,215.56,0.80712,0.47671,0.3483,-86.856,0.33732,-0.85652,0.39063,155.64
    10068 
    10069 > view matrix models
    10070 > #5,0.45306,-0.064033,-0.88918,206.75,0.74408,0.5765,0.33762,-90.406,0.491,-0.81458,0.30884,140.38
    10071 
    10072 > ui mousemode right "translate selected models"
    10073 
    10074 > view matrix models
    10075 > #5,0.45306,-0.064033,-0.88918,254.92,0.74408,0.5765,0.33762,-51.664,0.491,-0.81458,0.30884,143.9
    10076 
    10077 > ui mousemode right "rotate selected models"
    10078 
    10079 > view matrix models
    10080 > #5,0.050603,-0.42079,-0.90575,360.63,0.8555,0.48621,-0.17809,17.185,0.51532,-0.76586,0.38459,123.41
    10081 
    10082 > fitmap #5 inMap #1
    10083 
    10084 Fit molecule 6qwl (#5) to map cryosparc_P605_J52_005_volume_map_sharp.mrc (#1)
    10085 using 10408 atoms 
    10086 average map value = 0.08691, steps = 136 
    10087 shifted from previous position = 4.69 
    10088 rotated from previous position = 9.6 degrees 
    10089 atoms outside contour = 8202, contour level = 0.18205 
    10090  
    10091 Position of 6qwl (#5) relative to cryosparc_P605_J52_005_volume_map_sharp.mrc
    10092 (#1) coordinates: 
    10093 Matrix rotation and translation 
    10094 -0.00388935 -0.38545341 -0.92271910 364.68437376 
    10095 0.76695492 0.59095802 -0.25009751 29.83861543 
    10096 0.64168919 -0.70865667 0.29332695 110.32807559 
    10097 Axis -0.22969067 -0.78360661 0.57723728 
    10098 Axis point 96.58544641 0.00000000 279.32739026 
    10099 Rotation angle (degrees) 93.42845885 
    10100 Shift along axis -43.46085772 
    10101  
    10102 
    10103 > view matrix models
    10104 > #5,-0.36242,-0.7007,-0.61455,413.61,-0.57983,-0.34674,0.73728,203.67,-0.7297,0.62353,-0.28062,195
    10105 
    10106 > ui mousemode right "translate selected models"
    10107 
    10108 > view matrix models
    10109 > #5,-0.36242,-0.7007,-0.61455,415.44,-0.57983,-0.34674,0.73728,210.86,-0.7297,0.62353,-0.28062,205.3
    10110 
    10111 > fitmap #5 inMap #1
    10112 
    10113 Fit molecule 6qwl (#5) to map cryosparc_P605_J52_005_volume_map_sharp.mrc (#1)
    10114 using 10408 atoms 
    10115 average map value = 0.08371, steps = 148 
    10116 shifted from previous position = 3.44 
    10117 rotated from previous position = 13.1 degrees 
    10118 atoms outside contour = 8245, contour level = 0.18205 
    10119  
    10120 Position of 6qwl (#5) relative to cryosparc_P605_J52_005_volume_map_sharp.mrc
    10121 (#1) coordinates: 
    10122 Matrix rotation and translation 
    10123 -0.19479346 -0.75405376 -0.62726266 401.27085647 
    10124 -0.48729216 -0.48060891 0.72908259 214.91956598 
    10125 -0.85123549 0.44768069 -0.27382501 242.11910519 
    10126 Axis -0.62842894 0.50017791 0.59573411 
    10127 Axis point 0.00000000 289.01489686 291.84840551 
    10128 Rotation angle (degrees) 167.06219877 
    10129 Shift along axis -0.43359193 
    10130  
    10131 
    10132 > color #1 #73fdff7d models
    10133 
    10134 > color #1 #919191ff models
    10135 
    10136 > transparency #1.1 50
    10137 
    10138 > ui mousemode right "rotate selected models"
    10139 
    10140 > view matrix models
    10141 > #5,-0.31775,-0.22971,-0.91993,387.18,-0.68979,-0.60968,0.3905,307.14,-0.65056,0.75863,0.035272,129.44
    10142 
    10143 > view matrix models
    10144 > #5,0.015877,-0.74253,-0.66962,376.93,-0.1707,-0.66189,0.72991,196.46,-0.98519,0.10272,-0.13726,288.4
    10145 
    10146 > view matrix models
    10147 > #5,0.16465,-0.65917,-0.73375,354.23,-0.49922,-0.69727,0.51438,275.94,-0.85069,0.2816,-0.44388,288.33
    10148 
    10149 > view matrix models
    10150 > #5,0.23017,-0.69119,-0.68504,342.92,-0.48299,-0.69225,0.53619,270.01,-0.84483,0.20746,-0.49317,304.5
    10151 
    10152 > view matrix models
    10153 > #5,-0.12458,-0.96183,-0.24366,366.73,-0.59043,-0.1255,0.79727,171.04,-0.79741,0.24319,-0.55226,301.39
    10154 
    10155 > fitmap #5 inMap #1
    10156 
    10157 Fit molecule 6qwl (#5) to map cryosparc_P605_J52_005_volume_map_sharp.mrc (#1)
    10158 using 10408 atoms 
    10159 average map value = 0.1689, steps = 148 
    10160 shifted from previous position = 3.71 
    10161 rotated from previous position = 25.5 degrees 
    10162 atoms outside contour = 6171, contour level = 0.18205 
    10163  
    10164 Position of 6qwl (#5) relative to cryosparc_P605_J52_005_volume_map_sharp.mrc
    10165 (#1) coordinates: 
    10166 Matrix rotation and translation 
    10167 -0.20150913 -0.96146112 0.18704702 316.27169043 
    10168 -0.47814198 0.26322294 0.83791045 97.14518435 
    10169 -0.85485339 0.07941158 -0.51275675 322.91174794 
    10170 Axis -0.55107483 0.75697553 0.35114753 
    10171 Axis point 277.39544968 0.00000000 53.77065303 
    10172 Rotation angle (degrees) 136.51224532 
    10173 Shift along axis 12.63682405 
    10174  
    10175 
    10176 > ui tool show Matchmaker
    10177 
    10178 > matchmaker #!4 to #5
    10179 
    10180 Parameters 
    10181 --- 
    10182 Chain pairing | bb 
    10183 Alignment algorithm | Needleman-Wunsch 
    10184 Similarity matrix | BLOSUM-62 
    10185 SS fraction | 0.3 
    10186 Gap open (HH/SS/other) | 18/18/6 
    10187 Gap extend | 1 
    10188 SS matrix |  |  | H | S | O 
    10189 ---|---|---|--- 
    10190 H | 6 | -9 | -6 
    10191 S |  | 6 | -6 
    10192 O |  |  | 4 
    10193 Iteration cutoff | 2 
    10194  
    10195 Matchmaker 6qwl, chain K (#5) with copy of
    10196 fold_lee_rdrp_trimer_dimer_model_0.cif, chain D (#4), sequence alignment score
    10197 = 3220.4 
    10198 RMSD between 304 pruned atom pairs is 1.202 angstroms; (across all 539 pairs:
    10199 3.076) 
    10200  
    10201 
    10202 > show #!4 models
    10203 
    10204 > select subtract #5
    10205 
    10206 Nothing selected 
    10207 
    10208 > select add #4
    10209 
    10210 17915 atoms, 18256 bonds, 2248 residues, 1 model selected 
    10211 
    10212 > show #!17 models
    10213 
    10214 > hide #!17 models
    10215 
    10216 > show #16 models
    10217 
    10218 > fitmap #16 inMap #1
    10219 
    10220 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
    10221 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    10222 average map value = 0.02551, steps = 60 
    10223 shifted from previous position = 0.0203 
    10224 rotated from previous position = 0.00899 degrees 
    10225 atoms outside contour = 33282, contour level = 0.18205 
    10226  
    10227 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
    10228 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    10229 Matrix rotation and translation 
    10230 -0.39853761 -0.54398284 -0.73841074 190.01468401 
    10231 0.79662785 0.19364235 -0.57261393 186.77367422 
    10232 0.45447975 -0.81644674 0.35617813 271.88910101 
    10233 Axis -0.13464073 -0.65869580 0.74026463 
    10234 Axis point 24.64103535 298.98613745 0.00000000 
    10235 Rotation angle (degrees) 115.11006970 
    10236 Shift along axis 52.65913301 
    10237  
    10238 
    10239 > select subtract #4
    10240 
    10241 3 models selected 
    10242 
    10243 > select add #16
    10244 
    10245 35830 atoms, 36512 bonds, 4496 residues, 1 model selected 
    10246 
    10247 > show #!17 models
    10248 
    10249 > hide #!17 models
    10250 
    10251 > view matrix models
    10252 > #16,0.1141,0.64355,0.75685,187.13,-0.64769,-0.52948,0.54786,183.77,0.75332,-0.55271,0.35641,272.03
    10253 
    10254 > ui mousemode right "translate selected models"
    10255 
    10256 > view matrix models
    10257 > #16,0.1141,0.64355,0.75685,184.9,-0.64769,-0.52948,0.54786,187.5,0.75332,-0.55271,0.35641,265.25
    10258 
    10259 > hide #!4 models
    10260 
    10261 > hide #!5 models
    10262 
    10263 > fitmap #16 inMap #1
    10264 
    10265 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
    10266 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    10267 average map value = 0.02838, steps = 180 
    10268 shifted from previous position = 5.62 
    10269 rotated from previous position = 6.17 degrees 
    10270 atoms outside contour = 33146, contour level = 0.18205 
    10271  
    10272 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
    10273 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    10274 Matrix rotation and translation 
    10275 0.01994521 0.60736919 0.79416928 179.51516129 
    10276 -0.65851942 -0.58971028 0.46754034 187.91497589 
    10277 0.75229940 -0.53230108 0.38820251 264.25538255 
    10278 Axis -0.61960961 0.02594710 -0.78448115 
    10279 Axis point 48.77609816 103.12159126 0.00000000 
    10280 Rotation angle (degrees) 126.21246966 
    10281 Shift along axis -313.65683750 
    10282  
    10283 
    10284 > vop flip #1
    10285 
    10286 Opened cryosparc_P605_J52_005_volume_map_sharp.mrc z flip as #6, grid size
    10287 256,256,256, pixel 1.45, shown at step 1, values float32 
    10288 
    10289 > ui mousemode right "rotate selected models"
    10290 
    10291 > view matrix models
    10292 > #16,-0.12133,0.699,0.70475,180.06,-0.68181,-0.5747,0.45262,188,0.7214,-0.42559,0.54631,264
    10293 
    10294 > hide #16 models
    10295 
    10296 > show #16 models
    10297 
    10298 > hide #!6 models
    10299 
    10300 > show sel atoms
    10301 
    10302 > show #!6 models
    10303 
    10304 > hide sel atoms
    10305 
    10306 > view matrix models
    10307 > #16,0.718,0.68504,0.12328,180.9,-0.38388,0.24199,0.89111,187.77,0.58061,-0.68715,0.43672,264.03
    10308 
    10309 > fitmap #16 inMap #1
    10310 
    10311 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
    10312 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    10313 average map value = 0.0249, steps = 80 
    10314 shifted from previous position = 4.65 
    10315 rotated from previous position = 3.41 degrees 
    10316 atoms outside contour = 33562, contour level = 0.18205 
    10317  
    10318 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
    10319 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    10320 Matrix rotation and translation 
    10321 0.73487227 0.67465663 0.06929052 176.95703039 
    10322 -0.33353775 0.27055661 0.90307901 185.23447248 
    10323 0.59052124 -0.68675872 0.42384800 263.64725060 
    10324 Axis -0.81388768 -0.26683432 -0.51612624 
    10325 Axis point 0.00000000 135.09748730 1.37325732 
    10326 Rotation angle (degrees) 77.60568353 
    10327 Shift along axis -329.52532511 
    10328  
    10329 
    10330 > hide #!6 models
    10331 
    10332 > show #!6 models
    10333 
    10334 > hide #16 models
    10335 
    10336 > show #16 models
    10337 
    10338 > hide #16 models
    10339 
    10340 > show #16 models
    10341 
    10342 > hide #!6 models
    10343 
    10344 > view matrix models
    10345 > #16,-0.33118,-0.35995,0.87221,174,-0.69289,-0.53469,-0.48375,188.27,0.64049,-0.76455,-0.07233,264.9
    10346 
    10347 > view matrix models
    10348 > #16,0.36725,0.23087,0.90101,174.2,-0.79748,-0.42039,0.43277,185.92,0.47869,-0.87748,0.029722,264.58
    10349 
    10350 > show #!6 models
    10351 
    10352 > ui mousemode right "translate selected models"
    10353 
    10354 > view matrix models
    10355 > #16,0.36725,0.23087,0.90101,186.71,-0.79748,-0.42039,0.43277,192.68,0.47869,-0.87748,0.029722,264.67
    10356 
    10357 > ui mousemode right "rotate selected models"
    10358 
    10359 > view matrix models
    10360 > #16,0.43264,0.14693,0.88951,186.54,-0.76249,-0.46683,0.44797,192.53,0.48107,-0.87206,-0.089941,265.02
    10361 
    10362 > ui mousemode right "translate selected models"
    10363 
    10364 > view matrix models
    10365 > #16,0.43264,0.14693,0.88951,208.68,-0.76249,-0.46683,0.44797,180.75,0.48107,-0.87206,-0.089941,252.54
    10366 
    10367 > ui mousemode right "rotate selected models"
    10368 
    10369 > view matrix models
    10370 > #16,0.76702,0.58202,0.27005,210.84,-0.39907,0.10318,0.9111,179.99,0.50241,-0.8066,0.31141,251.46
    10371 
    10372 > ui mousemode right "translate selected models"
    10373 
    10374 > view matrix models
    10375 > #16,0.76702,0.58202,0.27005,208.01,-0.39907,0.10318,0.9111,172.91,0.50241,-0.8066,0.31141,251.22
    10376 
    10377 > view matrix models
    10378 > #16,0.76702,0.58202,0.27005,211.96,-0.39907,0.10318,0.9111,171.63,0.50241,-0.8066,0.31141,260.99
    10379 
    10380 > fitmap #16 inMap #1
    10381 
    10382 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
    10383 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    10384 average map value = 0.02231, steps = 224 
    10385 shifted from previous position = 10.2 
    10386 rotated from previous position = 1.79 degrees 
    10387 atoms outside contour = 33327, contour level = 0.18205 
    10388  
    10389 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
    10390 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    10391 Matrix rotation and translation 
    10392 0.77823158 0.56022746 0.28372663 203.52624885 
    10393 -0.39690425 0.08867892 0.91356613 177.34075699 
    10394 0.48664427 -0.82357830 0.29136940 261.79638330 
    10395 Axis -0.87130505 -0.10177805 -0.48007159 
    10396 Axis point 0.00000000 143.66502300 -15.03836672 
    10397 Rotation angle (degrees) 85.46086838 
    10398 Shift along axis -321.06385108 
    10399  
    10400 
    10401 > fitmap #16 inMap #1
    10402 
    10403 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
    10404 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    10405 average map value = 0.02231, steps = 76 
    10406 shifted from previous position = 0.0173 
    10407 rotated from previous position = 0.0136 degrees 
    10408 atoms outside contour = 33332, contour level = 0.18205 
    10409  
    10410 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
    10411 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    10412 Matrix rotation and translation 
    10413 0.77827265 0.56020428 0.28365971 203.53331789 
    10414 -0.39673355 0.08853928 0.91365382 177.35615554 
    10415 0.48671776 -0.82360909 0.29115953 261.79855369 
    10416 Axis -0.87135379 -0.10184722 -0.47996846 
    10417 Axis point 0.00000000 143.67151066 -15.00059713 
    10418 Rotation angle (degrees) 85.46973200 
    10419 Shift along axis -321.06780743 
    10420  
    10421 
    10422 > ui tool show "Side View"
    10423 
    10424 > ui mousemode right "rotate selected models"
    10425 
    10426 > view matrix models
    10427 > #16,0.40022,-0.13753,-0.90604,206.2,0.7783,0.57297,0.25682,178.9,0.48381,-0.80795,0.33636,261.7
    10428 
    10429 > ui mousemode right "translate selected models"
    10430 
    10431 > view matrix models
    10432 > #16,0.40022,-0.13753,-0.90604,180.47,0.7783,0.57297,0.25682,184.54,0.48381,-0.80795,0.33636,262.43
    10433 
    10434 > ui mousemode right "rotate selected models"
    10435 
    10436 > view matrix models
    10437 > #16,0.4171,-0.16282,-0.89416,180.38,0.76534,0.59354,0.24893,184.61,0.49018,-0.78816,0.37218,262.35
    10438 
    10439 > view matrix models
    10440 > #16,0.11268,-0.37325,-0.92086,180.41,0.85955,0.50154,-0.098114,185.37,0.49847,-0.78047,0.37734,262.34
    10441 
    10442 > ui mousemode right "translate selected models"
    10443 
    10444 > view matrix models
    10445 > #16,0.11268,-0.37325,-0.92086,189.14,0.85955,0.50154,-0.098114,183.83,0.49847,-0.78047,0.37734,262.09
    10446 
    10447 > fitmap #16 inMap #1
    10448 
    10449 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
    10450 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    10451 average map value = 0.0263, steps = 152 
    10452 shifted from previous position = 13.4 
    10453 rotated from previous position = 11.6 degrees 
    10454 atoms outside contour = 33251, contour level = 0.18205 
    10455  
    10456 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
    10457 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    10458 Matrix rotation and translation 
    10459 0.12557152 -0.41925935 -0.89914037 192.02988513 
    10460 0.94026202 0.33938439 -0.02693680 196.79813862 
    10461 0.31644771 -0.84204502 0.43683065 261.31997154 
    10462 Axis -0.40804640 -0.60852821 0.68058178 
    10463 Axis point 45.33098925 343.75436544 0.00000000 
    10464 Rotation angle (degrees) 92.81473995 
    10465 Shift along axis -20.26471141 
    10466  
    10467 
    10468 > show #!4 models
    10469 
    10470 > show #!5 models
    10471 
    10472 > hide #!4 models
    10473 
    10474 > hide #16 models
    10475 
    10476 > select add #5
    10477 
    10478 46238 atoms, 47180 bonds, 24 pseudobonds, 5766 residues, 4 models selected 
    10479 
    10480 > ui mousemode right "rotate selected models"
    10481 
    10482 > view matrix models
    10483 > #16,0.28708,-0.49781,-0.81839,210.95,0.95538,0.21078,0.20692,219.86,0.069488,-0.84128,0.53611,253.35,#5,-0.38682,-0.89832,0.2083,329.92,-0.61393,0.41941,0.66872,117.84,-0.68809,0.13079,-0.71374,321.16
    10484 
    10485 > ui mousemode right "translate selected models"
    10486 
    10487 > view matrix models
    10488 > #16,0.28708,-0.49781,-0.81839,195.41,0.95538,0.21078,0.20692,252.11,0.069488,-0.84128,0.53611,262.37,#5,-0.38682,-0.89832,0.2083,314.38,-0.61393,0.41941,0.66872,150.08,-0.68809,0.13079,-0.71374,330.18
    10489 
    10490 > ui mousemode right "rotate selected models"
    10491 
    10492 > view matrix models
    10493 > #16,0.19764,-0.39104,-0.8989,177.32,0.95757,0.27323,0.091673,241.3,0.20976,-0.87888,0.42845,268.29,#5,-0.23715,-0.93829,0.25172,293.43,-0.55479,0.34351,0.75777,140.01,-0.79748,0.040055,-0.60202,341.9
    10494 
    10495 > view matrix models
    10496 > #16,0.19657,-0.2309,-0.95291,159.56,0.97474,-0.059079,0.21539,279.39,-0.10603,-0.97118,0.21345,252.54,#5,-0.12386,-0.91849,0.37555,258.1,-0.80313,0.31506,0.50568,212.72,-0.58278,-0.23899,-0.77669,375.03
    10497 
    10498 > ui mousemode right "translate selected models"
    10499 
    10500 > view matrix models
    10501 > #16,0.19657,-0.2309,-0.95291,176.42,0.97474,-0.059079,0.21539,269.81,-0.10603,-0.97118,0.21345,238.14,#5,-0.12386,-0.91849,0.37555,274.96,-0.80313,0.31506,0.50568,203.13,-0.58278,-0.23899,-0.77669,360.63
    10502 
    10503 > ui mousemode right "rotate selected models"
    10504 
    10505 > view matrix models
    10506 > #16,0.3438,-0.70901,0.61572,296.36,-0.80947,0.10861,0.57704,181.51,-0.47599,-0.69679,-0.53658,161.69,#5,-0.82191,0.29977,-0.48436,323.33,0.56961,0.43803,-0.69547,166.6,0.0036824,-0.84751,-0.53077,329.65
    10507 
    10508 > show #!1 models
    10509 
    10510 > hide #!6 models
    10511 
    10512 > view matrix models
    10513 > #16,0.35091,-0.69647,0.62593,295.94,-0.81158,0.10724,0.57432,181.42,-0.46712,-0.70953,-0.52761,163.73,#5,-0.82099,0.31529,-0.47598,319.92,0.57079,0.4347,-0.69658,167.05,-0.012718,-0.84358,-0.53686,332.19
    10514 
    10515 > ui mousemode right "translate selected models"
    10516 
    10517 > view matrix models
    10518 > #16,0.35091,-0.69647,0.62593,299.05,-0.81158,0.10724,0.57432,160.11,-0.46712,-0.70953,-0.52761,171.09,#5,-0.82099,0.31529,-0.47598,323.03,0.57079,0.4347,-0.69658,145.74,-0.012718,-0.84358,-0.53686,339.55
    10519 
    10520 > ui mousemode right "rotate selected models"
    10521 
    10522 > view matrix models
    10523 > #16,0.35176,-0.70192,0.61933,299.33,-0.79299,0.12813,0.59561,159.92,-0.49743,-0.70064,-0.51154,169.43,#5,-0.82394,0.30722,-0.47617,324.56,0.56653,0.46541,-0.68002,139.83,0.012699,-0.83006,-0.55752,337.12
    10524 
    10525 > view matrix models
    10526 > #16,0.35088,-0.69633,0.6261,299.04,-0.81204,0.10671,0.57377,160.12,-0.46634,-0.70974,-0.528,171.13,#5,-0.82092,0.3155,-0.47598,322.99,0.57089,0.43392,-0.69699,145.89,-0.013365,-0.84391,-0.53633,339.61
    10527 
    10528 > view matrix models
    10529 > #16,0.35157,-0.70048,0.62107,299.26,-0.79798,0.12267,0.59007,159.97,-0.48952,-0.70305,-0.51584,169.87,#5,-0.82319,0.30935,-0.4761,324.16,0.56774,0.45739,-0.68445,141.38,0.006026,-0.83373,-0.55214,337.78
    10530 
    10531 > view matrix models
    10532 > #16,0.85038,0.4804,-0.21463,174.52,-0.34197,0.81463,0.46843,110.56,0.39988,-0.32495,0.85703,235.48,#5,-0.28695,0.14214,0.94734,76.122,0.69391,0.71262,0.10326,-20.104,-0.66042,0.687,-0.30312,186.43
    10533 
    10534 > view matrix models
    10535 > #16,-0.10842,-0.79896,0.59153,284.91,0.81019,-0.41582,-0.41314,248.05,0.57606,0.43446,0.69239,164.02,#5,-0.53824,0.17122,-0.82521,352.76,-0.79679,-0.42246,0.43205,291.78,-0.27464,0.89006,0.36381,13.539
    10536 
    10537 > view matrix models
    10538 > #16,-0.095734,-0.93158,-0.35071,258.24,0.86458,0.096785,-0.49309,197.97,0.4933,-0.35042,0.79616,239.92,#5,-0.46384,-0.72385,-0.51077,421,-0.49387,-0.26737,0.82741,174.46,-0.73549,0.63604,-0.23348,193.91
    10539 
    10540 > fitmap #5 inMap #1
    10541 
    10542 Fit molecule 6qwl (#5) to map cryosparc_P605_J52_005_volume_map_sharp.mrc (#1)
    10543 using 10408 atoms 
    10544 average map value = 0.08261, steps = 64 
    10545 shifted from previous position = 3.52 
    10546 rotated from previous position = 4.5 degrees 
    10547 atoms outside contour = 8207, contour level = 0.18205 
    10548  
    10549 Position of 6qwl (#5) relative to cryosparc_P605_J52_005_volume_map_sharp.mrc
    10550 (#1) coordinates: 
    10551 Matrix rotation and translation 
    10552 -0.52522278 -0.70629917 -0.47463926 424.09664524 
    10553 -0.48619116 -0.20869868 0.84856523 159.72829574 
    10554 -0.69839753 0.67645123 -0.23378313 183.98646498 
    10555 Axis -0.48081314 0.62508522 0.61488795 
    10556 Axis point 286.35485513 -0.00000000 -17.48781489 
    10557 Rotation angle (degrees) 169.68951791 
    10558 Shift along axis 9.06361897 
    10559  
    10560 
    10561 > ui tool show Matchmaker
    10562 
    10563 > hide #!5 models
    10564 
    10565 > show #16 models
    10566 
    10567 > show #!4 models
    10568 
    10569 > hide #16 models
    10570 
    10571 > view matrix models
    10572 > #16,-0.095734,-0.93158,-0.35071,258.24,0.86458,0.096785,-0.49309,197.97,0.4933,-0.35042,0.79616,239.92,#5,-0.52522,-0.7063,-0.47464,424.1,-0.48619,-0.2087,0.84857,159.73,-0.6984,0.67645,-0.23378,183.99
    10573 
    10574 [Repeated 1 time(s)]
    10575 
    10576 > select add #4
    10577 
    10578 64153 atoms, 65436 bonds, 24 pseudobonds, 8014 residues, 5 models selected 
    10579 
    10580 > select subtract #5
    10581 
    10582 53745 atoms, 54768 bonds, 6744 residues, 5 models selected 
    10583 
    10584 > select subtract #16
    10585 
    10586 17915 atoms, 18256 bonds, 2248 residues, 4 models selected 
    10587 
    10588 > view matrix models
    10589 > #4,0.12001,0.77876,0.61573,157.32,-0.2814,0.62146,-0.73116,160.92,-0.95206,-0.085517,0.29372,112.9
    10590 
    10591 > view matrix models
    10592 > #4,0.76586,-0.38531,0.51478,200.44,0.51252,0.84925,-0.12684,171.4,-0.38831,0.36098,0.84789,113.04
    10593 
    10594 > view matrix models
    10595 > #4,0.12295,0.16061,0.97933,180.58,0.87446,0.44909,-0.18343,187.81,-0.46927,0.87893,-0.08523,85.222
    10596 
    10597 > view matrix models
    10598 > #4,-0.43952,-0.22993,0.8683,183.88,0.41758,0.80356,0.42416,177.95,-0.79526,0.54902,-0.25717,89.068
    10599 
    10600 > view matrix models
    10601 > #4,0.051839,-0.32189,0.94536,194.08,0.19194,0.93219,0.30689,169.66,-0.98004,0.16554,0.11011,102.68
    10602 
    10603 > view matrix models
    10604 > #4,-0.026092,-0.17933,0.98344,189.11,0.068017,0.98118,0.18073,165.06,-0.99734,0.071606,-0.013403,103.91
    10605 
    10606 > view matrix models
    10607 > #4,0.20985,-0.34753,0.91389,196.58,0.57629,0.79904,0.17153,177.25,-0.78984,0.49067,0.36796,98.189
    10608 
    10609 > view matrix models
    10610 > #4,-0.227,-0.084103,0.97026,183.38,0.77067,0.59359,0.23176,186.82,-0.59543,0.80036,-0.069928,86.151
    10611 
    10612 > ui mousemode right "translate selected models"
    10613 
    10614 > view matrix models
    10615 > #4,-0.227,-0.084103,0.97026,190.01,0.77067,0.59359,0.23176,179.8,-0.59543,0.80036,-0.069928,102.93
    10616 
    10617 > color bfactor sel
    10618 
    10619 17915 atoms, 2248 residues, 3 surfaces, atom bfactor range 19 to 94.1 
    10620 
    10621 > ui mousemode right "rotate selected models"
    10622 
    10623 > view matrix models
    10624 > #4,-0.24769,-0.059219,0.96703,188.94,0.60416,0.77085,0.20195,171.81,-0.75739,0.63426,-0.15515,104.91
    10625 
    10626 > view matrix models
    10627 > #4,-0.05944,-0.77535,0.62873,209.5,0.90828,0.21928,0.35628,194.56,-0.41411,0.59224,0.6912,120.55
    10628 
    10629 > view matrix models
    10630 > #4,0.13056,-0.76461,0.63113,211.71,0.90117,0.35692,0.24598,188.96,-0.41334,0.53664,0.73565,122.78
    10631 
    10632 > ui mousemode right "translate selected models"
    10633 
    10634 > view matrix models
    10635 > #4,0.13056,-0.76461,0.63113,208.73,0.90117,0.35692,0.24598,197.7,-0.41334,0.53664,0.73565,119.29
    10636 
    10637 > view matrix models
    10638 > #4,0.13056,-0.76461,0.63113,213.47,0.90117,0.35692,0.24598,202.67,-0.41334,0.53664,0.73565,126.05
    10639 
    10640 > ui mousemode right "rotate selected models"
    10641 
    10642 > view matrix models
    10643 > #4,-0.1573,-0.59734,0.78641,206.34,0.89413,0.25194,0.37021,207.24,-0.41927,0.76139,0.49447,116.27
    10644 
    10645 > fitmap #4 inMap #1
    10646 
    10647 Fit molecule copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) to map
    10648 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 17915 atoms 
    10649 average map value = 0.06099, steps = 116 
    10650 shifted from previous position = 8.74 
    10651 rotated from previous position = 13.4 degrees 
    10652 atoms outside contour = 15474, contour level = 0.18205 
    10653  
    10654 Position of copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) relative to
    10655 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    10656 Matrix rotation and translation 
    10657 -0.19703977 -0.54596940 0.81430506 201.04356649 
    10658 0.78030079 0.41552336 0.46740879 192.89864757 
    10659 -0.59355370 0.72750100 0.34414574 113.06645958 
    10660 Axis 0.13327189 0.72139032 0.67958414 
    10661 Axis point 53.88533173 0.00000000 -127.94224637 
    10662 Rotation angle (degrees) 102.63182812 
    10663 Shift along axis 242.78684689 
    10664  
    10665 
    10666 > hide #!4 models
    10667 
    10668 > show #!4 models
    10669 
    10670 > view matrix models
    10671 > #4,-0.19926,0.97952,0.028807,145.01,-0.94836,-0.20016,0.24608,186.46,0.24681,0.021715,0.96882,153.09
    10672 
    10673 > ui mousemode right "translate selected models"
    10674 
    10675 > view matrix models
    10676 > #4,-0.19926,0.97952,0.028807,156.36,-0.94836,-0.20016,0.24608,173.98,0.24681,0.021715,0.96882,151.67
    10677 
    10678 > hide #!4 models
    10679 
    10680 > volume #1 level 0.1094
    10681 
    10682 > show #!4 models
    10683 
    10684 > ui mousemode right "rotate selected models"
    10685 
    10686 > view matrix models
    10687 > #4,0.022809,0.80442,0.59362,171.23,-0.99753,-0.021166,0.067012,165.75,0.066471,-0.59368,0.80195,166.27
    10688 
    10689 > ui mousemode right "translate selected models"
    10690 
    10691 > view matrix models
    10692 > #4,0.022809,0.80442,0.59362,98.79,-0.99753,-0.021166,0.067012,275.2,0.066471,-0.59368,0.80195,172.18
    10693 
    10694 > ui mousemode right "rotate selected models"
    10695 
    10696 > view matrix models
    10697 > #4,-0.73891,0.39731,0.5442,100.69,-0.64653,-0.64554,-0.40655,293.52,0.18977,-0.65224,0.73387,174.82
    10698 
    10699 > view matrix models
    10700 > #4,0.98592,0.12003,0.1164,126.98,-0.16612,0.7821,0.6006,267.67,-0.018951,-0.61149,0.79103,171.48
    10701 
    10702 > ui mousemode right "translate selected models"
    10703 
    10704 > view matrix models
    10705 > #4,0.98592,0.12003,0.1164,222.02,-0.16612,0.7821,0.6006,166.57,-0.018951,-0.61149,0.79103,159.37
    10706 
    10707 > hide #!4 models
    10708 
    10709 > show #!4 models
    10710 
    10711 > ui mousemode right "rotate selected models"
    10712 
    10713 > view matrix models
    10714 > #4,0.98592,0.12031,0.11614,222,-0.16618,0.78223,0.60042,166.56,-0.018612,-0.61127,0.7912,159.37
    10715 
    10716 > fitmap #4 inMap #1
    10717 
    10718 Fit molecule copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) to map
    10719 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 17915 atoms 
    10720 average map value = 0.05453, steps = 152 
    10721 shifted from previous position = 9.82 
    10722 rotated from previous position = 11.5 degrees 
    10723 atoms outside contour = 13536, contour level = 0.1094 
    10724  
    10725 Position of copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) relative to
    10726 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    10727 Matrix rotation and translation 
    10728 0.97217171 -0.01254972 0.23393303 223.36029917 
    10729 -0.15245228 0.72430588 0.67241302 165.83582297 
    10730 -0.17787766 -0.68936453 0.70223648 165.20229996 
    10731 Axis -0.95259510 0.28807116 -0.09786510 
    10732 Axis point 0.00000000 300.72095953 -200.94465099 
    10733 Rotation angle (degrees) 45.62455794 
    10734 Shift along axis -181.16694792 
    10735  
    10736 
    10737 > view matrix models
    10738 > #4,0.86307,-0.36978,0.34406,234.18,-0.030955,0.64118,0.76677,171.09,-0.50414,-0.67242,0.54194,158.52
    10739 
    10740 > view matrix models
    10741 > #4,0.89101,-0.3832,0.24346,233.79,0.065971,0.63985,0.76567,172.39,-0.44917,-0.66615,0.59539,159.67
    10742 
    10743 > ui mousemode right "translate selected models"
    10744 
    10745 > view matrix models
    10746 > #4,0.89101,-0.3832,0.24346,230.38,0.065971,0.63985,0.76567,180.48,-0.44917,-0.66615,0.59539,154.39
    10747 
    10748 > volume #1 level 0.1366
    10749 
    10750 > fitmap #4 inMap #1
    10751 
    10752 Fit molecule copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) to map
    10753 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 17915 atoms 
    10754 average map value = 0.05184, steps = 176 
    10755 shifted from previous position = 2.77 
    10756 rotated from previous position = 7.83 degrees 
    10757 atoms outside contour = 14456, contour level = 0.13664 
    10758  
    10759 Position of copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) relative to
    10760 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    10761 Matrix rotation and translation 
    10762 0.93448535 -0.30507923 0.18347696 227.72992244 
    10763 0.08887493 0.69898574 0.70959154 180.48371967 
    10764 -0.34472942 -0.64679639 0.68030585 159.10532733 
    10765 Axis -0.89947611 0.35027518 0.26124705 
    10766 Axis point 0.00000000 360.86693294 -150.65521239 
    10767 Rotation angle (degrees) 48.93700041 
    10768 Shift along axis -100.05285970 
    10769  
    10770 
    10771 > hide #!1 models
    10772 
    10773 > show #!1 models
    10774 
    10775 > hide #!4 models
    10776 
    10777 > show #!4 models
    10778 
    10779 > hide #!1 models
    10780 
    10781 > hide sel atoms
    10782 
    10783 > show sel atoms
    10784 
    10785 > show #!1 models
    10786 
    10787 > view matrix models
    10788 > #4,0.93449,-0.30508,0.18348,226.03,0.088875,0.69899,0.70959,172.04,-0.34473,-0.6468,0.68031,147.35
    10789 
    10790 > ui mousemode right "rotate selected models"
    10791 
    10792 > view matrix models
    10793 > #4,0.41524,-0.15837,0.89582,222.68,-0.12436,0.9656,0.22835,155.48,-0.90117,-0.20622,0.38126,122.91
    10794 
    10795 > view matrix models
    10796 > #4,0.65316,0.056418,0.75511,217.98,-0.1375,0.98948,0.045006,152.44,-0.74463,-0.13322,0.65405,126.12
    10797 
    10798 > fitmap #4 inMap #1
    10799 
    10800 Fit molecule copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) to map
    10801 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 17915 atoms 
    10802 average map value = 0.05826, steps = 276 
    10803 shifted from previous position = 9.35 
    10804 rotated from previous position = 19.3 degrees 
    10805 atoms outside contour = 14372, contour level = 0.13664 
    10806  
    10807 Position of copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) relative to
    10808 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    10809 Matrix rotation and translation 
    10810 0.40150631 0.01758552 0.91568741 207.61560984 
    10811 -0.00312739 0.99983612 -0.01783030 153.30769219 
    10812 -0.91585092 0.00429528 0.40149552 119.72764544 
    10813 Axis 0.01207867 0.99986311 -0.01130748 
    10814 Axis point 195.82877209 0.00000000 -96.70099800 
    10815 Rotation angle (degrees) 66.33308465 
    10816 Shift along axis 154.44060928 
    10817  
    10818 
    10819 > show #16 models
    10820 
    10821 > select subtract #4
    10822 
    10823 3 models selected 
    10824 
    10825 > select add #16
    10826 
    10827 35830 atoms, 36512 bonds, 4496 residues, 1 model selected 
    10828 
    10829 > ui mousemode right "move picked models"
    10830 
    10831 > ui mousemode right "translate selected models"
    10832 
    10833 > view matrix models
    10834 > #16,-0.095734,-0.93158,-0.35071,202.16,0.86458,0.096785,-0.49309,212.39,0.4933,-0.35042,0.79616,261.14
    10835 
    10836 > ui mousemode right "rotate selected models"
    10837 
    10838 > view matrix models
    10839 > #16,0.34584,-0.35632,-0.868,204.15,0.66259,0.74775,-0.042959,212.34,0.66435,-0.56027,0.4947,261.5
    10840 
    10841 > view matrix models
    10842 > #16,0.39645,-0.51568,-0.75954,203.53,0.66701,0.73027,-0.14766,212.61,0.63082,-0.44808,0.63347,261.31
    10843 
    10844 > view matrix models
    10845 > #16,0.45271,-0.4045,-0.79463,203.76,0.37733,0.89436,-0.2403,213.42,0.80788,-0.19105,0.55752,261.78
    10846 
    10847 > ui mousemode right "translate selected models"
    10848 
    10849 > view matrix models
    10850 > #16,0.45271,-0.4045,-0.79463,204.43,0.37733,0.89436,-0.2403,173.74,0.80788,-0.19105,0.55752,268.46
    10851 
    10852 > select clear
    10853 
    10854 > ui mousemode right select
    10855 
    10856 Drag select of 1835 residues 
    10857 
    10858 > select up
    10859 
    10860 16068 atoms, 16358 bonds, 2017 residues, 1 model selected 
    10861 
    10862 > select up
    10863 
    10864 17915 atoms, 18256 bonds, 2248 residues, 1 model selected 
    10865 
    10866 > select up
    10867 
    10868 35830 atoms, 36512 bonds, 4496 residues, 1 model selected 
    10869 
    10870 > select down
    10871 
    10872 17915 atoms, 18256 bonds, 2248 residues, 1 model selected 
    10873 
    10874 > hide sel cartoons
    10875 
    10876 > select clear
    10877 
    10878 > select add #16
    10879 
    10880 35830 atoms, 36512 bonds, 4496 residues, 1 model selected 
    10881 
    10882 > hide #!4 models
    10883 
    10884 > ui mousemode right rotate
    10885 
    10886 > ui mousemode right "rotate selected models"
    10887 
    10888 > view matrix models
    10889 > #16,-0.54138,0.0051342,0.84076,197.72,-0.13278,-0.98796,-0.079463,226.73,0.83023,-0.15465,0.53554,267.38
    10890 
    10891 > ui mousemode right "translate selected models"
    10892 
    10893 > view matrix models
    10894 > #16,-0.54138,0.0051342,0.84076,199.35,-0.13278,-0.98796,-0.079463,205.16,0.83023,-0.15465,0.53554,260.48
    10895 
    10896 > ui mousemode right "rotate selected models"
    10897 
    10898 > view matrix models
    10899 > #16,-0.4976,0.42472,0.75631,186.05,-0.32904,-0.89918,0.28847,204.12,0.80258,-0.10532,0.58718,259.2
    10900 
    10901 > ui mousemode right "translate selected models"
    10902 
    10903 > view matrix models
    10904 > #16,-0.4976,0.42472,0.75631,175.06,-0.32904,-0.89918,0.28847,199.34,0.80258,-0.10532,0.58718,263.42
    10905 
    10906 > fitmap #16 inMap #1
    10907 
    10908 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
    10909 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    10910 average map value = 0.02909, steps = 212 
    10911 shifted from previous position = 14.7 
    10912 rotated from previous position = 2.89 degrees 
    10913 atoms outside contour = 32381, contour level = 0.13664 
    10914  
    10915 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
    10916 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    10917 Matrix rotation and translation 
    10918 -0.52233503 0.40277560 0.75162349 165.43127810 
    10919 -0.28536142 -0.91316451 0.29103154 209.90195815 
    10920 0.80357634 -0.06246839 0.59191445 260.24620435 
    10921 Axis -0.45591309 -0.06700420 -0.88749856 
    10922 Axis point 37.28592338 92.92989442 0.00000000 
    10923 Rotation angle (degrees) 157.18956560 
    10924 Shift along axis -320.45473009 
    10925  
    10926 
    10927 > view matrix models
    10928 > #16,-0.52234,0.40278,0.75162,165.4,-0.28536,-0.91316,0.29103,210.7,0.80358,-0.062468,0.59191,261.7
    10929 
    10930 > ui mousemode right "rotate selected models"
    10931 
    10932 > view matrix models
    10933 > #16,-0.47306,0.41046,0.77957,166.14,-0.32277,-0.90407,0.28015,209.8,0.81978,-0.11909,0.56016,263.29
    10934 
    10935 > view matrix models
    10936 > #16,-0.64642,0.35817,0.67368,164.23,-0.26174,-0.93348,0.24516,211.1,0.71668,-0.017851,0.69717,260.41
    10937 
    10938 > view matrix models
    10939 > #16,-0.52667,0.28914,0.79939,169.39,0.094315,-0.9147,0.39298,216.93,0.84482,0.28237,0.45447,250.05
    10940 
    10941 > ui mousemode right "translate selected models"
    10942 
    10943 > view matrix models
    10944 > #16,-0.52667,0.28914,0.79939,168.62,0.094315,-0.9147,0.39298,223.02,0.84482,0.28237,0.45447,267.49
    10945 
    10946 > ui mousemode right "rotate selected models"
    10947 
    10948 > view matrix models
    10949 > #16,0.53768,-0.65639,-0.5292,196.29,0.25863,0.72578,-0.63746,162.8,0.8025,0.20588,0.56,270.51
    10950 
    10951 > view matrix models
    10952 > #16,0.49896,-0.59259,-0.63236,192.62,0.47673,0.79704,-0.37074,166.59,0.72371,-0.11648,0.6802,280.77
    10953 
    10954 > ui mousemode right "translate selected models"
    10955 
    10956 > view matrix models
    10957 > #16,0.49896,-0.59259,-0.63236,204.96,0.47673,0.79704,-0.37074,136.45,0.72371,-0.11648,0.6802,264.56
    10958 
    10959 > fitmap #16 inMap #1
    10960 
    10961 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
    10962 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    10963 average map value = 0.02129, steps = 184 
    10964 shifted from previous position = 22.2 
    10965 rotated from previous position = 18.6 degrees 
    10966 atoms outside contour = 33069, contour level = 0.13664 
    10967  
    10968 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
    10969 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    10970 Matrix rotation and translation 
    10971 0.62149755 -0.30828276 -0.72021004 195.59553321 
    10972 0.32020110 0.93898469 -0.12561420 156.84094955 
    10973 0.71499092 -0.15254315 0.68228918 264.00282331 
    10974 Axis -0.01718493 -0.91588527 0.40107213 
    10975 Axis point -220.55886546 0.00000000 386.51343740 
    10976 Rotation angle (degrees) 51.58260133 
    10977 Shift along axis -41.12543605 
    10978  
    10979 
    10980 > view matrix models
    10981 > #16,0.6215,-0.30828,-0.72021,192.21,0.3202,0.93898,-0.12561,167.12,0.71499,-0.15254,0.68229,273.52
    10982 
    10983 > ui mousemode right "rotate selected models"
    10984 
    10985 > view matrix models
    10986 > #16,-0.056266,-0.89171,0.44909,214.77,0.99064,0.0061552,0.13634,207.67,-0.12434,0.45256,0.88302,246.18
    10987 
    10988 > view matrix models
    10989 > #16,0.0021121,-0.7606,0.64922,213.84,0.77471,-0.40927,-0.482,210.41,0.63232,0.50397,0.58837,251.16
    10990 
    10991 > view matrix models
    10992 > #16,0.59757,-0.012686,0.80171,200.47,0.75676,0.33937,-0.5587,186.28,-0.26499,0.94057,0.2124,221.55
    10993 
    10994 > view matrix models
    10995 > #16,0.57421,0.1476,0.80529,195.28,0.81698,-0.16727,-0.55188,202.72,0.053247,0.9748,-0.21664,219.71
    10996 
    10997 > ui mousemode right "translate selected models"
    10998 
    10999 > view matrix models
    11000 > #16,0.57421,0.1476,0.80529,197.81,0.81698,-0.16727,-0.55188,195.44,0.053247,0.9748,-0.21664,203.05
    11001 
    11002 > view matrix models
    11003 > #16,0.57421,0.1476,0.80529,225.26,0.81698,-0.16727,-0.55188,217.29,0.053247,0.9748,-0.21664,202.64
    11004 
    11005 > view matrix models
    11006 > #16,0.57421,0.1476,0.80529,233.63,0.81698,-0.16727,-0.55188,207.03,0.053247,0.9748,-0.21664,195.36
    11007 
    11008 > ui mousemode right "rotate selected models"
    11009 
    11010 > view matrix models
    11011 > #16,0.61045,0.062325,0.7896,236.55,0.79197,-0.033119,-0.60967,201.91,-0.011846,0.99751,-0.069577,195.52
    11012 
    11013 > fitmap #16 inMap #1
    11014 
    11015 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
    11016 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    11017 average map value = 0.02255, steps = 232 
    11018 shifted from previous position = 19.9 
    11019 rotated from previous position = 16.3 degrees 
    11020 atoms outside contour = 32606, contour level = 0.13664 
    11021  
    11022 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
    11023 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    11024 Matrix rotation and translation 
    11025 0.55302812 -0.17299936 0.81500371 220.95865519 
    11026 0.79629036 -0.17803680 -0.57812155 214.10831876 
    11027 0.24511531 0.96869708 0.03929836 196.14545114 
    11028 Axis 0.80887290 0.29800991 0.50686756 
    11029 Axis point 0.00000000 55.91816647 80.13727705 
    11030 Rotation angle (degrees) 107.02896823 
    11031 Shift along axis 341.95363571 
    11032  
    11033 
    11034 > ui mousemode right "translate selected models"
    11035 
    11036 > view matrix models
    11037 > #16,0.55303,-0.173,0.815,213.74,0.79629,-0.17804,-0.57812,279.78,0.24512,0.9687,0.039298,231.16
    11038 
    11039 > ui mousemode right "rotate selected models"
    11040 
    11041 > view matrix models
    11042 > #16,0.81665,0.10362,0.56776,205.85,0.57709,-0.15843,-0.80116,273.7,0.0069366,0.98192,-0.18918,224.96
    11043 
    11044 > view matrix models
    11045 > #16,0.78482,0.050307,0.61768,207.64,0.61718,-0.15362,-0.77168,274.42,0.056065,0.98685,-0.15161,225.89
    11046 
    11047 > view matrix models
    11048 > #16,0.254,0.10957,0.96098,202.81,0.95993,-0.15023,-0.23659,285.05,0.11844,0.98256,-0.14333,226.94
    11049 
    11050 > view matrix models
    11051 > #16,0.27245,0.34696,0.89744,195.02,-0.40599,-0.80417,0.43415,294.93,0.87232,-0.48264,-0.078238,282.67
    11052 
    11053 > view matrix models
    11054 > #16,0.20124,0.22981,0.9522,198.32,0.52486,-0.84606,0.093268,304.53,0.82706,0.481,-0.29088,249.99
    11055 
    11056 > view matrix models
    11057 > #16,-0.55852,0.82834,-0.043759,158.35,-0.010181,0.045903,0.99889,280.57,0.82943,0.55834,-0.017204,250.82
    11058 
    11059 > ui mousemode right "translate selected models"
    11060 
    11061 > view matrix models
    11062 > #16,-0.55852,0.82834,-0.043759,167.21,-0.010181,0.045903,0.99889,180.79,0.82943,0.55834,-0.017204,245.87
    11063 
    11064 > view matrix models
    11065 > #16,-0.55852,0.82834,-0.043759,157.31,-0.010181,0.045903,0.99889,186.56,0.82943,0.55834,-0.017204,243.16
    11066 
    11067 > view matrix models
    11068 > #16,-0.55852,0.82834,-0.043759,156.65,-0.010181,0.045903,0.99889,179.03,0.82943,0.55834,-0.017204,237.99
    11069 
    11070 > ui mousemode right "rotate selected models"
    11071 
    11072 > view matrix models
    11073 > #16,-0.69199,0.65543,-0.30258,157.2,-0.15768,0.2718,0.94935,169.57,0.70447,0.70465,-0.084738,231.07
    11074 
    11075 > ui mousemode right "translate selected models"
    11076 
    11077 > view matrix models
    11078 > #16,-0.69199,0.65543,-0.30258,147.35,-0.15768,0.2718,0.94935,174.84,0.70447,0.70465,-0.084738,233.78
    11079 
    11080 > fitmap #16 inMap #1
    11081 
    11082 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
    11083 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    11084 average map value = 0.03092, steps = 2000 
    11085 shifted from previous position = 17.9 
    11086 rotated from previous position = 10.3 degrees 
    11087 atoms outside contour = 32151, contour level = 0.13664 
    11088  
    11089 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
    11090 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    11091 Matrix rotation and translation 
    11092 -0.71148024 0.62528943 -0.32063835 139.67150460 
    11093 -0.28929107 0.15519625 0.94457650 183.77785824 
    11094 0.64039559 0.76480532 0.07047158 220.24411436 
    11095 Axis -0.13427874 -0.71783715 -0.68313911 
    11096 Axis point 48.76072910 0.00000000 49.22202875 
    11097 Rotation angle (degrees) 137.97957241 
    11098 Shift along axis -301.13485642 
    11099  
    11100 
    11101 > fitmap #16 inMap #1
    11102 
    11103 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
    11104 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    11105 average map value = 0.03095, steps = 2000 
    11106 shifted from previous position = 0.387 
    11107 rotated from previous position = 0.512 degrees 
    11108 atoms outside contour = 32133, contour level = 0.13664 
    11109  
    11110 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
    11111 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    11112 Matrix rotation and translation 
    11113 -0.70814881 0.62512107 -0.32825124 139.70967030 
    11114 -0.29721084 0.15779215 0.94168324 183.41548583 
    11115 0.64046152 0.76441168 0.07405242 220.14895902 
    11116 Axis -0.13138344 -0.71795398 -0.68357917 
    11117 Axis point 49.09536930 0.00000000 49.84896274 
    11118 Rotation angle (degrees) 137.57424163 
    11119 Shift along axis -300.52865711 
    11120  
    11121 
    11122 > ui mousemode right "rotate selected models"
    11123 
    11124 > ui mousemode right "translate selected models"
    11125 
    11126 > view matrix models
    11127 > #16,-0.70815,0.62512,-0.32825,136.04,-0.29721,0.15779,0.94168,183.17,0.64046,0.76441,0.074052,252.44
    11128 
    11129 > ui mousemode right "rotate selected models"
    11130 
    11131 > view matrix models
    11132 > #16,-0.6233,0.55555,0.55033,149.5,0.093262,-0.64593,0.75768,210.89,0.7764,0.52359,0.3508,264.84
    11133 
    11134 > view matrix models
    11135 > #16,-0.1756,0.69795,0.69428,152.69,-0.93224,-0.34454,0.11058,180.59,0.31639,-0.62782,0.71116,298.35
    11136 
    11137 > ui mousemode right "translate selected models"
    11138 
    11139 > view matrix models
    11140 > #16,-0.1756,0.69795,0.69428,166.41,-0.93224,-0.34454,0.11058,156.52,0.31639,-0.62782,0.71116,272.48
    11141 
    11142 > view matrix models
    11143 > #16,-0.1756,0.69795,0.69428,146.74,-0.93224,-0.34454,0.11058,156.47,0.31639,-0.62782,0.71116,277.99
    11144 
    11145 > view matrix models
    11146 > #16,-0.1756,0.69795,0.69428,147.96,-0.93224,-0.34454,0.11058,145.21,0.31639,-0.62782,0.71116,274.19
    11147 
    11148 > ui mousemode right "rotate selected models"
    11149 
    11150 > view matrix models
    11151 > #16,-0.64863,0.58056,0.49217,142.99,-0.75307,-0.58326,-0.30445,150.09,0.11032,-0.56812,0.81552,270.85
    11152 
    11153 > ui mousemode right "translate selected models"
    11154 
    11155 > view matrix models
    11156 > #16,-0.64863,0.58056,0.49217,136.59,-0.75307,-0.58326,-0.30445,166.85,0.11032,-0.56812,0.81552,258.42
    11157 
    11158 > view matrix models
    11159 > #16,-0.64863,0.58056,0.49217,149.85,-0.75307,-0.58326,-0.30445,179.93,0.11032,-0.56812,0.81552,239.12
    11160 
    11161 > ui mousemode right "rotate selected models"
    11162 
    11163 > view matrix models
    11164 > #16,-0.69534,0.48106,0.53394,152.78,-0.71,-0.57496,-0.4066,179.06,0.11139,-0.66182,0.74134,241.16
    11165 
    11166 > view matrix models
    11167 > #16,-0.72428,0.42227,0.54508,154.33,-0.67968,-0.57021,-0.4614,178.68,0.11597,-0.70466,0.7,242.05
    11168 
    11169 > view matrix models
    11170 > #16,-0.65542,0.17459,0.73481,165.06,-0.47636,-0.85055,-0.22281,192.74,0.58609,-0.49607,0.64064,241.15
    11171 
    11172 > ui mousemode right "translate selected models"
    11173 
    11174 > view matrix models
    11175 > #16,-0.65542,0.17459,0.73481,165.43,-0.47636,-0.85055,-0.22281,179.69,0.58609,-0.49607,0.64064,283.32
    11176 
    11177 > view matrix models
    11178 > #16,-0.65542,0.17459,0.73481,146.37,-0.47636,-0.85055,-0.22281,192.24,0.58609,-0.49607,0.64064,281.06
    11179 
    11180 > ui mousemode right "rotate selected models"
    11181 
    11182 > view matrix models
    11183 > #16,-0.8779,0.19599,0.4369,139.32,-0.27393,-0.95392,-0.12249,199.25,0.39276,-0.22721,0.89113,273.16
    11184 
    11185 > view matrix models
    11186 > #16,-0.5996,-0.80007,0.01884,168.75,0.13726,-0.126,-0.98249,169.24,0.78844,-0.58652,0.18537,281.22
    11187 
    11188 > view matrix models
    11189 > #16,-0.73006,-0.64273,-0.23218,159.28,0.36691,-0.082027,-0.92663,171.56,0.57653,-0.76169,0.29571,285.09
    11190 
    11191 > ui mousemode right "translate selected models"
    11192 
    11193 > view matrix models
    11194 > #16,-0.73006,-0.64273,-0.23218,164.89,0.36691,-0.082027,-0.92663,173.23,0.57653,-0.76169,0.29571,278.73
    11195 
    11196 > ui mousemode right "rotate selected models"
    11197 
    11198 > view matrix models
    11199 > #16,-0.6319,-0.7618,-0.1427,170.88,0.3235,-0.091936,-0.94175,172.78,0.70431,-0.64125,0.30454,276.81
    11200 
    11201 > view matrix models
    11202 > #16,-0.51597,-0.83593,-0.18706,174.17,0.72684,-0.31167,-0.61202,188.68,0.45331,-0.45175,0.7684,273.06
    11203 
    11204 > ui mousemode right "translate selected models"
    11205 
    11206 > view matrix models
    11207 > #16,-0.51597,-0.83593,-0.18706,181.22,0.72684,-0.31167,-0.61202,214.39,0.45331,-0.45175,0.7684,258.71
    11208 
    11209 > view matrix models
    11210 > #16,-0.51597,-0.83593,-0.18706,192.41,0.72684,-0.31167,-0.61202,210,0.45331,-0.45175,0.7684,262.72
    11211 
    11212 > view matrix models
    11213 > #16,-0.51597,-0.83593,-0.18706,200.06,0.72684,-0.31167,-0.61202,206,0.45331,-0.45175,0.7684,268.21
    11214 
    11215 > ui mousemode right "rotate selected models"
    11216 
    11217 > view matrix models
    11218 > #16,-0.3668,-0.93028,0.0063014,207.17,0.64943,-0.2609,-0.71426,202.24,0.6661,-0.2579,0.69985,264.26
    11219 
    11220 > fitmap #16 inMap #1
    11221 
    11222 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
    11223 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    11224 average map value = 0.02716, steps = 112 
    11225 shifted from previous position = 5.62 
    11226 rotated from previous position = 6.71 degrees 
    11227 atoms outside contour = 32389, contour level = 0.13664 
    11228  
    11229 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
    11230 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    11231 Matrix rotation and translation 
    11232 -0.46294298 -0.88524776 0.04494576 202.10023072 
    11233 0.58718413 -0.34426500 -0.73259564 204.27061025 
    11234 0.66400193 -0.31275858 0.67917852 263.18768658 
    11235 Axis 0.25421107 -0.37483811 0.89155657 
    11236 Axis point -20.20289521 201.53711085 0.00000000 
    11237 Rotation angle (degrees) 124.33390122 
    11238 Shift along axis 209.45441787 
    11239  
    11240 
    11241 > volume #1 level 0.3288
    11242 
    11243 > view matrix models
    11244 > #16,-0.36388,-0.19403,0.91101,192.21,0.56616,-0.82272,0.050911,227.79,0.73963,0.5343,0.40923,235.02
    11245 
    11246 > view matrix models
    11247 > #16,0.096215,-0.09288,0.99102,196.1,0.050987,-0.99387,-0.098097,224.53,0.99405,0.059968,-0.09089,247.15
    11248 
    11249 > ui mousemode right "translate selected models"
    11250 
    11251 > view matrix models
    11252 > #16,0.096215,-0.09288,0.99102,206.89,0.050987,-0.99387,-0.098097,212.98,0.99405,0.059968,-0.09089,257.96
    11253 
    11254 > ui mousemode right "rotate selected models"
    11255 
    11256 > view matrix models
    11257 > #16,-0.32217,-0.059422,0.94481,199.81,-0.10114,-0.99016,-0.096762,210.88,0.94126,-0.12673,0.31299,267.69
    11258 
    11259 > fitmap #16 inMap #1
    11260 
    11261 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
    11262 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    11263 average map value = 0.03495, steps = 208 
    11264 shifted from previous position = 8.8 
    11265 rotated from previous position = 19.7 degrees 
    11266 atoms outside contour = 34764, contour level = 0.32879 
    11267  
    11268 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
    11269 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    11270 Matrix rotation and translation 
    11271 -0.36314223 -0.36164125 0.85868695 193.06663054 
    11272 0.12976179 -0.93224971 -0.33774588 213.20942943 
    11273 0.92265354 -0.01122504 0.38546646 262.91050364 
    11274 Axis 0.55020655 -0.10778742 0.82804265 
    11275 Axis point -13.32797262 126.23533585 0.00000000 
    11276 Rotation angle (degrees) 162.73895372 
    11277 Shift along axis 300.94634066 
    11278  
    11279 
    11280 > ui mousemode right "translate selected models"
    11281 
    11282 > view matrix models
    11283 > #16,-0.36314,-0.36164,0.85869,187.29,0.12976,-0.93225,-0.33775,212.38,0.92265,-0.011225,0.38547,258.33
    11284 
    11285 > ui mousemode right "rotate selected models"
    11286 
    11287 > view matrix models
    11288 > #16,-0.31042,-0.41938,0.85309,189.69,0.12198,-0.90758,-0.40178,210.77,0.94274,-0.020664,0.33289,258.27
    11289 
    11290 > view matrix models
    11291 > #16,-0.55722,-0.4977,0.66468,186.66,0.046121,-0.81778,-0.57368,205.02,0.82908,-0.28901,0.47864,266.71
    11292 
    11293 > fitmap #16 inMap #1
    11294 
    11295 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
    11296 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    11297 average map value = 0.06504, steps = 2000 
    11298 shifted from previous position = 6.14 
    11299 rotated from previous position = 7.78 degrees 
    11300 atoms outside contour = 32995, contour level = 0.32879 
    11301  
    11302 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
    11303 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    11304 Matrix rotation and translation 
    11305 -0.44811604 -0.50799300 0.73561884 190.05353685 
    11306 -0.00091451 -0.82260157 -0.56861739 200.41729782 
    11307 0.89397491 -0.25547932 0.36815640 268.46426211 
    11308 Axis 0.50780288 -0.25679940 0.82230791 
    11309 Axis point -13.68004374 147.41995834 0.00000000 
    11310 Rotation angle (degrees) 162.04159872 
    11311 Shift along axis 265.80297966 
    11312  
    11313 
    11314 > fitmap #16 inMap #1
    11315 
    11316 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map
    11317 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 35830 atoms 
    11318 average map value = 0.0648, steps = 2000 
    11319 shifted from previous position = 0.798 
    11320 rotated from previous position = 0.775 degrees 
    11321 atoms outside contour = 33032, contour level = 0.32879 
    11322  
    11323 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to
    11324 cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates: 
    11325 Matrix rotation and translation 
    11326 -0.45856838 -0.50379365 0.73205666 189.70318165 
    11327 0.00428134 -0.82501957 -0.56508788 200.79929944 
    11328 0.88864879 -0.25599726 0.38048480 267.87409526 
    11329 Axis 0.50260411 -0.25463034 0.82616736 
    11330 Axis point -12.22457591 147.04370353 0.00000000 
    11331 Rotation angle (degrees) 162.09201978 
    11332 Shift along axis 265.52483862 
    11333  
    11334 
    11335 > save /Users/oswanson/Desktop/RdRp.cxs
    11336 
    11337 > close #6
    11338 
    11339 > show #!4 models
    11340 
    11341 > hide #16 models
    11342 
    11343 > show #16 models
     3043[deleted to fit within ticket limits]
    113443044
    113453045> select subtract #16