Changes between Initial Version and Version 1 of Ticket #17082


Ignore:
Timestamp:
Mar 13, 2025, 2:42:57 PM (7 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #17082

    • Property Component Unassigned → Window Toolkit
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Crash on Mac waking from sleep

  • Ticket #17082 – Description

    initial v1  
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     149[deleted to fit within ticket limits]
    1810150],
    1811151  "sharedCache" : {
    … …  
    2042382> hide #!1 models
    2043383
    2044 > open 2ady fromDatabase pdb format mmcif
    2045 
    2046 Summary of feedback from opening 2ady fetched from pdb 
    2047 --- 
    2048 note | Fetching compressed mmCIF 2ady from http://files.rcsb.org/download/2ady.cif 
    2049  
    2050 2ady title: 
    2051 Structural Basis of DNA Recognition by p53 Tetramers (complex IV) [more
    2052 info...] 
    2053  
    2054 Chain information for 2ady #3 
    2055 --- 
    2056 Chain | Description | UniProt 
    2057 A B | Cellular tumor antigen p53 | P53_HUMAN 94-293 
    2058 E F | 5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3' |   
    2059  
    2060 Non-standard residues in 2ady #3 
    2061 --- 
    2062 ZN — zinc ion 
    2063  
    2064 2ady mmCIF Assemblies 
    2065 --- 
    2066 1| author_defined_assembly 
    2067  
    2068 3 atoms have alternate locations. Control/examine alternate locations with
    2069 Altloc Explorer [start tool...] or the altlocs command. 
    2070 
    2071 > open 2ahi fromDatabase pdb format mmcif
    2072 
    2073 Summary of feedback from opening 2ahi fetched from pdb 
    2074 --- 
    2075 note | Fetching compressed mmCIF 2ahi from http://files.rcsb.org/download/2ahi.cif 
    2076  
    2077 2ahi title: 
    2078 Structural Basis of DNA Recognition by p53 Tetramers (complex III) [more
    2079 info...] 
    2080  
    2081 Chain information for 2ahi #4 
    2082 --- 
    2083 Chain | Description | UniProt 
    2084 A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-293 
    2085 E F G H | 5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3' |   
    2086  
    2087 Non-standard residues in 2ahi #4 
    2088 --- 
    2089 ZN — zinc ion 
    2090  
    2091 23 atoms have alternate locations. Control/examine alternate locations with
    2092 Altloc Explorer [start tool...] or the altlocs command. 
    2093 
    2094 > open 2ata fromDatabase pdb format mmcif
    2095 
    2096 Summary of feedback from opening 2ata fetched from pdb 
    2097 --- 
    2098 note | Fetching compressed mmCIF 2ata from http://files.rcsb.org/download/2ata.cif 
    2099  
    2100 2ata title: 
    2101 Structural Basis of DNA Recognition by p53 Tetramers (complex II) [more
    2102 info...] 
    2103  
    2104 Chain information for 2ata #5 
    2105 --- 
    2106 Chain | Description | UniProt 
    2107 A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-293 
    2108 E F G H | 5'-D(*AP*AP*GP*GP*CP*AP*TP*GP*CP*CP*TP*T)-3' |   
    2109  
    2110 Non-standard residues in 2ata #5 
    2111 --- 
    2112 ZN — zinc ion 
    2113  
    2114 9 atoms have alternate locations. Control/examine alternate locations with
    2115 Altloc Explorer [start tool...] or the altlocs command. 
    2116 
    2117 > select add #2
    2118 
    2119 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected 
    2120 
    2121 > select subtract #2
    2122 
    2123 Nothing selected 
    2124 
    2125 > select add #2
    2126 
    2127 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected 
    2128 
    2129 > select add #4
    2130 
    2131 16245 atoms, 14689 bonds, 152 pseudobonds, 3729 residues, 6 models selected 
    2132 
    2133 > select add #3
    2134 
    2135 20034 atoms, 18391 bonds, 189 pseudobonds, 4364 residues, 9 models selected 
    2136 
    2137 > select add #5
    2138 
    2139 27815 atoms, 25698 bonds, 259 pseudobonds, 5919 residues, 12 models selected 
    2140 
    2141 > hide sel atoms
    2142 
    2143 > show sel cartoons
    2144 
    2145 > hide #!2 models
    2146 
    2147 > hide #!4 models
    2148 
    2149 > hide #!5 models
    2150 
    2151 > show #!5 models
    2152 
    2153 > hide #!3 models
    2154 
    2155 > show #!3 models
    2156 
    2157 > show #!4 models
    2158 
    2159 > show #!2 models
    2160 
    2161 > ui tool show Matchmaker
    2162 
    2163 > matchmaker #!3 to #2
    2164 
    2165 Parameters 
    2166 --- 
    2167 Chain pairing | bb 
    2168 Alignment algorithm | Needleman-Wunsch 
    2169 Similarity matrix | BLOSUM-62 
    2170 SS fraction | 0.3 
    2171 Gap open (HH/SS/other) | 18/18/6 
    2172 Gap extend | 1 
    2173 SS matrix |  |  | H | S | O 
    2174 ---|---|---|--- 
    2175 H | 6 | -9 | -6 
    2176 S |  | 6 | -6 
    2177 O |  |  | 4 
    2178 Iteration cutoff | 2 
    2179  
    2180 Matchmaker 2ac0, chain D (#2) with 2ady, chain A (#3), sequence alignment
    2181 score = 1041 
    2182 RMSD between 194 pruned atom pairs is 0.457 angstroms; (across all 196 pairs:
    2183 0.530) 
    2184  
    2185 
    2186 > hide #!5 models
    2187 
    2188 > hide #!4 models
    2189 
    2190 > hide #!2 models
    2191 
    2192 > show #!2 models
    2193 
    2194 > show #!4 models
    2195 
    2196 > show #!5 models
    2197 
    2198 > style sel sphere
    2199 
    2200 Changed 27815 atom styles 
    2201 
    2202 > show sel atoms
    2203 
    2204 > hide sel cartoons
    2205 
    2206 > style sel stick
    2207 
    2208 Changed 27815 atom styles 
    2209 
    2210 > hide #!4 models
    2211 
    2212 > hide #!5 models
    2213 
    2214 > hide #!2 models
    2215 
    2216 > nucleotides sel & #!3 atoms
    2217 
    2218 > style nucleic & sel & #!3 stick
    2219 
    2220 Changed 486 atom styles 
    2221 
    2222 > show #!4 models
    2223 
    2224 > show #!2 models
    2225 
    2226 > show #!5 models
    2227 
    2228 > show sel surfaces
    2229 
    2230 > hide sel surfaces
    2231 
    2232 > select subtract #2
    2233 
    2234 19605 atoms, 18290 bonds, 181 pseudobonds, 4023 residues, 37 models selected 
    2235 
    2236 > select subtract #3
    2237 
    2238 15816 atoms, 14588 bonds, 144 pseudobonds, 3388 residues, 26 models selected 
    2239 
    2240 > select subtract #4
    2241 
    2242 7781 atoms, 7307 bonds, 70 pseudobonds, 1555 residues, 19 models selected 
    2243 
    2244 > select subtract #5
    2245 
    2246 8 models selected 
    2247 
    2248 > show #!1 models
    2249 
    2250 > matchmaker #!1 to #2
    2251 
    2252 Parameters 
    2253 --- 
    2254 Chain pairing | bb 
    2255 Alignment algorithm | Needleman-Wunsch 
    2256 Similarity matrix | BLOSUM-62 
    2257 SS fraction | 0.3 
    2258 Gap open (HH/SS/other) | 18/18/6 
    2259 Gap extend | 1 
    2260 SS matrix |  |  | H | S | O 
    2261 ---|---|---|--- 
    2262 H | 6 | -9 | -6 
    2263 S |  | 6 | -6 
    2264 O |  |  | 4 
    2265 Iteration cutoff | 2 
    2266  
    2267 Matchmaker 2ac0, chain A (#2) with 1tup, chain A (#1), sequence alignment
    2268 score = 1024.8 
    2269 RMSD between 191 pruned atom pairs is 0.546 angstroms; (across all 196 pairs:
    2270 1.132) 
    2271  
    2272 
    2273 > hide #!5 models
    2274 
    2275 > hide #!4 models
    2276 
    2277 > hide #!3 models
    2278 
    2279 > hide #!2 models
    2280 
    2281 > show #!2 models
    2282 
    2283 > hide #!2 models
    2284 
    2285 > show #!2 models
    2286 
    2287 > hide #!2 models
    2288 
    2289 > select add #1
    2290 
    2291 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected 
    2292 
    2293 > show sel atoms
    2294 
    2295 > style sel stick
    2296 
    2297 Changed 5828 atom styles 
    2298 
    2299 > hide sel cartoons
    2300 
    2301 > select subtract #1
    2302 
    2303 Nothing selected 
    2304 
    2305 > show #!2 models
    2306 
    2307 > hide #!1 models
    2308 
    2309 > show #!1 models
    2310 
    2311 > hide #!1 models
    2312 
    2313 > show #!1 models
    2314 
    2315 > hide #!2 models
    2316 
    2317 > show #!2 models
    2318 
    2319 > hide #!1 models
    2320 
    2321 > show #!1 models
    2322 
    2323 > hide #!1 models
    2324 
    2325 > show #!1 models
    2326 
    2327 > hide #!1 models
    2328 
    2329 > show #!1 models
    2330 
    2331 > hide #!2 models
    2332 
    2333 > show #!2 models
    2334 
    2335 > hide #!2 models
    2336 
    2337 > show #!2 models
    2338 
    2339 > hide #!1 models
    2340 
    2341 > show #!1 models
    2342 
    2343 > hide #!1 models
    2344 
    2345 > show #!1 models
    2346 
    2347 > hide #!1 models
    2348 
    2349 > show #!1 models
    2350 
    2351 > hide #!2 models
    2352 
    2353 > show #!2 models
    2354 
    2355 > select add #1
    2356 
    2357 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected 
    2358 
    2359 > ui mousemode right rotate
    2360 
    2361 > ui mousemode right "rotate selected models"
    2362 
    2363 > view matrix models
    2364 > #1,0.33546,-0.80914,-0.48246,77.205,0.20225,-0.43834,0.87576,-68.732,-0.92009,-0.39136,0.016605,93.096
    2365 
    2366 > ui mousemode right "translate selected models"
    2367 
    2368 > view matrix models
    2369 > #1,0.33546,-0.80914,-0.48246,75.538,0.20225,-0.43834,0.87576,-81.654,-0.92009,-0.39136,0.016605,70.995
    2370 
    2371 > select subtract #1
    2372 
    2373 Nothing selected 
    2374 
    2375 > select add #2
    2376 
    2377 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected 
    2378 
    2379 > select add #1
    2380 
    2381 14038 atoms, 13057 bonds, 133 pseudobonds, 2910 residues, 14 models selected 
    2382 
    2383 > show sel cartoons
    2384 
    2385 > hide sel atoms
    2386 
    2387 > select subtract #2
    2388 
    2389 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 11 models selected 
    2390 
    2391 > view matrix models
    2392 > #1,0.33546,-0.80914,-0.48246,83.959,0.20225,-0.43834,0.87576,-27.201,-0.92009,-0.39136,0.016605,56.212
    2393 
    2394 > ui mousemode right "rotate selected models"
    2395 
    2396 > view matrix models
    2397 > #1,0.47854,-0.70175,0.52777,0.92818,-0.3715,0.3828,0.84584,-5.1579,-0.7956,-0.60084,-0.077517,59.209
    2398 
    2399 > view matrix models
    2400 > #1,0.66211,-0.70583,0.25184,10.847,0.14066,-0.21303,-0.96687,106.96,0.73609,0.67559,-0.04177,-47.372
    2401 
    2402 > view matrix models
    2403 > #1,-0.22202,0.86187,0.45595,22.171,0.41802,-0.33833,0.84308,-38.3,0.88089,0.37778,-0.28516,-33.349
    2404 
    2405 > ui mousemode right "translate selected models"
    2406 
    2407 > view matrix models
    2408 > #1,-0.22202,0.86187,0.45595,17.518,0.41802,-0.33833,0.84308,-75.138,0.88089,0.37778,-0.28516,-18.673
    2409 
    2410 > view matrix models
    2411 > #1,-0.22202,0.86187,0.45595,-30.27,0.41802,-0.33833,0.84308,-66.789,0.88089,0.37778,-0.28516,-17.681
    2412 
    2413 > view matrix models
    2414 > #1,-0.22202,0.86187,0.45595,-32.908,0.41802,-0.33833,0.84308,-66.426,0.88089,0.37778,-0.28516,-19.539
    2415 
    2416 > ui mousemode right "rotate selected models"
    2417 
    2418 > view matrix models
    2419 > #1,0.58924,-0.80159,-0.10128,-13.083,0.17546,0.24931,-0.9524,69.057,0.78868,0.54342,0.28755,-58.505
    2420 
    2421 > view matrix models
    2422 > #1,0.080048,-0.6908,0.7186,-46.019,-0.56887,0.56032,0.60202,-7.1708,-0.81852,-0.45698,-0.34813,91.867
    2423 
    2424 > ui mousemode right "translate selected models"
    2425 
    2426 > view matrix models
    2427 > #1,0.080048,-0.6908,0.7186,-15.014,-0.56887,0.56032,0.60202,-25.742,-0.81852,-0.45698,-0.34813,109
    2428 
    2429 > matchmaker #!1 to #2
    2430 
    2431 Parameters 
    2432 --- 
    2433 Chain pairing | bb 
    2434 Alignment algorithm | Needleman-Wunsch 
    2435 Similarity matrix | BLOSUM-62 
    2436 SS fraction | 0.3 
    2437 Gap open (HH/SS/other) | 18/18/6 
    2438 Gap extend | 1 
    2439 SS matrix |  |  | H | S | O 
    2440 ---|---|---|--- 
    2441 H | 6 | -9 | -6 
    2442 S |  | 6 | -6 
    2443 O |  |  | 4 
    2444 Iteration cutoff | 2 
    2445  
    2446 Matchmaker 2ac0, chain A (#2) with 1tup, chain A (#1), sequence alignment
    2447 score = 1024.8 
    2448 RMSD between 191 pruned atom pairs is 0.546 angstroms; (across all 196 pairs:
    2449 1.132) 
    2450  
    2451 
    2452 > matchmaker #1/E to #2/E pairing ss
    2453 
    2454 Using Nucleic matrix instead of BLOSUM-62 to match 1tup #1/E to 2ac0 #2/E 
    2455 Parameters 
    2456 --- 
    2457 Chain pairing | ss 
    2458 Alignment algorithm | Needleman-Wunsch 
    2459 Similarity matrix | Nucleic 
    2460 SS fraction | 0.3 
    2461 Gap open (HH/SS/other) | 18/18/6 
    2462 Gap extend | 1 
    2463 SS matrix |  |  | H | S | O 
    2464 ---|---|---|--- 
    2465 H | 6 | -9 | -6 
    2466 S |  | 6 | -6 
    2467 O |  |  | 4 
    2468 Iteration cutoff | 2 
    2469  
    2470 Matchmaker 2ac0, chain E (#2) with 1tup, chain E (#1), sequence alignment
    2471 score = 23.5 
    2472 RMSD between 8 pruned atom pairs is 1.096 angstroms; (across all 12 pairs:
    2473 3.330) 
    2474  
    2475 
    2476 > matchmaker #1/F to #2/F pairing ss
    2477 
    2478 Using Nucleic matrix instead of BLOSUM-62 to match 1tup #1/F to 2ac0 #2/F 
    2479 Parameters 
    2480 --- 
    2481 Chain pairing | ss 
    2482 Alignment algorithm | Needleman-Wunsch 
    2483 Similarity matrix | Nucleic 
    2484 SS fraction | 0.3 
    2485 Gap open (HH/SS/other) | 18/18/6 
    2486 Gap extend | 1 
    2487 SS matrix |  |  | H | S | O 
    2488 ---|---|---|--- 
    2489 H | 6 | -9 | -6 
    2490 S |  | 6 | -6 
    2491 O |  |  | 4 
    2492 Iteration cutoff | 2 
    2493  
    2494 Matchmaker 2ac0, chain F (#2) with 1tup, chain F (#1), sequence alignment
    2495 score = 23.5 
    2496 RMSD between 9 pruned atom pairs is 1.079 angstroms; (across all 12 pairs:
    2497 2.836) 
    2498  
    2499 
    2500 > show #!3 models
    2501 
    2502 > show #!4 models
    2503 
    2504 > show #!5 models
    2505 
    2506 > hide #!1 models
    2507 
    2508 > matchmaker #1/E to #2/E pairing ss
    2509 
    2510 Using Nucleic matrix instead of BLOSUM-62 to match 1tup #1/E to 2ac0 #2/E 
    2511 Parameters 
    2512 --- 
    2513 Chain pairing | ss 
    2514 Alignment algorithm | Needleman-Wunsch 
    2515 Similarity matrix | Nucleic 
    2516 SS fraction | 0.3 
    2517 Gap open (HH/SS/other) | 18/18/6 
    2518 Gap extend | 1 
    2519 SS matrix |  |  | H | S | O 
    2520 ---|---|---|--- 
    2521 H | 6 | -9 | -6 
    2522 S |  | 6 | -6 
    2523 O |  |  | 4 
    2524 Iteration cutoff | 2 
    2525  
    2526 Matchmaker 2ac0, chain E (#2) with 1tup, chain E (#1), sequence alignment
    2527 score = 23.5 
    2528 RMSD between 8 pruned atom pairs is 1.096 angstroms; (across all 12 pairs:
    2529 3.330) 
    2530  
    2531 
    2532 > show #!1 models
    2533 
    2534 > hide #!3 models
    2535 
    2536 > hide #!4 models
    2537 
    2538 > hide #!5 models
    2539 
    2540 > matchmaker #1/B to #2/B pairing ss
    2541 
    2542 Parameters 
    2543 --- 
    2544 Chain pairing | ss 
    2545 Alignment algorithm | Needleman-Wunsch 
    2546 Similarity matrix | BLOSUM-62 
    2547 SS fraction | 0.3 
    2548 Gap open (HH/SS/other) | 18/18/6 
    2549 Gap extend | 1 
    2550 SS matrix |  |  | H | S | O 
    2551 ---|---|---|--- 
    2552 H | 6 | -9 | -6 
    2553 S |  | 6 | -6 
    2554 O |  |  | 4 
    2555 Iteration cutoff | 2 
    2556  
    2557 Matchmaker 2ac0, chain B (#2) with 1tup, chain B (#1), sequence alignment
    2558 score = 1007.4 
    2559 RMSD between 191 pruned atom pairs is 0.597 angstroms; (across all 194 pairs:
    2560 0.710) 
    2561  
    2562 
    2563 > hide #!2 models
    2564 
    2565 > show #!2 models
    2566 
    2567 > hide #!1 models
    2568 
    2569 > show #!1 models
    2570 
    2571 > show #!3 models
    2572 
    2573 > show #!4 models
    2574 
    2575 > hide #!4 models
    2576 
    2577 > select add #3
    2578 
    2579 9617 atoms, 9351 bonds, 92 pseudobonds, 1649 residues, 6 models selected 
    2580 
    2581 > select subtract #1
    2582 
    2583 3789 atoms, 3702 bonds, 37 pseudobonds, 635 residues, 7 models selected 
    2584 
    2585 > close #3
    2586 
    2587 > show #!4 models
    2588 
    2589 > show #!5 models
    2590 
    2591 > hide #!1 models
    2592 
    2593 > hide #!5 models
    2594 
    2595 > hide #!4 models
    2596 
    2597 > open 5lgy fromDatabase pdb format mmcif
    2598 
    2599 Summary of feedback from opening 5lgy fetched from pdb 
    2600 --- 
    2601 note | Fetching compressed mmCIF 5lgy from http://files.rcsb.org/download/5lgy.cif 
    2602  
    2603 5lgy title: 
    2604 Lysine 120-acetylated P53 DNA binding domain in a complex with the BAX
    2605 response element. [more info...] 
    2606  
    2607 Chain information for 5lgy #3 
    2608 --- 
    2609 Chain | Description | UniProt 
    2610 A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-291 
    2611 E | DNA (5'-D(*TP*CP*AP*CP*AP*AP*GP*TP*TP*AP*GP*AP*GP*AP*CP*AP*AP*GP*CP*CP*T)-3') |   
    2612 F | DNA (5'-D(*AP*GP*GP*CP*TP*TP*GP*TP*CP*TP*CP*TP*AP*AP*CP*TP*TP*GP*TP*GP*A)-3') |   
    2613  
    2614 Non-standard residues in 5lgy #3 
    2615 --- 
    2616 ALY — N(6)-acetyllysine 
    2617 ZN — zinc ion 
    2618  
    2619 3 atoms have alternate locations. Control/examine alternate locations with
    2620 Altloc Explorer [start tool...] or the altlocs command. 
    2621 
    2622 > open 5bua fromDatabase pdb format mmcif
    2623 
    2624 Summary of feedback from opening 5bua fetched from pdb 
    2625 --- 
    2626 note | Fetching compressed mmCIF 5bua from http://files.rcsb.org/download/5bua.cif 
    2627  
    2628 5bua title: 
    2629 Lysine 120-acetylated P53 DNA binding domain in a complex with DNA. [more
    2630 info...] 
    2631  
    2632 Chain information for 5bua #6 
    2633 --- 
    2634 Chain | Description | UniProt 
    2635 A | Cellular tumor antigen p53 | P53_HUMAN 94-293 
    2636 B | DNA (5'-D(P*GP*GP*AP*CP*AP*TP*GP*TP*CP*C)-3') |   
    2637  
    2638 Non-standard residues in 5bua #6 
    2639 --- 
    2640 ALY — N(6)-acetyllysine 
    2641 ZN — zinc ion 
    2642  
    2643 5bua mmCIF Assemblies 
    2644 --- 
    2645 1| author_and_software_defined_assembly 
    2646  
    2647 58 atoms have alternate locations. Control/examine alternate locations with
    2648 Altloc Explorer [start tool...] or the altlocs command. 
    2649 
    2650 > hide #!2 models
    2651 
    2652 > show #!2 models
    2653 
    2654 > hide #!3 models
    2655 
    2656 > hide #!6 models
    2657 
    2658 > show #!3 models
    2659 
    2660 > show #!6 models
    2661 
    2662 > matchmaker #6/A to #2/B pairing ss
    2663 
    2664 Parameters 
    2665 --- 
    2666 Chain pairing | ss 
    2667 Alignment algorithm | Needleman-Wunsch 
    2668 Similarity matrix | BLOSUM-62 
    2669 SS fraction | 0.3 
    2670 Gap open (HH/SS/other) | 18/18/6 
    2671 Gap extend | 1 
    2672 SS matrix |  |  | H | S | O 
    2673 ---|---|---|--- 
    2674 H | 6 | -9 | -6 
    2675 S |  | 6 | -6 
    2676 O |  |  | 4 
    2677 Iteration cutoff | 2 
    2678  
    2679 Matchmaker 2ac0, chain B (#2) with 5bua, chain A (#6), sequence alignment
    2680 score = 1001.4 
    2681 RMSD between 187 pruned atom pairs is 0.507 angstroms; (across all 198 pairs:
    2682 1.246) 
    2683  
    2684 
    2685 > hide #!3 models
    2686 
    2687 > hide #!2 models
    2688 
    2689 > show #!2 models
    2690 
    2691 > hide #!2 models
    2692 
    2693 > show #!2 models
    2694 
    2695 > hide #!6 models
    2696 
    2697 > show #!6 models
    2698 
    2699 > hide #!6 models
    2700 
    2701 > show #!3 models
    2702 
    2703 > hide #!2 models
    2704 
    2705 > select add #3
    2706 
    2707 7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 3 models selected 
    2708 
    2709 > hide sel atoms
    2710 
    2711 > style sel stick
    2712 
    2713 Changed 7093 atom styles 
    2714 
    2715 > show sel atoms
    2716 
    2717 > show sel cartoons
    2718 
    2719 > hide sel atoms
    2720 
    2721 > show #!2 models
    2722 
    2723 > matchmaker #3/C to #2/B pairing ss
    2724 
    2725 Parameters 
    2726 --- 
    2727 Chain pairing | ss 
    2728 Alignment algorithm | Needleman-Wunsch 
    2729 Similarity matrix | BLOSUM-62 
    2730 SS fraction | 0.3 
    2731 Gap open (HH/SS/other) | 18/18/6 
    2732 Gap extend | 1 
    2733 SS matrix |  |  | H | S | O 
    2734 ---|---|---|--- 
    2735 H | 6 | -9 | -6 
    2736 S |  | 6 | -6 
    2737 O |  |  | 4 
    2738 Iteration cutoff | 2 
    2739  
    2740 Matchmaker 2ac0, chain B (#2) with 5lgy, chain C (#3), sequence alignment
    2741 score = 1018.3 
    2742 RMSD between 196 pruned atom pairs is 0.474 angstroms; (across all 197 pairs:
    2743 0.534) 
    2744  
    2745 
    2746 > matchmaker #3/D to #2/B pairing ss
    2747 
    2748 Parameters 
    2749 --- 
    2750 Chain pairing | ss 
    2751 Alignment algorithm | Needleman-Wunsch 
    2752 Similarity matrix | BLOSUM-62 
    2753 SS fraction | 0.3 
    2754 Gap open (HH/SS/other) | 18/18/6 
    2755 Gap extend | 1 
    2756 SS matrix |  |  | H | S | O 
    2757 ---|---|---|--- 
    2758 H | 6 | -9 | -6 
    2759 S |  | 6 | -6 
    2760 O |  |  | 4 
    2761 Iteration cutoff | 2 
    2762  
    2763 Matchmaker 2ac0, chain B (#2) with 5lgy, chain D (#3), sequence alignment
    2764 score = 1015.3 
    2765 RMSD between 194 pruned atom pairs is 0.536 angstroms; (across all 197 pairs:
    2766 0.673) 
    2767  
    2768 
    2769 > open 4mzr fromDatabase pdb format mmcif
    2770 
    2771 Summary of feedback from opening 4mzr fetched from pdb 
    2772 --- 
    2773 note | Fetching compressed mmCIF 4mzr from http://files.rcsb.org/download/4mzr.cif 
    2774  
    2775 4mzr title: 
    2776 Crystal structure of a polypeptide p53 mutant bound to DNA [more info...] 
    2777  
    2778 Chain information for 4mzr #7 
    2779 --- 
    2780 Chain | Description | UniProt 
    2781 A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-358 
    2782 K | consensus DNA sense strand |   
    2783 L | consensus DNA anti-sense strand |   
    2784  
    2785 Non-standard residues in 4mzr #7 
    2786 --- 
    2787 ZN — zinc ion 
    2788  
    2789 
    2790 > matchmaker #7/A to #2/B pairing ss
    2791 
    2792 Parameters 
    2793 --- 
    2794 Chain pairing | ss 
    2795 Alignment algorithm | Needleman-Wunsch 
    2796 Similarity matrix | BLOSUM-62 
    2797 SS fraction | 0.3 
    2798 Gap open (HH/SS/other) | 18/18/6 
    2799 Gap extend | 1 
    2800 SS matrix |  |  | H | S | O 
    2801 ---|---|---|--- 
    2802 H | 6 | -9 | -6 
    2803 S |  | 6 | -6 
    2804 O |  |  | 4 
    2805 Iteration cutoff | 2 
    2806  
    2807 Matchmaker 2ac0, chain B (#2) with 4mzr, chain A (#7), sequence alignment
    2808 score = 948.8 
    2809 RMSD between 186 pruned atom pairs is 0.543 angstroms; (across all 198 pairs:
    2810 2.117) 
    2811  
    2812 
    2813 > select add #7
    2814 
    2815 15686 atoms, 16125 bonds, 130 pseudobonds, 1916 residues, 6 models selected 
    2816 
    2817 > select subtract #3
    2818 
    2819 8593 atoms, 8812 bonds, 73 pseudobonds, 1061 residues, 3 models selected 
    2820 
    2821 > style sel stick
    2822 
    2823 Changed 8593 atom styles 
    2824 
    2825 > show sel cartoons
    2826 
    2827 > hide sel atoms
    2828 
    2829 > matchmaker #7/B to #2/B pairing ss
    2830 
    2831 Parameters 
    2832 --- 
    2833 Chain pairing | ss 
    2834 Alignment algorithm | Needleman-Wunsch 
    2835 Similarity matrix | BLOSUM-62 
    2836 SS fraction | 0.3 
    2837 Gap open (HH/SS/other) | 18/18/6 
    2838 Gap extend | 1 
    2839 SS matrix |  |  | H | S | O 
    2840 ---|---|---|--- 
    2841 H | 6 | -9 | -6 
    2842 S |  | 6 | -6 
    2843 O |  |  | 4 
    2844 Iteration cutoff | 2 
    2845  
    2846 Matchmaker 2ac0, chain B (#2) with 4mzr, chain B (#7), sequence alignment
    2847 score = 843.2 
    2848 RMSD between 190 pruned atom pairs is 0.842 angstroms; (across all 198 pairs:
    2849 1.070) 
    2850  
    2851 
    2852 > hide #!2 models
    2853 
    2854 > hide #!3 models
    2855 
    2856 > show #!2 models
    2857 
    2858 > matchmaker #7/C to #2/B pairing ss
    2859 
    2860 Parameters 
    2861 --- 
    2862 Chain pairing | ss 
    2863 Alignment algorithm | Needleman-Wunsch 
    2864 Similarity matrix | BLOSUM-62 
    2865 SS fraction | 0.3 
    2866 Gap open (HH/SS/other) | 18/18/6 
    2867 Gap extend | 1 
    2868 SS matrix |  |  | H | S | O 
    2869 ---|---|---|--- 
    2870 H | 6 | -9 | -6 
    2871 S |  | 6 | -6 
    2872 O |  |  | 4 
    2873 Iteration cutoff | 2 
    2874  
    2875 Matchmaker 2ac0, chain B (#2) with 4mzr, chain C (#7), sequence alignment
    2876 score = 933.2 
    2877 RMSD between 193 pruned atom pairs is 0.571 angstroms; (across all 198 pairs:
    2878 0.889) 
    2879  
    2880 
    2881 > matchmaker #7/D to #2/B pairing ss
    2882 
    2883 Parameters 
    2884 --- 
    2885 Chain pairing | ss 
    2886 Alignment algorithm | Needleman-Wunsch 
    2887 Similarity matrix | BLOSUM-62 
    2888 SS fraction | 0.3 
    2889 Gap open (HH/SS/other) | 18/18/6 
    2890 Gap extend | 1 
    2891 SS matrix |  |  | H | S | O 
    2892 ---|---|---|--- 
    2893 H | 6 | -9 | -6 
    2894 S |  | 6 | -6 
    2895 O |  |  | 4 
    2896 Iteration cutoff | 2 
    2897  
    2898 Matchmaker 2ac0, chain B (#2) with 4mzr, chain D (#7), sequence alignment
    2899 score = 948.8 
    2900 RMSD between 186 pruned atom pairs is 0.544 angstroms; (across all 198 pairs:
    2901 2.118) 
    2902  
    2903 
    2904 > matchmaker #7/A to #2/B pairing ss
    2905 
    2906 Parameters 
    2907 --- 
    2908 Chain pairing | ss 
    2909 Alignment algorithm | Needleman-Wunsch 
    2910 Similarity matrix | BLOSUM-62 
    2911 SS fraction | 0.3 
    2912 Gap open (HH/SS/other) | 18/18/6 
    2913 Gap extend | 1 
    2914 SS matrix |  |  | H | S | O 
    2915 ---|---|---|--- 
    2916 H | 6 | -9 | -6 
    2917 S |  | 6 | -6 
    2918 O |  |  | 4 
    2919 Iteration cutoff | 2 
    2920  
    2921 Matchmaker 2ac0, chain B (#2) with 4mzr, chain A (#7), sequence alignment
    2922 score = 948.8 
    2923 RMSD between 186 pruned atom pairs is 0.543 angstroms; (across all 198 pairs:
    2924 2.117) 
    2925  
    2926 
    2927 > select subtract #7
    2928 
    2929 Nothing selected 
    2930 
    2931 > matchmaker #7/C to #2/B pairing ss
    2932 
    2933 Parameters 
    2934 --- 
    2935 Chain pairing | ss 
    2936 Alignment algorithm | Needleman-Wunsch 
    2937 Similarity matrix | BLOSUM-62 
    2938 SS fraction | 0.3 
    2939 Gap open (HH/SS/other) | 18/18/6 
    2940 Gap extend | 1 
    2941 SS matrix |  |  | H | S | O 
    2942 ---|---|---|--- 
    2943 H | 6 | -9 | -6 
    2944 S |  | 6 | -6 
    2945 O |  |  | 4 
    2946 Iteration cutoff | 2 
    2947  
    2948 Matchmaker 2ac0, chain B (#2) with 4mzr, chain C (#7), sequence alignment
    2949 score = 933.2 
    2950 RMSD between 193 pruned atom pairs is 0.571 angstroms; (across all 198 pairs:
    2951 0.889) 
    2952  
    2953 
    2954 > matchmaker #7/B to #2/B pairing ss
    2955 
    2956 Parameters 
    2957 --- 
    2958 Chain pairing | ss 
    2959 Alignment algorithm | Needleman-Wunsch 
    2960 Similarity matrix | BLOSUM-62 
    2961 SS fraction | 0.3 
    2962 Gap open (HH/SS/other) | 18/18/6 
    2963 Gap extend | 1 
    2964 SS matrix |  |  | H | S | O 
    2965 ---|---|---|--- 
    2966 H | 6 | -9 | -6 
    2967 S |  | 6 | -6 
    2968 O |  |  | 4 
    2969 Iteration cutoff | 2 
    2970  
    2971 Matchmaker 2ac0, chain B (#2) with 4mzr, chain B (#7), sequence alignment
    2972 score = 843.2 
    2973 RMSD between 190 pruned atom pairs is 0.842 angstroms; (across all 198 pairs:
    2974 1.070) 
    2975  
    2976 
    2977 > matchmaker #7/D to #2/B pairing ss
    2978 
    2979 Parameters 
    2980 --- 
    2981 Chain pairing | ss 
    2982 Alignment algorithm | Needleman-Wunsch 
    2983 Similarity matrix | BLOSUM-62 
    2984 SS fraction | 0.3 
    2985 Gap open (HH/SS/other) | 18/18/6 
    2986 Gap extend | 1 
    2987 SS matrix |  |  | H | S | O 
    2988 ---|---|---|--- 
    2989 H | 6 | -9 | -6 
    2990 S |  | 6 | -6 
    2991 O |  |  | 4 
    2992 Iteration cutoff | 2 
    2993  
    2994 Matchmaker 2ac0, chain B (#2) with 4mzr, chain D (#7), sequence alignment
    2995 score = 948.8 
    2996 RMSD between 186 pruned atom pairs is 0.544 angstroms; (across all 198 pairs:
    2997 2.118) 
    2998  
    2999 
    3000 > open 4ibu fromDatabase pdb format mmcif
    3001 
    3002 Summary of feedback from opening 4ibu fetched from pdb 
    3003 --- 
    3004 note | Fetching compressed mmCIF 4ibu from http://files.rcsb.org/download/4ibu.cif 
    3005  
    3006 4ibu title: 
    3007 Human p53 core domain with hot spot mutation R273C and second-site suppressor
    3008 mutation T284R in sequence-specific complex with DNA [more info...] 
    3009  
    3010 Chain information for 4ibu #8 
    3011 --- 
    3012 Chain | Description | UniProt 
    3013 A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-293 
    3014 E F G H | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') |   
    3015  
    3016 Non-standard residues in 4ibu #8 
    3017 --- 
    3018 ACT — acetate ion 
    3019 EDO — 1,2-ethanediol (ethylene glycol) 
    3020 ZN — zinc ion 
    3021  
    3022 382 atoms have alternate locations. Control/examine alternate locations with
    3023 Altloc Explorer [start tool...] or the altlocs command. 
    3024 
    3025 > open 4ibv fromDatabase pdb format mmcif
    3026 
    3027 Summary of feedback from opening 4ibv fetched from pdb 
    3028 --- 
    3029 note | Fetching compressed mmCIF 4ibv from http://files.rcsb.org/download/4ibv.cif 
    3030  
    3031 4ibv title: 
    3032 Human p53 core domain with hot spot mutation R273C and second-site suppressor
    3033 mutation S240R in sequence-specific complex with DNA [more info...] 
    3034  
    3035 Chain information for 4ibv #9 
    3036 --- 
    3037 Chain | Description | UniProt 
    3038 A | Cellular tumor antigen p53 | P53_HUMAN 94-293 
    3039 B | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') |   
    3040  
    3041 Non-standard residues in 4ibv #9 
    3042 --- 
    3043 EDO — 1,2-ethanediol (ethylene glycol) 
    3044 ZN — zinc ion 
    3045  
    3046 4ibv mmCIF Assemblies 
    3047 --- 
    3048 1| author_and_software_defined_assembly 
    3049  
    3050 98 atoms have alternate locations. Control/examine alternate locations with
    3051 Altloc Explorer [start tool...] or the altlocs command. 
    3052 
    3053 > open 4ibw fromDatabase pdb format mmcif
    3054 
    3055 Summary of feedback from opening 4ibw fetched from pdb 
    3056 --- 
    3057 note | Fetching compressed mmCIF 4ibw from http://files.rcsb.org/download/4ibw.cif 
    3058  
    3059 4ibw title: 
    3060 Human p53 core domain with hot spot mutation R273H and second-site suppressor
    3061 mutation T284R in sequence-specific complex with DNA [more info...] 
    3062  
    3063 Chain information for 4ibw #10 
    3064 --- 
    3065 Chain | Description | UniProt 
    3066 A | Cellular tumor antigen p53 | P53_HUMAN 94-293 
    3067 B | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') |   
    3068  
    3069 Non-standard residues in 4ibw #10 
    3070 --- 
    3071 EDO — 1,2-ethanediol (ethylene glycol) 
    3072 ZN — zinc ion 
    3073  
    3074 4ibw mmCIF Assemblies 
    3075 --- 
    3076 1| author_defined_assembly 
    3077  
    3078 140 atoms have alternate locations. Control/examine alternate locations with
    3079 Altloc Explorer [start tool...] or the altlocs command. 
    3080 
    3081 > open 4hje fromDatabase pdb format mmcif
    3082 
    3083 Summary of feedback from opening 4hje fetched from pdb 
    3084 --- 
    3085 note | Fetching compressed mmCIF 4hje from http://files.rcsb.org/download/4hje.cif 
    3086  
    3087 4hje title: 
    3088 Crystal structure of p53 core domain in complex with DNA [more info...] 
    3089  
    3090 Chain information for 4hje #11 
    3091 --- 
    3092 Chain | Description | UniProt 
    3093 A B C D | Cellular tumor antigen p53 | P53_HUMAN 92-291 
    3094 E | DNA (5'-D(*TP*CP*AP*CP*AP*AP*GP*TP*TP*AP*GP*AP*GP*AP*CP*AP*AP*GP*CP*CP*T)-3') |   
    3095 F | DNA (5'-D(*AP*GP*GP*CP*TP*TP*GP*TP*CP*TP*CP*TP*AP*AP*CP*TP*TP*GP*TP*GP*A)-3') |   
    3096  
    3097 Non-standard residues in 4hje #11 
    3098 --- 
    3099 ZN — zinc ion 
    3100  
    3101 
    3102 > select add #11
    3103 
    3104 7975 atoms, 7386 bonds, 63 pseudobonds, 1678 residues, 3 models selected 
    3105 
    3106 > select add #10
    3107 
    3108 10147 atoms, 9266 bonds, 68 pseudobonds, 2240 residues, 6 models selected 
    3109 
    3110 > select add #9
    3111 
    3112 12096 atoms, 11103 bonds, 73 pseudobonds, 2620 residues, 9 models selected 
    3113 
    3114 > select add #8
    3115 
    3116 20184 atoms, 18460 bonds, 154 pseudobonds, 4433 residues, 12 models selected 
    3117 
    3118 > select add #7
    3119 
    3120 28777 atoms, 27272 bonds, 227 pseudobonds, 5494 residues, 15 models selected 
    3121 
    3122 > style sel stick
    3123 
    3124 Changed 28777 atom styles 
    3125 
    3126 > hide sel atoms
    3127 
    3128 > show sel cartoons
    3129 
    3130 > ui mousemode right select
    3131 
    3132 > select clear
    3133 
    3134 > matchmaker #11/B to #2/B pairing ss
    3135 
    3136 Parameters 
    3137 --- 
    3138 Chain pairing | ss 
    3139 Alignment algorithm | Needleman-Wunsch 
    3140 Similarity matrix | BLOSUM-62 
    3141 SS fraction | 0.3 
    3142 Gap open (HH/SS/other) | 18/18/6 
    3143 Gap extend | 1 
    3144 SS matrix |  |  | H | S | O 
    3145 ---|---|---|--- 
    3146 H | 6 | -9 | -6 
    3147 S |  | 6 | -6 
    3148 O |  |  | 4 
    3149 Iteration cutoff | 2 
    3150  
    3151 Matchmaker 2ac0, chain B (#2) with 4hje, chain B (#11), sequence alignment
    3152 score = 1018.3 
    3153 RMSD between 195 pruned atom pairs is 0.356 angstroms; (across all 198 pairs:
    3154 0.530) 
    3155  
    3156 
    3157 > matchmaker #10/B to #2/B pairing ss
    3158 
    3159 Match chain (4ibw (#10) chain B) not compatible with BLOSUM-62 similarity
    3160 matrix 
    3161 
    3162 > hide #!11 models
    3163 
    3164 > hide #!2 models
    3165 
    3166 > hide #!7 models
    3167 
    3168 > hide #!8 models
    3169 
    3170 > hide #!9 models
    3171 
    3172 > show #!2 models
    3173 
    3174 > matchmaker #10/A to #2/B pairing ss
    3175 
    3176 Parameters 
    3177 --- 
    3178 Chain pairing | ss 
    3179 Alignment algorithm | Needleman-Wunsch 
    3180 Similarity matrix | BLOSUM-62 
    3181 SS fraction | 0.3 
    3182 Gap open (HH/SS/other) | 18/18/6 
    3183 Gap extend | 1 
    3184 SS matrix |  |  | H | S | O 
    3185 ---|---|---|--- 
    3186 H | 6 | -9 | -6 
    3187 S |  | 6 | -6 
    3188 O |  |  | 4 
    3189 Iteration cutoff | 2 
    3190  
    3191 Matchmaker 2ac0, chain B (#2) with 4ibw, chain A (#10), sequence alignment
    3192 score = 1011.7 
    3193 RMSD between 188 pruned atom pairs is 0.497 angstroms; (across all 195 pairs:
    3194 0.717) 
    3195  
    3196 
    3197 > show #!1 models
    3198 
    3199 > show #!3 models
    3200 
    3201 > show #!4 models
    3202 
    3203 > show #!5 models
    3204 
    3205 > show #!6 models
    3206 
    3207 > show #!7 models
    3208 
    3209 > matchmaker #9/A to #2/B pairing ss
    3210 
    3211 Parameters 
    3212 --- 
    3213 Chain pairing | ss 
    3214 Alignment algorithm | Needleman-Wunsch 
    3215 Similarity matrix | BLOSUM-62 
    3216 SS fraction | 0.3 
    3217 Gap open (HH/SS/other) | 18/18/6 
    3218 Gap extend | 1 
    3219 SS matrix |  |  | H | S | O 
    3220 ---|---|---|--- 
    3221 H | 6 | -9 | -6 
    3222 S |  | 6 | -6 
    3223 O |  |  | 4 
    3224 Iteration cutoff | 2 
    3225  
    3226 Matchmaker 2ac0, chain B (#2) with 4ibv, chain A (#9), sequence alignment
    3227 score = 1000.1 
    3228 RMSD between 185 pruned atom pairs is 0.508 angstroms; (across all 195 pairs:
    3229 1.235) 
    3230  
    3231 
    3232 > show #!9 models
    3233 
    3234 > show #!8 models
    3235 
    3236 > hide #!9 models
    3237 
    3238 > show #!9 models
    3239 
    3240 > matchmaker #8/B to #2/B pairing ss
    3241 
    3242 Parameters 
    3243 --- 
    3244 Chain pairing | ss 
    3245 Alignment algorithm | Needleman-Wunsch 
    3246 Similarity matrix | BLOSUM-62 
    3247 SS fraction | 0.3 
    3248 Gap open (HH/SS/other) | 18/18/6 
    3249 Gap extend | 1 
    3250 SS matrix |  |  | H | S | O 
    3251 ---|---|---|--- 
    3252 H | 6 | -9 | -6 
    3253 S |  | 6 | -6 
    3254 O |  |  | 4 
    3255 Iteration cutoff | 2 
    3256  
    3257 Matchmaker 2ac0, chain B (#2) with 4ibu, chain B (#8), sequence alignment
    3258 score = 1018 
    3259 RMSD between 196 pruned atom pairs is 0.320 angstroms; (across all 198 pairs:
    3260 0.451) 
    3261  
    3262 
    3263 > select add #1
    3264 
    3265 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected 
    3266 
    3267 > select subtract #1
    3268 
    3269 Nothing selected 
    3270 
    3271 > select add #10
    3272 
    3273 2172 atoms, 1880 bonds, 5 pseudobonds, 562 residues, 3 models selected 
    3274 
    3275 > select add #9
    3276 
    3277 4121 atoms, 3717 bonds, 10 pseudobonds, 942 residues, 6 models selected 
    3278 
    3279 > show #!11 models
    3280 
    3281 > matchmaker #11/B to #2/B pairing ss
    3282 
    3283 Parameters 
    3284 --- 
    3285 Chain pairing | ss 
    3286 Alignment algorithm | Needleman-Wunsch 
    3287 Similarity matrix | BLOSUM-62 
    3288 SS fraction | 0.3 
    3289 Gap open (HH/SS/other) | 18/18/6 
    3290 Gap extend | 1 
    3291 SS matrix |  |  | H | S | O 
    3292 ---|---|---|--- 
    3293 H | 6 | -9 | -6 
    3294 S |  | 6 | -6 
    3295 O |  |  | 4 
    3296 Iteration cutoff | 2 
    3297  
    3298 Matchmaker 2ac0, chain B (#2) with 4hje, chain B (#11), sequence alignment
    3299 score = 1018.3 
    3300 RMSD between 195 pruned atom pairs is 0.356 angstroms; (across all 198 pairs:
    3301 0.530) 
    3302  
    3303 
    3304 > matchmaker #11/A to #2/B pairing ss
    3305 
    3306 Parameters 
    3307 --- 
    3308 Chain pairing | ss 
    3309 Alignment algorithm | Needleman-Wunsch 
    3310 Similarity matrix | BLOSUM-62 
    3311 SS fraction | 0.3 
    3312 Gap open (HH/SS/other) | 18/18/6 
    3313 Gap extend | 1 
    3314 SS matrix |  |  | H | S | O 
    3315 ---|---|---|--- 
    3316 H | 6 | -9 | -6 
    3317 S |  | 6 | -6 
    3318 O |  |  | 4 
    3319 Iteration cutoff | 2 
    3320  
    3321 Matchmaker 2ac0, chain B (#2) with 4hje, chain A (#11), sequence alignment
    3322 score = 1018.3 
    3323 RMSD between 196 pruned atom pairs is 0.344 angstroms; (across all 198 pairs:
    3324 0.482) 
    3325  
    3326 
    3327 > select add #11
    3328 
    3329 12096 atoms, 11103 bonds, 73 pseudobonds, 2620 residues, 9 models selected 
    3330 
    3331 > select add #8
    3332 
    3333 20184 atoms, 18460 bonds, 154 pseudobonds, 4433 residues, 12 models selected 
    3334 
    3335 > select add #7
    3336 
    3337 28777 atoms, 27272 bonds, 227 pseudobonds, 5494 residues, 15 models selected 
    3338 
    3339 > select add #6
    3340 
    3341 30709 atoms, 29107 bonds, 231 pseudobonds, 5860 residues, 17 models selected 
    3342 
    3343 > select add #5
    3344 
    3345 38490 atoms, 36414 bonds, 301 pseudobonds, 7415 residues, 20 models selected 
    3346 
    3347 > select add #4
    3348 
    3349 46525 atoms, 43695 bonds, 375 pseudobonds, 9248 residues, 31 models selected 
    3350 
    3351 > select add #3
    3352 
    3353 53618 atoms, 51008 bonds, 432 pseudobonds, 10103 residues, 42 models selected 
    3354 
    3355 > select add #2
    3356 
    3357 61828 atoms, 58416 bonds, 510 pseudobonds, 11999 residues, 45 models selected 
    3358 
    3359 > select add #1
    3360 
    3361 67656 atoms, 64065 bonds, 565 pseudobonds, 13013 residues, 56 models selected 
    3362 
    3363 > style sel stick
    3364 
    3365 Changed 67656 atom styles 
    3366 
    3367 > hide sel atoms
    3368 
    3369 > show sel cartoons
    3370 
    3371 > select clear
    3372 
    3373 > select O
    3374 
    3375 18203 atoms, 12968 residues, 11 models selected 
    3376 
    3377 > show sel atoms
    3378 
    3379 > select clear
    3380 
    3381 > select add #1
    3382 
    3383 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected 
    3384 
    3385 > select add #2
    3386 
    3387 14038 atoms, 13057 bonds, 133 pseudobonds, 2910 residues, 6 models selected 
    3388 
    3389 > select add #3
    3390 
    3391 21131 atoms, 20370 bonds, 190 pseudobonds, 3765 residues, 17 models selected 
    3392 
    3393 > select add #5
    3394 
    3395 28912 atoms, 27677 bonds, 260 pseudobonds, 5320 residues, 20 models selected 
    3396 
    3397 > select add #4
    3398 
    3399 36947 atoms, 34958 bonds, 334 pseudobonds, 7153 residues, 31 models selected 
    3400 
    3401 > select add #6
    3402 
    3403 38879 atoms, 36793 bonds, 338 pseudobonds, 7519 residues, 41 models selected 
    3404 
    3405 > select add #7
    3406 
    3407 47472 atoms, 45605 bonds, 411 pseudobonds, 8580 residues, 44 models selected 
    3408 
    3409 > select add #8
    3410 
    3411 55560 atoms, 52962 bonds, 492 pseudobonds, 10393 residues, 47 models selected 
    3412 
    3413 > select add #9
    3414 
    3415 57509 atoms, 54799 bonds, 497 pseudobonds, 10773 residues, 50 models selected 
    3416 
    3417 > select add #10
    3418 
    3419 59681 atoms, 56679 bonds, 502 pseudobonds, 11335 residues, 53 models selected 
    3420 
    3421 > select add #11
    3422 
    3423 67656 atoms, 64065 bonds, 565 pseudobonds, 13013 residues, 56 models selected 
    3424 
    3425 > hide sel atoms
    3426 
    3427 > show sel atoms
    3428 
    3429 > hide sel cartoons
    3430 
    3431 > select H
    3432 
    3433 Nothing selected 
    3434 
    3435 > show atoms
    3436 
    3437 > select hydroxyl
    3438 
    3439 1506 atoms, 1466 residues, 11 models selected 
    3440 
    3441 > show sel atoms
    3442 
    3443 > select add #1
    3444 
    3445 7211 atoms, 5649 bonds, 55 pseudobonds, 2357 residues, 37 models selected 
    3446 
    3447 > select subtract #1
    3448 
    3449 1383 atoms, 1343 residues, 34 models selected 
    3450 
    3451 > select clear
    3452 
    3453 > select add #1
    3454 
    3455 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected 
    3456 
    3457 > select add #2
    3458 
    3459 14038 atoms, 13057 bonds, 133 pseudobonds, 2910 residues, 6 models selected 
    3460 
    3461 > select add #3
    3462 
    3463 21131 atoms, 20370 bonds, 190 pseudobonds, 3765 residues, 17 models selected 
    3464 
    3465 > select add #4
    3466 
    3467 29166 atoms, 27651 bonds, 264 pseudobonds, 5598 residues, 20 models selected 
    3468 
    3469 > select add #5
    3470 
    3471 36947 atoms, 34958 bonds, 334 pseudobonds, 7153 residues, 31 models selected 
    3472 
    3473 > select add #6
    3474 
    3475 38879 atoms, 36793 bonds, 338 pseudobonds, 7519 residues, 41 models selected 
    3476 
    3477 > select add #7
    3478 
    3479 47472 atoms, 45605 bonds, 411 pseudobonds, 8580 residues, 44 models selected 
    3480 
    3481 > select add #9
    3482 
    3483 49421 atoms, 47442 bonds, 416 pseudobonds, 8960 residues, 47 models selected 
    3484 
    3485 > select add #8
    3486 
    3487 57509 atoms, 54799 bonds, 497 pseudobonds, 10773 residues, 50 models selected 
    3488 
    3489 > select add #10
    3490 
    3491 59681 atoms, 56679 bonds, 502 pseudobonds, 11335 residues, 53 models selected 
    3492 
    3493 > select add #11
    3494 
    3495 67656 atoms, 64065 bonds, 565 pseudobonds, 13013 residues, 56 models selected 
    3496 
    3497 > show sel cartoons
    3498 
    3499 > hide sel atoms
    3500 
    3501 > open 3ts8 fromDatabase pdb format mmcif
    3502 
    3503 Summary of feedback from opening 3ts8 fetched from pdb 
    3504 --- 
    3505 note | Fetching compressed mmCIF 3ts8 from http://files.rcsb.org/download/3ts8.cif 
    3506  
    3507 3ts8 title: 
    3508 Crystal structure of a multidomain human p53 tetramer bound to the natural
    3509 CDKN1A(p21) p53-response element [more info...] 
    3510  
    3511 Chain information for 3ts8 #12 
    3512 --- 
    3513 Chain | Description | UniProt 
    3514 A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-291 321-356 
    3515 K | CDKN1A(p21) sense strand |   
    3516 L | CDKN1A(p21) anti-sense strand |   
    3517  
    3518 Non-standard residues in 3ts8 #12 
    3519 --- 
    3520 ZN — zinc ion 
    3521  
    3522 
    3523 > select clear
    3524 
    3525 > select add #12
    3526 
    3527 8621 atoms, 8800 bonds, 71 pseudobonds, 1097 residues, 3 models selected 
    3528 
    3529 > style sel stick
    3530 
    3531 Changed 8621 atom styles 
    3532 
    3533 > show sel cartoons
    3534 
    3535 > hide sel atoms
    3536 
    3537 > matchmaker #12/B to #2/B pairing ss
    3538 
    3539 Parameters 
    3540 --- 
    3541 Chain pairing | ss 
    3542 Alignment algorithm | Needleman-Wunsch 
    3543 Similarity matrix | BLOSUM-62 
    3544 SS fraction | 0.3 
    3545 Gap open (HH/SS/other) | 18/18/6 
    3546 Gap extend | 1 
    3547 SS matrix |  |  | H | S | O 
    3548 ---|---|---|--- 
    3549 H | 6 | -9 | -6 
    3550 S |  | 6 | -6 
    3551 O |  |  | 4 
    3552 Iteration cutoff | 2 
    3553  
    3554 Matchmaker 2ac0, chain B (#2) with 3ts8, chain B (#12), sequence alignment
    3555 score = 893.7 
    3556 RMSD between 183 pruned atom pairs is 0.874 angstroms; (across all 198 pairs:
    3557 1.399) 
    3558  
    3559 
    3560 > matchmaker #12/A to #2/B pairing ss
    3561 
    3562 Parameters 
    3563 --- 
    3564 Chain pairing | ss 
    3565 Alignment algorithm | Needleman-Wunsch 
    3566 Similarity matrix | BLOSUM-62 
    3567 SS fraction | 0.3 
    3568 Gap open (HH/SS/other) | 18/18/6 
    3569 Gap extend | 1 
    3570 SS matrix |  |  | H | S | O 
    3571 ---|---|---|--- 
    3572 H | 6 | -9 | -6 
    3573 S |  | 6 | -6 
    3574 O |  |  | 4 
    3575 Iteration cutoff | 2 
    3576  
    3577 Matchmaker 2ac0, chain B (#2) with 3ts8, chain A (#12), sequence alignment
    3578 score = 947.1 
    3579 RMSD between 186 pruned atom pairs is 0.545 angstroms; (across all 198 pairs:
    3580 2.430) 
    3581  
    3582 
    3583 > matchmaker #11/C to #2/B pairing ss
    3584 
    3585 Parameters 
    3586 --- 
    3587 Chain pairing | ss 
    3588 Alignment algorithm | Needleman-Wunsch 
    3589 Similarity matrix | BLOSUM-62 
    3590 SS fraction | 0.3 
    3591 Gap open (HH/SS/other) | 18/18/6 
    3592 Gap extend | 1 
    3593 SS matrix |  |  | H | S | O 
    3594 ---|---|---|--- 
    3595 H | 6 | -9 | -6 
    3596 S |  | 6 | -6 
    3597 O |  |  | 4 
    3598 Iteration cutoff | 2 
    3599  
    3600 Matchmaker 2ac0, chain B (#2) with 4hje, chain C (#11), sequence alignment
    3601 score = 1018.3 
    3602 RMSD between 196 pruned atom pairs is 0.349 angstroms; (across all 198 pairs:
    3603 0.485) 
    3604  
    3605 
    3606 > matchmaker #12/D to #2/B pairing ss
    3607 
    3608 Parameters 
    3609 --- 
    3610 Chain pairing | ss 
    3611 Alignment algorithm | Needleman-Wunsch 
    3612 Similarity matrix | BLOSUM-62 
    3613 SS fraction | 0.3 
    3614 Gap open (HH/SS/other) | 18/18/6 
    3615 Gap extend | 1 
    3616 SS matrix |  |  | H | S | O 
    3617 ---|---|---|--- 
    3618 H | 6 | -9 | -6 
    3619 S |  | 6 | -6 
    3620 O |  |  | 4 
    3621 Iteration cutoff | 2 
    3622  
    3623 Matchmaker 2ac0, chain B (#2) with 3ts8, chain D (#12), sequence alignment
    3624 score = 950.1 
    3625 RMSD between 186 pruned atom pairs is 0.547 angstroms; (across all 198 pairs:
    3626 2.431) 
    3627  
    3628 
    3629 > hide #!11 models
    3630 
    3631 > hide #!10 models
    3632 
    3633 > hide #!9 models
    3634 
    3635 > hide #!8 models
    3636 
    3637 > hide #!7 models
    3638 
    3639 > hide #!6 models
    3640 
    3641 > hide #!5 models
    3642 
    3643 > hide #!4 models
    3644 
    3645 > hide #!3 models
    3646 
    3647 > hide #!2 models
    3648 
    3649 > hide #!1 models
    3650 
    3651 > show #!1 models
    3652 
    3653 > hide #!1 models
    3654 
    3655 > show #!1 models
    3656 
    3657 > hide #!1 models
    3658 
    3659 > show #!11 models
    3660 
    3661 > show #!2 models
    3662 
    3663 > hide #!11 models
    3664 
    3665 > matchmaker #12/A to #2/B pairing ss
    3666 
    3667 Parameters 
    3668 --- 
    3669 Chain pairing | ss 
    3670 Alignment algorithm | Needleman-Wunsch 
    3671 Similarity matrix | BLOSUM-62 
    3672 SS fraction | 0.3 
    3673 Gap open (HH/SS/other) | 18/18/6 
    3674 Gap extend | 1 
    3675 SS matrix |  |  | H | S | O 
    3676 ---|---|---|--- 
    3677 H | 6 | -9 | -6 
    3678 S |  | 6 | -6 
    3679 O |  |  | 4 
    3680 Iteration cutoff | 2 
    3681  
    3682 Matchmaker 2ac0, chain B (#2) with 3ts8, chain A (#12), sequence alignment
    3683 score = 947.1 
    3684 RMSD between 186 pruned atom pairs is 0.545 angstroms; (across all 198 pairs:
    3685 2.430) 
    3686  
    3687 
    3688 > matchmaker #12/B to #2/B pairing ss
    3689 
    3690 Parameters 
    3691 --- 
    3692 Chain pairing | ss 
    3693 Alignment algorithm | Needleman-Wunsch 
    3694 Similarity matrix | BLOSUM-62 
    3695 SS fraction | 0.3 
    3696 Gap open (HH/SS/other) | 18/18/6 
    3697 Gap extend | 1 
    3698 SS matrix |  |  | H | S | O 
    3699 ---|---|---|--- 
    3700 H | 6 | -9 | -6 
    3701 S |  | 6 | -6 
    3702 O |  |  | 4 
    3703 Iteration cutoff | 2 
    3704  
    3705 Matchmaker 2ac0, chain B (#2) with 3ts8, chain B (#12), sequence alignment
    3706 score = 893.7 
    3707 RMSD between 183 pruned atom pairs is 0.874 angstroms; (across all 198 pairs:
    3708 1.399) 
    3709  
    3710 
    3711 > matchmaker #12/C to #2/B pairing ss
    3712 
    3713 Parameters 
    3714 --- 
    3715 Chain pairing | ss 
    3716 Alignment algorithm | Needleman-Wunsch 
    3717 Similarity matrix | BLOSUM-62 
    3718 SS fraction | 0.3 
    3719 Gap open (HH/SS/other) | 18/18/6 
    3720 Gap extend | 1 
    3721 SS matrix |  |  | H | S | O 
    3722 ---|---|---|--- 
    3723 H | 6 | -9 | -6 
    3724 S |  | 6 | -6 
    3725 O |  |  | 4 
    3726 Iteration cutoff | 2 
    3727  
    3728 Matchmaker 2ac0, chain B (#2) with 3ts8, chain C (#12), sequence alignment
    3729 score = 939.3 
    3730 RMSD between 192 pruned atom pairs is 0.573 angstroms; (across all 198 pairs:
    3731 0.928) 
    3732  
    3733 
    3734 > matchmaker #12/D to #2/B pairing ss
    3735 
    3736 Parameters 
    3737 --- 
    3738 Chain pairing | ss 
    3739 Alignment algorithm | Needleman-Wunsch 
    3740 Similarity matrix | BLOSUM-62 
    3741 SS fraction | 0.3 
    3742 Gap open (HH/SS/other) | 18/18/6 
    3743 Gap extend | 1 
    3744 SS matrix |  |  | H | S | O 
    3745 ---|---|---|--- 
    3746 H | 6 | -9 | -6 
    3747 S |  | 6 | -6 
    3748 O |  |  | 4 
    3749 Iteration cutoff | 2 
    3750  
    3751 Matchmaker 2ac0, chain B (#2) with 3ts8, chain D (#12), sequence alignment
    3752 score = 950.1 
    3753 RMSD between 186 pruned atom pairs is 0.547 angstroms; (across all 198 pairs:
    3754 2.431) 
    3755  
    3756 
    3757 > hide #!12 models
    3758 
    3759 > show #!12 models
    3760 
    3761 > hide #!2 models
    3762 
    3763 > show #!2 models
    3764 
    3765 > matchmaker #12/L to #2/E pairing ss
    3766 
    3767 Using Nucleic matrix instead of BLOSUM-62 to match 3ts8 #12/L to 2ac0 #2/E 
    3768 Parameters 
    3769 --- 
    3770 Chain pairing | ss 
    3771 Alignment algorithm | Needleman-Wunsch 
    3772 Similarity matrix | Nucleic 
    3773 SS fraction | 0.3 
    3774 Gap open (HH/SS/other) | 18/18/6 
    3775 Gap extend | 1 
    3776 SS matrix |  |  | H | S | O 
    3777 ---|---|---|--- 
    3778 H | 6 | -9 | -6 
    3779 S |  | 6 | -6 
    3780 O |  |  | 4 
    3781 Iteration cutoff | 2 
    3782  
    3783 Matchmaker 2ac0, chain E (#2) with 3ts8, chain L (#12), sequence alignment
    3784 score = 23.5 
    3785 RMSD between 8 pruned atom pairs is 1.000 angstroms; (across all 12 pairs:
    3786 3.750) 
    3787  
    3788 
    3789 > matchmaker #12/K to #2/E pairing ss
    3790 
    3791 Using Nucleic matrix instead of BLOSUM-62 to match 3ts8 #12/K to 2ac0 #2/E 
    3792 Parameters 
    3793 --- 
    3794 Chain pairing | ss 
    3795 Alignment algorithm | Needleman-Wunsch 
    3796 Similarity matrix | Nucleic 
    3797 SS fraction | 0.3 
    3798 Gap open (HH/SS/other) | 18/18/6 
    3799 Gap extend | 1 
    3800 SS matrix |  |  | H | S | O 
    3801 ---|---|---|--- 
    3802 H | 6 | -9 | -6 
    3803 S |  | 6 | -6 
    3804 O |  |  | 4 
    3805 Iteration cutoff | 2 
    3806  
    3807 Matchmaker 2ac0, chain E (#2) with 3ts8, chain K (#12), sequence alignment
    3808 score = 23.5 
    3809 RMSD between 9 pruned atom pairs is 1.158 angstroms; (across all 12 pairs:
    3810 3.771) 
    3811  
    3812 
    3813 > matchmaker #12/L to #2/E pairing ss
    3814 
    3815 Using Nucleic matrix instead of BLOSUM-62 to match 3ts8 #12/L to 2ac0 #2/E 
    3816 Parameters 
    3817 --- 
    3818 Chain pairing | ss 
    3819 Alignment algorithm | Needleman-Wunsch 
    3820 Similarity matrix | Nucleic 
    3821 SS fraction | 0.3 
    3822 Gap open (HH/SS/other) | 18/18/6 
    3823 Gap extend | 1 
    3824 SS matrix |  |  | H | S | O 
    3825 ---|---|---|--- 
    3826 H | 6 | -9 | -6 
    3827 S |  | 6 | -6 
    3828 O |  |  | 4 
    3829 Iteration cutoff | 2 
    3830  
    3831 Matchmaker 2ac0, chain E (#2) with 3ts8, chain L (#12), sequence alignment
    3832 score = 23.5 
    3833 RMSD between 8 pruned atom pairs is 1.000 angstroms; (across all 12 pairs:
    3834 3.750) 
    3835  
    3836 
    3837 > hide #!2 models
    3838 
    3839 > select clear
    3840 
    3841 > show #!11 models
    3842 
    3843 > matchmaker #11/A to #12/A pairing ss
    3844 
    3845 Parameters 
    3846 --- 
    3847 Chain pairing | ss 
    3848 Alignment algorithm | Needleman-Wunsch 
    3849 Similarity matrix | BLOSUM-62 
    3850 SS fraction | 0.3 
    3851 Gap open (HH/SS/other) | 18/18/6 
    3852 Gap extend | 1 
    3853 SS matrix |  |  | H | S | O 
    3854 ---|---|---|--- 
    3855 H | 6 | -9 | -6 
    3856 S |  | 6 | -6 
    3857 O |  |  | 4 
    3858 Iteration cutoff | 2 
    3859  
    3860 Matchmaker 3ts8, chain A (#12) with 4hje, chain A (#11), sequence alignment
    3861 score = 941.4 
    3862 RMSD between 185 pruned atom pairs is 0.482 angstroms; (across all 198 pairs:
    3863 2.439) 
    3864  
    3865 
    3866 > matchmaker #11/B to #12/A pairing ss
    3867 
    3868 Parameters 
    3869 --- 
    3870 Chain pairing | ss 
    3871 Alignment algorithm | Needleman-Wunsch 
    3872 Similarity matrix | BLOSUM-62 
    3873 SS fraction | 0.3 
    3874 Gap open (HH/SS/other) | 18/18/6 
    3875 Gap extend | 1 
    3876 SS matrix |  |  | H | S | O 
    3877 ---|---|---|--- 
    3878 H | 6 | -9 | -6 
    3879 S |  | 6 | -6 
    3880 O |  |  | 4 
    3881 Iteration cutoff | 2 
    3882  
    3883 Matchmaker 3ts8, chain A (#12) with 4hje, chain B (#11), sequence alignment
    3884 score = 941.4 
    3885 RMSD between 183 pruned atom pairs is 0.461 angstroms; (across all 198 pairs:
    3886 2.441) 
    3887  
    3888 
    3889 > matchmaker #11/C to #12/A pairing ss
    3890 
    3891 Parameters 
    3892 --- 
    3893 Chain pairing | ss 
    3894 Alignment algorithm | Needleman-Wunsch 
    3895 Similarity matrix | BLOSUM-62 
    3896 SS fraction | 0.3 
    3897 Gap open (HH/SS/other) | 18/18/6 
    3898 Gap extend | 1 
    3899 SS matrix |  |  | H | S | O 
    3900 ---|---|---|--- 
    3901 H | 6 | -9 | -6 
    3902 S |  | 6 | -6 
    3903 O |  |  | 4 
    3904 Iteration cutoff | 2 
    3905  
    3906 Matchmaker 3ts8, chain A (#12) with 4hje, chain C (#11), sequence alignment
    3907 score = 941.4 
    3908 RMSD between 185 pruned atom pairs is 0.477 angstroms; (across all 198 pairs:
    3909 2.433) 
    3910  
    3911 
    3912 > matchmaker #11/D to #12/A pairing ss
    3913 
    3914 Parameters 
    3915 --- 
    3916 Chain pairing | ss 
    3917 Alignment algorithm | Needleman-Wunsch 
    3918 Similarity matrix | BLOSUM-62 
    3919 SS fraction | 0.3 
    3920 Gap open (HH/SS/other) | 18/18/6 
    3921 Gap extend | 1 
    3922 SS matrix |  |  | H | S | O 
    3923 ---|---|---|--- 
    3924 H | 6 | -9 | -6 
    3925 S |  | 6 | -6 
    3926 O |  |  | 4 
    3927 Iteration cutoff | 2 
    3928  
    3929 Matchmaker 3ts8, chain A (#12) with 4hje, chain D (#11), sequence alignment
    3930 score = 941.4 
    3931 RMSD between 183 pruned atom pairs is 0.466 angstroms; (across all 198 pairs:
    3932 2.450) 
    3933  
    3934 
    3935 > matchmaker #11/A to #12/A pairing ss
    3936 
    3937 Parameters 
    3938 --- 
    3939 Chain pairing | ss 
    3940 Alignment algorithm | Needleman-Wunsch 
    3941 Similarity matrix | BLOSUM-62 
    3942 SS fraction | 0.3 
    3943 Gap open (HH/SS/other) | 18/18/6 
    3944 Gap extend | 1 
    3945 SS matrix |  |  | H | S | O 
    3946 ---|---|---|--- 
    3947 H | 6 | -9 | -6 
    3948 S |  | 6 | -6 
    3949 O |  |  | 4 
    3950 Iteration cutoff | 2 
    3951  
    3952 Matchmaker 3ts8, chain A (#12) with 4hje, chain A (#11), sequence alignment
    3953 score = 941.4 
    3954 RMSD between 185 pruned atom pairs is 0.482 angstroms; (across all 198 pairs:
    3955 2.439) 
    3956  
    3957 
    3958 > hide #!11 models
    3959 
    3960 > show #!10 models
    3961 
    3962 > matchmaker #10/A to #12/A pairing ss
    3963 
    3964 Parameters 
    3965 --- 
    3966 Chain pairing | ss 
    3967 Alignment algorithm | Needleman-Wunsch 
    3968 Similarity matrix | BLOSUM-62 
    3969 SS fraction | 0.3 
    3970 Gap open (HH/SS/other) | 18/18/6 
    3971 Gap extend | 1 
    3972 SS matrix |  |  | H | S | O 
    3973 ---|---|---|--- 
    3974 H | 6 | -9 | -6 
    3975 S |  | 6 | -6 
    3976 O |  |  | 4 
    3977 Iteration cutoff | 2 
    3978  
    3979 Matchmaker 3ts8, chain A (#12) with 4ibw, chain A (#10), sequence alignment
    3980 score = 942.4 
    3981 RMSD between 184 pruned atom pairs is 0.577 angstroms; (across all 197 pairs:
    3982 2.357) 
    3983  
    3984 
    3985 > hide #!10 models
    3986 
    3987 > show #!9 models
    3988 
    3989 > matchmaker #9/A to #12/A pairing ss
    3990 
    3991 Parameters 
    3992 --- 
    3993 Chain pairing | ss 
    3994 Alignment algorithm | Needleman-Wunsch 
    3995 Similarity matrix | BLOSUM-62 
    3996 SS fraction | 0.3 
    3997 Gap open (HH/SS/other) | 18/18/6 
    3998 Gap extend | 1 
    3999 SS matrix |  |  | H | S | O 
    4000 ---|---|---|--- 
    4001 H | 6 | -9 | -6 
    4002 S |  | 6 | -6 
    4003 O |  |  | 4 
    4004 Iteration cutoff | 2 
    4005  
    4006 Matchmaker 3ts8, chain A (#12) with 4ibv, chain A (#9), sequence alignment
    4007 score = 944 
    4008 RMSD between 181 pruned atom pairs is 0.577 angstroms; (across all 197 pairs:
    4009 2.583) 
    4010  
    4011 
    4012 > hide #!9 models
    4013 
    4014 > show #!8 models
    4015 
    4016 > matchmaker #8/A to #12/A pairing ss
    4017 
    4018 Parameters 
    4019 --- 
    4020 Chain pairing | ss 
    4021 Alignment algorithm | Needleman-Wunsch 
    4022 Similarity matrix | BLOSUM-62 
    4023 SS fraction | 0.3 
    4024 Gap open (HH/SS/other) | 18/18/6 
    4025 Gap extend | 1 
    4026 SS matrix |  |  | H | S | O 
    4027 ---|---|---|--- 
    4028 H | 6 | -9 | -6 
    4029 S |  | 6 | -6 
    4030 O |  |  | 4 
    4031 Iteration cutoff | 2 
    4032  
    4033 Matchmaker 3ts8, chain A (#12) with 4ibu, chain A (#8), sequence alignment
    4034 score = 928.3 
    4035 RMSD between 184 pruned atom pairs is 0.578 angstroms; (across all 197 pairs:
    4036 2.491) 
    4037  
    4038 
    4039 > hide #!12 models
    4040 
    4041 > show #!12 models
    4042 
    4043 > matchmaker #8/B to #12/A pairing ss
    4044 
    4045 Parameters 
    4046 --- 
    4047 Chain pairing | ss 
    4048 Alignment algorithm | Needleman-Wunsch 
    4049 Similarity matrix | BLOSUM-62 
    4050 SS fraction | 0.3 
    4051 Gap open (HH/SS/other) | 18/18/6 
    4052 Gap extend | 1 
    4053 SS matrix |  |  | H | S | O 
    4054 ---|---|---|--- 
    4055 H | 6 | -9 | -6 
    4056 S |  | 6 | -6 
    4057 O |  |  | 4 
    4058 Iteration cutoff | 2 
    4059  
    4060 Matchmaker 3ts8, chain A (#12) with 4ibu, chain B (#8), sequence alignment
    4061 score = 915.7 
    4062 RMSD between 185 pruned atom pairs is 0.556 angstroms; (across all 198 pairs:
    4063 2.406) 
    4064  
    4065 
    4066 > matchmaker #8/D to #12/A pairing ss
    4067 
    4068 Parameters 
    4069 --- 
    4070 Chain pairing | ss 
    4071 Alignment algorithm | Needleman-Wunsch 
    4072 Similarity matrix | BLOSUM-62 
    4073 SS fraction | 0.3 
    4074 Gap open (HH/SS/other) | 18/18/6 
    4075 Gap extend | 1 
    4076 SS matrix |  |  | H | S | O 
    4077 ---|---|---|--- 
    4078 H | 6 | -9 | -6 
    4079 S |  | 6 | -6 
    4080 O |  |  | 4 
    4081 Iteration cutoff | 2 
    4082  
    4083 Matchmaker 3ts8, chain A (#12) with 4ibu, chain D (#8), sequence alignment
    4084 score = 910.9 
    4085 RMSD between 187 pruned atom pairs is 0.556 angstroms; (across all 196 pairs:
    4086 2.334) 
    4087  
    4088 
    4089 > show #!9 models
    4090 
    4091 > hide #!9 models
    4092 
    4093 > matchmaker #8/B to #12/A pairing ss
    4094 
    4095 Parameters 
    4096 --- 
    4097 Chain pairing | ss 
    4098 Alignment algorithm | Needleman-Wunsch 
    4099 Similarity matrix | BLOSUM-62 
    4100 SS fraction | 0.3 
    4101 Gap open (HH/SS/other) | 18/18/6 
    4102 Gap extend | 1 
    4103 SS matrix |  |  | H | S | O 
    4104 ---|---|---|--- 
    4105 H | 6 | -9 | -6 
    4106 S |  | 6 | -6 
    4107 O |  |  | 4 
    4108 Iteration cutoff | 2 
    4109  
    4110 Matchmaker 3ts8, chain A (#12) with 4ibu, chain B (#8), sequence alignment
    4111 score = 915.7 
    4112 RMSD between 185 pruned atom pairs is 0.556 angstroms; (across all 198 pairs:
    4113 2.406) 
    4114  
    4115 
    4116 > matchmaker #8/A to #12/A pairing ss
    4117 
    4118 Parameters 
    4119 --- 
    4120 Chain pairing | ss 
    4121 Alignment algorithm | Needleman-Wunsch 
    4122 Similarity matrix | BLOSUM-62 
    4123 SS fraction | 0.3 
    4124 Gap open (HH/SS/other) | 18/18/6 
    4125 Gap extend | 1 
    4126 SS matrix |  |  | H | S | O 
    4127 ---|---|---|--- 
    4128 H | 6 | -9 | -6 
    4129 S |  | 6 | -6 
    4130 O |  |  | 4 
    4131 Iteration cutoff | 2 
    4132  
    4133 Matchmaker 3ts8, chain A (#12) with 4ibu, chain A (#8), sequence alignment
    4134 score = 928.3 
    4135 RMSD between 184 pruned atom pairs is 0.578 angstroms; (across all 197 pairs:
    4136 2.491) 
    4137  
    4138 
    4139 > hide #!12 models
    4140 
    4141 > show #!12 models
    4142 
    4143 > hide #!12 models
    4144 
    4145 > show #!12 models
    4146 
    4147 > hide #!12 models
    4148 
    4149 > show #!12 models
    4150 
    4151 > hide #!8 models
    4152 
    4153 > show #!7 models
    4154 
    4155 > matchmaker #7/A to #12/A pairing ss
    4156 
    4157 Parameters 
    4158 --- 
    4159 Chain pairing | ss 
    4160 Alignment algorithm | Needleman-Wunsch 
    4161 Similarity matrix | BLOSUM-62 
    4162 SS fraction | 0.3 
    4163 Gap open (HH/SS/other) | 18/18/6 
    4164 Gap extend | 1 
    4165 SS matrix |  |  | H | S | O 
    4166 ---|---|---|--- 
    4167 H | 6 | -9 | -6 
    4168 S |  | 6 | -6 
    4169 O |  |  | 4 
    4170 Iteration cutoff | 2 
    4171  
    4172 Matchmaker 3ts8, chain A (#12) with 4mzr, chain A (#7), sequence alignment
    4173 score = 1190.7 
    4174 RMSD between 226 pruned atom pairs is 0.355 angstroms; (across all 234 pairs:
    4175 0.747) 
    4176  
    4177 
    4178 > show #!6 models
    4179 
    4180 > hide #!7 models
    4181 
    4182 > matchmaker #6/A to #12/A pairing ss
    4183 
    4184 Parameters 
    4185 --- 
    4186 Chain pairing | ss 
    4187 Alignment algorithm | Needleman-Wunsch 
    4188 Similarity matrix | BLOSUM-62 
    4189 SS fraction | 0.3 
    4190 Gap open (HH/SS/other) | 18/18/6 
    4191 Gap extend | 1 
    4192 SS matrix |  |  | H | S | O 
    4193 ---|---|---|--- 
    4194 H | 6 | -9 | -6 
    4195 S |  | 6 | -6 
    4196 O |  |  | 4 
    4197 Iteration cutoff | 2 
    4198  
    4199 Matchmaker 3ts8, chain A (#12) with 5bua, chain A (#6), sequence alignment
    4200 score = 951.9 
    4201 RMSD between 184 pruned atom pairs is 0.599 angstroms; (across all 200 pairs:
    4202 2.577) 
    4203  
    4204 
    4205 > hide #!6 models
    4206 
    4207 > show #!5 models
    4208 
    4209 > matchmaker #5/A to #12/A pairing ss
    4210 
    4211 Parameters 
    4212 --- 
    4213 Chain pairing | ss 
    4214 Alignment algorithm | Needleman-Wunsch 
    4215 Similarity matrix | BLOSUM-62 
    4216 SS fraction | 0.3 
    4217 Gap open (HH/SS/other) | 18/18/6 
    4218 Gap extend | 1 
    4219 SS matrix |  |  | H | S | O 
    4220 ---|---|---|--- 
    4221 H | 6 | -9 | -6 
    4222 S |  | 6 | -6 
    4223 O |  |  | 4 
    4224 Iteration cutoff | 2 
    4225  
    4226 Matchmaker 3ts8, chain A (#12) with 2ata, chain A (#5), sequence alignment
    4227 score = 945.3 
    4228 RMSD between 186 pruned atom pairs is 0.585 angstroms; (across all 197 pairs:
    4229 2.459) 
    4230  
    4231 
    4232 > show #!11 models
    4233 
    4234 > hide #!11 models
    4235 
    4236 > show #!10 models
    4237 
    4238 > hide #!10 models
    4239 
    4240 > show #!8 models
    4241 
    4242 > hide #!8 models
    4243 
    4244 > show #!8 models
    4245 
    4246 > hide #!8 models
    4247 
    4248 > show #!8 models
    4249 
    4250 > hide #!8 models
    4251 
    4252 > show #!4 models
    4253 
    4254 > hide #!5 models
    4255 
    4256 > matchmaker #4/A to #12/A pairing ss
    4257 
    4258 Parameters 
    4259 --- 
    4260 Chain pairing | ss 
    4261 Alignment algorithm | Needleman-Wunsch 
    4262 Similarity matrix | BLOSUM-62 
    4263 SS fraction | 0.3 
    4264 Gap open (HH/SS/other) | 18/18/6 
    4265 Gap extend | 1 
    4266 SS matrix |  |  | H | S | O 
    4267 ---|---|---|--- 
    4268 H | 6 | -9 | -6 
    4269 S |  | 6 | -6 
    4270 O |  |  | 4 
    4271 Iteration cutoff | 2 
    4272  
    4273 Matchmaker 3ts8, chain A (#12) with 2ahi, chain A (#4), sequence alignment
    4274 score = 947.7 
    4275 RMSD between 184 pruned atom pairs is 0.578 angstroms; (across all 197 pairs:
    4276 2.473) 
    4277  
    4278 
    4279 > show #!5 models
    4280 
    4281 > hide #!5 models
    4282 
    4283 > hide #!4 models
    4284 
    4285 > show #!3 models
    4286 
    4287 > matchmaker #3/A to #12/A pairing ss
    4288 
    4289 Parameters 
    4290 --- 
    4291 Chain pairing | ss 
    4292 Alignment algorithm | Needleman-Wunsch 
    4293 Similarity matrix | BLOSUM-62 
    4294 SS fraction | 0.3 
    4295 Gap open (HH/SS/other) | 18/18/6 
    4296 Gap extend | 1 
    4297 SS matrix |  |  | H | S | O 
    4298 ---|---|---|--- 
    4299 H | 6 | -9 | -6 
    4300 S |  | 6 | -6 
    4301 O |  |  | 4 
    4302 Iteration cutoff | 2 
    4303  
    4304 Matchmaker 3ts8, chain A (#12) with 5lgy, chain A (#3), sequence alignment
    4305 score = 944.4 
    4306 RMSD between 185 pruned atom pairs is 0.528 angstroms; (across all 197 pairs:
    4307 2.320) 
    4308  
    4309 
    4310 > hide #!3 models
    4311 
    4312 > show #!2 models
    4313 
    4314 > matchmaker #2/A to #12/A pairing ss
    4315 
    4316 Parameters 
    4317 --- 
    4318 Chain pairing | ss 
    4319 Alignment algorithm | Needleman-Wunsch 
    4320 Similarity matrix | BLOSUM-62 
    4321 SS fraction | 0.3 
    4322 Gap open (HH/SS/other) | 18/18/6 
    4323 Gap extend | 1 
    4324 SS matrix |  |  | H | S | O 
    4325 ---|---|---|--- 
    4326 H | 6 | -9 | -6 
    4327 S |  | 6 | -6 
    4328 O |  |  | 4 
    4329 Iteration cutoff | 2 
    4330  
    4331 Matchmaker 3ts8, chain A (#12) with 2ac0, chain A (#2), sequence alignment
    4332 score = 950.7 
    4333 RMSD between 187 pruned atom pairs is 0.618 angstroms; (across all 198 pairs:
    4334 2.423) 
    4335  
    4336 
    4337 > hide #!2 models
    4338 
    4339 > show #!1 models
    4340 
    4341 > matchmaker #1/A to #12/A pairing ss
    4342 
    4343 Parameters 
    4344 --- 
    4345 Chain pairing | ss 
    4346 Alignment algorithm | Needleman-Wunsch 
    4347 Similarity matrix | BLOSUM-62 
    4348 SS fraction | 0.3 
    4349 Gap open (HH/SS/other) | 18/18/6 
    4350 Gap extend | 1 
    4351 SS matrix |  |  | H | S | O 
    4352 ---|---|---|--- 
    4353 H | 6 | -9 | -6 
    4354 S |  | 6 | -6 
    4355 O |  |  | 4 
    4356 Iteration cutoff | 2 
    4357  
    4358 Matchmaker 3ts8, chain A (#12) with 1tup, chain A (#1), sequence alignment
    4359 score = 931.1 
    4360 RMSD between 184 pruned atom pairs is 0.596 angstroms; (across all 196 pairs:
    4361 2.426) 
    4362  
    4363 
    4364 > matchmaker #1/B to #12/A pairing ss
    4365 
    4366 Parameters 
    4367 --- 
    4368 Chain pairing | ss 
    4369 Alignment algorithm | Needleman-Wunsch 
    4370 Similarity matrix | BLOSUM-62 
    4371 SS fraction | 0.3 
    4372 Gap open (HH/SS/other) | 18/18/6 
    4373 Gap extend | 1 
    4374 SS matrix |  |  | H | S | O 
    4375 ---|---|---|--- 
    4376 H | 6 | -9 | -6 
    4377 S |  | 6 | -6 
    4378 O |  |  | 4 
    4379 Iteration cutoff | 2 
    4380  
    4381 Matchmaker 3ts8, chain A (#12) with 1tup, chain B (#1), sequence alignment
    4382 score = 919.1 
    4383 RMSD between 178 pruned atom pairs is 0.574 angstroms; (across all 194 pairs:
    4384 2.414) 
    4385  
    4386 
    4387 > select add #1
    4388 
    4389 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected 
    4390 
    4391 > select subtract #1
    4392 
    4393 Nothing selected 
    4394 
    4395 > show #!11 models
    4396 
    4397 > hide #!11 models
    4398 
    4399 > show #!11 models
    4400 
    4401 > hide #!1 models
    4402 
    4403 > hide #!12 models
    4404 
    4405 > hide #!11 models
    4406 
    4407 > show #!12 models
    4408 
    4409 > show #!11 models
    4410 
    4411 > hide #!11 models
    4412 
    4413 > show #!1 models
    4414 
    4415 > matchmaker #1/C to #12/A pairing ss
    4416 
    4417 Parameters 
    4418 --- 
    4419 Chain pairing | ss 
    4420 Alignment algorithm | Needleman-Wunsch 
    4421 Similarity matrix | BLOSUM-62 
    4422 SS fraction | 0.3 
    4423 Gap open (HH/SS/other) | 18/18/6 
    4424 Gap extend | 1 
    4425 SS matrix |  |  | H | S | O 
    4426 ---|---|---|--- 
    4427 H | 6 | -9 | -6 
    4428 S |  | 6 | -6 
    4429 O |  |  | 4 
    4430 Iteration cutoff | 2 
    4431  
    4432 Matchmaker 3ts8, chain A (#12) with 1tup, chain C (#1), sequence alignment
    4433 score = 913.7 
    4434 RMSD between 182 pruned atom pairs is 0.634 angstroms; (across all 195 pairs:
    4435 2.442) 
    4436  
    4437 
    4438 > show #!2 models
    4439 
    4440 > hide #!2 models
    4441 
    4442 > show #!2 models
    4443 
    4444 > hide #!2 models
    4445 
    4446 > show #!2 models
    4447 
    4448 > hide #!2 models
    4449 
    4450 > show #!3 models
    4451 
    4452 > hide #!3 models
    4453 
    4454 > show #!4 models
    4455 
    4456 > hide #!4 models
    4457 
    4458 > show #!4 models
    4459 
    4460 > hide #!4 models
    4461 
    4462 > show #!4 models
    4463 
    4464 > hide #!4 models
    4465 
    4466 > hide #!12 models
    4467 
    4468 > show #!12 models
    4469 
    4470 > matchmaker #1/B to #12/A pairing ss
    4471 
    4472 Parameters 
    4473 --- 
    4474 Chain pairing | ss 
    4475 Alignment algorithm | Needleman-Wunsch 
    4476 Similarity matrix | BLOSUM-62 
    4477 SS fraction | 0.3 
    4478 Gap open (HH/SS/other) | 18/18/6 
    4479 Gap extend | 1 
    4480 SS matrix |  |  | H | S | O 
    4481 ---|---|---|--- 
    4482 H | 6 | -9 | -6 
    4483 S |  | 6 | -6 
    4484 O |  |  | 4 
    4485 Iteration cutoff | 2 
    4486  
    4487 Matchmaker 3ts8, chain A (#12) with 1tup, chain B (#1), sequence alignment
    4488 score = 919.1 
    4489 RMSD between 178 pruned atom pairs is 0.574 angstroms; (across all 194 pairs:
    4490 2.414) 
    4491  
    4492 
    4493 > hide #!1 models
    4494 
    4495 > show #!6 models
    4496 
    4497 > show #!3 models
    4498 
    4499 > hide #!12 models
    4500 
    4501 > show #!12 models
    4502 
    4503 > show #!11 models
    4504 
    4505 > show #!10 models
    4506 
    4507 > show #!9 models
    4508 
    4509 > show #!8 models
    4510 
    4511 > hide #!6 models
    4512 
    4513 > hide #!3 models
    4514 
    4515 > hide #!12 models
    4516 
    4517 > hide #!11 models
    4518 
    4519 > hide #!8 models
    4520 
    4521 > hide #!9 models
    4522 
    4523 > show #!9 models
    4524 
    4525 > show #!8 models
    4526 
    4527 > open /Users/kompa012/Desktop/P53/4ibv.pdb1
    4528 
    4529 4ibv.pdb1 title: 
    4530 Human P53 core domain with hot spot mutation R273C and second-site suppressor
    4531 mutation S240R In sequence-specific complex with DNA [more info...] 
    4532  
    4533 98 atoms have alternate locations. Control/examine alternate locations with
    4534 Altloc Explorer [start tool...] or the altlocs command. 
    4535 Chain information for 4ibv.pdb1 
    4536 --- 
    4537 Chain | Description 
    4538 13.1/A | No description available 
    4539 13.2/A | No description available 
    4540 13.1/B | No description available 
    4541 13.2/B | No description available 
    4542  
    4543 98 atoms have alternate locations. Control/examine alternate locations with
    4544 Altloc Explorer [start tool...] or the altlocs command. 
    4545 
    4546 > hide #!13 models
    4547 
    4548 > hide #!13.1 models
    4549 
    4550 > show #!13.1 models
    4551 
    4552 > hide #!10 models
    4553 
    4554 > hide #!9 models
    4555 
    4556 > hide #!8 models
    4557 
    4558 > hide #!13.2 models
    4559 
    4560 > show #!13.2 models
    4561 
    4562 > hide #!13.1 models
    4563 
    4564 > show #!13.1 models
    4565 
    4566 > hide #!13.2 models
    4567 
    4568 > show #!13.2 models
    4569 
    4570 > show #!12 models
    4571 
    4572 > matchmaker #13.1/A to #12/A pairing ss
    4573 
    4574 Parameters 
    4575 --- 
    4576 Chain pairing | ss 
    4577 Alignment algorithm | Needleman-Wunsch 
    4578 Similarity matrix | BLOSUM-62 
    4579 SS fraction | 0.3 
    4580 Gap open (HH/SS/other) | 18/18/6 
    4581 Gap extend | 1 
    4582 SS matrix |  |  | H | S | O 
    4583 ---|---|---|--- 
    4584 H | 6 | -9 | -6 
    4585 S |  | 6 | -6 
    4586 O |  |  | 4 
    4587 Iteration cutoff | 2 
    4588  
    4589 Matchmaker 3ts8, chain A (#12) with 4ibv.pdb1, chain A (#13.1), sequence
    4590 alignment score = 944 
    4591 RMSD between 181 pruned atom pairs is 0.577 angstroms; (across all 197 pairs:
    4592 2.583) 
    4593  
    4594 No reference and/or match structure/chain chosen 
    4595 
    4596 > hide #!13 models
    4597 
    4598 > matchmaker #13.2/B to #12/B pairing ss
    4599 
    4600 Match chain (4ibv.pdb1 (#13.2) chain B) not compatible with BLOSUM-62
    4601 similarity matrix 
    4602 
    4603 > show #!13 models
    4604 
    4605 > matchmaker #13.2/A to #12/A pairing ss
    4606 
    4607 Parameters 
    4608 --- 
    4609 Chain pairing | ss 
    4610 Alignment algorithm | Needleman-Wunsch 
    4611 Similarity matrix | BLOSUM-62 
    4612 SS fraction | 0.3 
    4613 Gap open (HH/SS/other) | 18/18/6 
    4614 Gap extend | 1 
    4615 SS matrix |  |  | H | S | O 
    4616 ---|---|---|--- 
    4617 H | 6 | -9 | -6 
    4618 S |  | 6 | -6 
    4619 O |  |  | 4 
    4620 Iteration cutoff | 2 
    4621  
    4622 Matchmaker 3ts8, chain A (#12) with 4ibv.pdb1, chain A (#13.2), sequence
    4623 alignment score = 923.8 
    4624 RMSD between 181 pruned atom pairs is 0.577 angstroms; (across all 197 pairs:
    4625 2.583) 
    4626  
    4627 No reference and/or match structure/chain chosen 
    4628 
    4629 > matchmaker #13.2/A to #12/B pairing ss
    4630 
    4631 Parameters 
    4632 --- 
    4633 Chain pairing | ss 
    4634 Alignment algorithm | Needleman-Wunsch 
    4635 Similarity matrix | BLOSUM-62 
    4636 SS fraction | 0.3 
    4637 Gap open (HH/SS/other) | 18/18/6 
    4638 Gap extend | 1 
    4639 SS matrix |  |  | H | S | O 
    4640 ---|---|---|--- 
    4641 H | 6 | -9 | -6 
    4642 S |  | 6 | -6 
    4643 O |  |  | 4 
    4644 Iteration cutoff | 2 
    4645  
    4646 Matchmaker 3ts8, chain B (#12) with 4ibv.pdb1, chain A (#13.2), sequence
    4647 alignment score = 889.6 
    4648 RMSD between 178 pruned atom pairs is 0.879 angstroms; (across all 197 pairs:
    4649 1.492) 
    4650  
    4651 
    4652 > hide #!12 models
    4653 
    4654 > close #13
    4655 
    4656 > show #!12 models
    4657 
    4658 > show #!11 models
    4659 
    4660 > show #!8 models
    4661 
    4662 > hide #!8 models
    4663 
    4664 > hide #!11 models
    4665 
    4666 > show #!7 models
    4667 
    4668 > hide #!7 models
    4669 
    4670 > open 3kmd fromDatabase pdb format mmcif
    4671 
    4672 Summary of feedback from opening 3kmd fetched from pdb 
    4673 --- 
    4674 note | Fetching compressed mmCIF 3kmd from http://files.rcsb.org/download/3kmd.cif 
    4675  
    4676 3kmd title: 
    4677 Crystal structure of the p53 core domain bound to a full consensus site as a
    4678 self-assembled tetramer [more info...] 
    4679  
    4680 Chain information for 3kmd #13 
    4681 --- 
    4682 Chain | Description | UniProt 
    4683 A B C D | Cellular tumor antigen p53 | P53_HUMAN 92-291 
    4684 E F | 5'-D(*GP*GP*GP*CP*AP*TP*GP*CP*CP*TP*AP*GP*GP*CP*AP*TP*GP*CP*C)-3' |   
    4685  
    4686 Non-standard residues in 3kmd #13 
    4687 --- 
    4688 ZN — zinc ion 
    4689  
    4690 
    4691 > select add #13
    4692 
    4693 7587 atoms, 7298 bonds, 64 pseudobonds, 1365 residues, 3 models selected 
    4694 
    4695 > style sel sphere
    4696 
    4697 Changed 7587 atom styles 
    4698 
    4699 > style sel stick
    4700 
    4701 Changed 7587 atom styles 
    4702 
    4703 > show sel cartoons
    4704 
    4705 > hide sel atoms
    4706 
    4707 > select clear
    4708 
    4709 > hide #!13 models
    4710 
    4711 > show #!13 models
    4712 
    4713 > hide #!13 models
    4714 
    4715 > show #!13 models
    4716 
    4717 > matchmaker #13/A to #12/A pairing ss
    4718 
    4719 Parameters 
    4720 --- 
    4721 Chain pairing | ss 
    4722 Alignment algorithm | Needleman-Wunsch 
    4723 Similarity matrix | BLOSUM-62 
    4724 SS fraction | 0.3 
    4725 Gap open (HH/SS/other) | 18/18/6 
    4726 Gap extend | 1 
    4727 SS matrix |  |  | H | S | O 
    4728 ---|---|---|--- 
    4729 H | 6 | -9 | -6 
    4730 S |  | 6 | -6 
    4731 O |  |  | 4 
    4732 Iteration cutoff | 2 
    4733  
    4734 Matchmaker 3ts8, chain A (#12) with 3kmd, chain A (#13), sequence alignment
    4735 score = 938.4 
    4736 RMSD between 185 pruned atom pairs is 0.477 angstroms; (across all 198 pairs:
    4737 2.352) 
    4738  
    4739 
    4740 > hide #!12 models
    4741 
    4742 > show #!12 models
    4743 
    4744 > hide #!13 models
    4745 
    4746 > open 3igk fromDatabase pdb format mmcif
    4747 
    4748 Summary of feedback from opening 3igk fetched from pdb 
    4749 --- 
    4750 note | Fetching compressed mmCIF 3igk from http://files.rcsb.org/download/3igk.cif 
    4751  
    4752 3igk title: 
    4753 Diversity in DNA recognition by p53 revealed by crystal structures with
    4754 Hoogsteen base pairs (p53-DNA complex 2) [more info...] 
    4755  
    4756 Chain information for 3igk #14 
    4757 --- 
    4758 Chain | Description | UniProt 
    4759 A | Cellular tumor antigen p53 | P53_HUMAN 94-293 
    4760 B | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') |   
    4761  
    4762 Non-standard residues in 3igk #14 
    4763 --- 
    4764 ZN — zinc ion 
    4765  
    4766 3igk mmCIF Assemblies 
    4767 --- 
    4768 1| author_and_software_defined_assembly 
    4769  
    4770 57 atoms have alternate locations. Control/examine alternate locations with
    4771 Altloc Explorer [start tool...] or the altlocs command. 
    4772 
    4773 > open 3igl fromDatabase pdb format mmcif
    4774 
    4775 Summary of feedback from opening 3igl fetched from pdb 
    4776 --- 
    4777 note | Fetching compressed mmCIF 3igl from http://files.rcsb.org/download/3igl.cif 
    4778  
    4779 3igl title: 
    4780 Diversity in DNA recognition by p53 revealed by crystal structures with
    4781 Hoogsteen base pairs (p53-DNA complex 1) [more info...] 
    4782  
    4783 Chain information for 3igl #15 
    4784 --- 
    4785 Chain | Description | UniProt 
    4786 A | Cellular tumor antigen p53 | P53_HUMAN 94-293 
    4787 B | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') |   
    4788  
    4789 Non-standard residues in 3igl #15 
    4790 --- 
    4791 EDO — 1,2-ethanediol (ethylene glycol) 
    4792 ZN — zinc ion 
    4793  
    4794 3igl mmCIF Assemblies 
    4795 --- 
    4796 1| author_and_software_defined_assembly 
    4797  
    4798 28 atoms have alternate locations. Control/examine alternate locations with
    4799 Altloc Explorer [start tool...] or the altlocs command. 
    4800 
    4801 > open 3kz8 fromDatabase pdb format mmcif
    4802 
    4803 Summary of feedback from opening 3kz8 fetched from pdb 
    4804 --- 
    4805 notes | Fetching compressed mmCIF 3kz8 from http://files.rcsb.org/download/3kz8.cif 
    4806 Fetching CCD IOD from
    4807 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/IOD/IOD.cif 
    4808  
    4809 3kz8 title: 
    4810 Diversity in DNA recognition by p53 revealed by crystal structures with
    4811 Hoogsteen base pairs (p53-DNA complex 3) [more info...] 
    4812  
    4813 Chain information for 3kz8 #16 
    4814 --- 
    4815 Chain | Description | UniProt 
    4816 A B | Cellular tumor antigen p53 | P53_HUMAN 94-293 
    4817 C | DNA (5'-D(*TP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*C)-3') |   
    4818  
    4819 Non-standard residues in 3kz8 #16 
    4820 --- 
    4821 IOD — iodide ion 
    4822 ZN — zinc ion 
    4823  
    4824 3kz8 mmCIF Assemblies 
    4825 --- 
    4826 1| author_defined_assembly 
    4827  
    4828 87 atoms have alternate locations. Control/examine alternate locations with
    4829 Altloc Explorer [start tool...] or the altlocs command. 
    4830 
    4831 > matchmaker #14/A to #12/A pairing ss
    4832 
    4833 Parameters 
    4834 --- 
    4835 Chain pairing | ss 
    4836 Alignment algorithm | Needleman-Wunsch 
    4837 Similarity matrix | BLOSUM-62 
    4838 SS fraction | 0.3 
    4839 Gap open (HH/SS/other) | 18/18/6 
    4840 Gap extend | 1 
    4841 SS matrix |  |  | H | S | O 
    4842 ---|---|---|--- 
    4843 H | 6 | -9 | -6 
    4844 S |  | 6 | -6 
    4845 O |  |  | 4 
    4846 Iteration cutoff | 2 
    4847  
    4848 Matchmaker 3ts8, chain A (#12) with 3igk, chain A (#14), sequence alignment
    4849 score = 934.3 
    4850 RMSD between 181 pruned atom pairs is 0.672 angstroms; (across all 197 pairs:
    4851 2.601) 
    4852  
    4853 
    4854 > matchmaker #15/A to #12/A pairing ss
    4855 
    4856 Parameters 
    4857 --- 
    4858 Chain pairing | ss 
    4859 Alignment algorithm | Needleman-Wunsch 
    4860 Similarity matrix | BLOSUM-62 
    4861 SS fraction | 0.3 
    4862 Gap open (HH/SS/other) | 18/18/6 
    4863 Gap extend | 1 
    4864 SS matrix |  |  | H | S | O 
    4865 ---|---|---|--- 
    4866 H | 6 | -9 | -6 
    4867 S |  | 6 | -6 
    4868 O |  |  | 4 
    4869 Iteration cutoff | 2 
    4870  
    4871 Matchmaker 3ts8, chain A (#12) with 3igl, chain A (#15), sequence alignment
    4872 score = 944.1 
    4873 RMSD between 182 pruned atom pairs is 0.630 angstroms; (across all 197 pairs:
    4874 2.594) 
    4875  
    4876 
    4877 > matchmaker #16/A to #12/A pairing ss
    4878 
    4879 Parameters 
    4880 --- 
    4881 Chain pairing | ss 
    4882 Alignment algorithm | Needleman-Wunsch 
    4883 Similarity matrix | BLOSUM-62 
    4884 SS fraction | 0.3 
    4885 Gap open (HH/SS/other) | 18/18/6 
    4886 Gap extend | 1 
    4887 SS matrix |  |  | H | S | O 
    4888 ---|---|---|--- 
    4889 H | 6 | -9 | -6 
    4890 S |  | 6 | -6 
    4891 O |  |  | 4 
    4892 Iteration cutoff | 2 
    4893  
    4894 Matchmaker 3ts8, chain A (#12) with 3kz8, chain A (#16), sequence alignment
    4895 score = 948.3 
    4896 RMSD between 180 pruned atom pairs is 0.603 angstroms; (across all 195 pairs:
    4897 2.497) 
    4898  
    4899 
    4900 > hide #!14 models
    4901 
    4902 > hide #!15 models
    4903 
    4904 > hide #!12 models
    4905 
    4906 > show #!12 models
    4907 
    4908 > hide #!16 models
    4909 
    4910 > open 3q05 fromDatabase pdb format mmcif
    4911 
    4912 Summary of feedback from opening 3q05 fetched from pdb 
    4913 --- 
    4914 note | Fetching compressed mmCIF 3q05 from http://files.rcsb.org/download/3q05.cif 
    4915  
    4916 3q05 title: 
    4917 An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence
    4918 specificity [more info...] 
    4919  
    4920 Chain information for 3q05 #17 
    4921 --- 
    4922 Chain | Description | UniProt 
    4923 A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-291 321-356 
    4924 K | DNA (26-MER) |   
    4925 L | DNA (26-MER) |   
    4926  
    4927 Non-standard residues in 3q05 #17 
    4928 --- 
    4929 ZN — zinc ion 
    4930  
    4931 
    4932 > open 3q06 fromDatabase pdb format mmcif
    4933 
    4934 Summary of feedback from opening 3q06 fetched from pdb 
    4935 --- 
    4936 note | Fetching compressed mmCIF 3q06 from http://files.rcsb.org/download/3q06.cif 
    4937  
    4938 3q06 title: 
    4939 An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence
    4940 specificity [more info...] 
    4941  
    4942 Chain information for 3q06 #18 
    4943 --- 
    4944 Chain | Description | UniProt 
    4945 A B C D | Cellular tumor antigen p53 | P53_HUMAN 96-292 321-354 
    4946 K | DNA (26-MER) |   
    4947 L | DNA (26-MER) |   
    4948  
    4949 Non-standard residues in 3q06 #18 
    4950 --- 
    4951 ZN — zinc ion 
    4952  
    4953 
    4954 > select add #17
    4955 
    4956 8677 atoms, 8800 bonds, 77 pseudobonds, 1153 residues, 3 models selected 
    4957 
    4958 > select add #18
    4959 
    4960 17133 atoms, 17540 bonds, 136 pseudobonds, 2133 residues, 6 models selected 
    4961 
    4962 > style sel stick
    4963 
    4964 Changed 17133 atom styles 
    4965 
    4966 > hide sel atoms
    4967 
    4968 > show sel cartoons
    4969 
    4970 > matchmaker #17/A to #12/A pairing ss
    4971 
    4972 Parameters 
    4973 --- 
    4974 Chain pairing | ss 
    4975 Alignment algorithm | Needleman-Wunsch 
    4976 Similarity matrix | BLOSUM-62 
    4977 SS fraction | 0.3 
    4978 Gap open (HH/SS/other) | 18/18/6 
    4979 Gap extend | 1 
    4980 SS matrix |  |  | H | S | O 
    4981 ---|---|---|--- 
    4982 H | 6 | -9 | -6 
    4983 S |  | 6 | -6 
    4984 O |  |  | 4 
    4985 Iteration cutoff | 2 
    4986  
    4987 Matchmaker 3ts8, chain A (#12) with 3q05, chain A (#17), sequence alignment
    4988 score = 1171 
    4989 RMSD between 223 pruned atom pairs is 0.512 angstroms; (across all 234 pairs:
    4990 1.303) 
    4991  
    4992 
    4993 > matchmaker #18/A to #12/A pairing ss
    4994 
    4995 Parameters 
    4996 --- 
    4997 Chain pairing | ss 
    4998 Alignment algorithm | Needleman-Wunsch 
    4999 Similarity matrix | BLOSUM-62 
    5000 SS fraction | 0.3 
    5001 Gap open (HH/SS/other) | 18/18/6 
    5002 Gap extend | 1 
    5003 SS matrix |  |  | H | S | O 
    5004 ---|---|---|--- 
    5005 H | 6 | -9 | -6 
    5006 S |  | 6 | -6 
    5007 O |  |  | 4 
    5008 Iteration cutoff | 2 
    5009  
    5010 Matchmaker 3ts8, chain A (#12) with 3q06, chain A (#18), sequence alignment
    5011 score = 1133.5 
    5012 RMSD between 221 pruned atom pairs is 0.602 angstroms; (across all 230 pairs:
    5013 1.295) 
    5014  
    5015 
    5016 > select subtract #17
    5017 
    5018 8456 atoms, 8740 bonds, 59 pseudobonds, 980 residues, 3 models selected 
    5019 
    5020 > select subtract #18
    5021 
    5022 Nothing selected 
    5023 
    5024 > hide #!17 models
    5025 
    5026 > hide #!18 models
    5027 
    5028 > open 3d0a fromDatabase pdb format mmcif
    5029 
    5030 Summary of feedback from opening 3d0a fetched from pdb 
    5031 --- 
    5032 warnings | Atom P has no neighbors to form bonds with according to residue template for DG /F:3 
    5033 Atom CE has no neighbors to form bonds with according to residue template for
    5034 MET /B:243 
    5035 note | Fetching compressed mmCIF 3d0a from http://files.rcsb.org/download/3d0a.cif 
    5036  
    5037 3d0a title: 
    5038 Human p53 core domain with hot spot mutation R249S and second site suppressor
    5039 mutation H168R in sequence-specific complex with DNA [more info...] 
    5040  
    5041 Chain information for 3d0a #19 
    5042 --- 
    5043 Chain | Description | UniProt 
    5044 A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-293 
    5045 E F G H | DNA (5'-D(*DCP*DGP*DGP*DGP*DCP*DAP*DTP*DGP*DCP*DCP*DCP*DG)-3') |   
    5046  
    5047 Non-standard residues in 3d0a #19 
    5048 --- 
    5049 ZN — zinc ion 
    5050  
    5051 3d0a mmCIF Assemblies 
    5052 --- 
    5053 1| author_and_software_defined_assembly 
    5054 2| author_and_software_defined_assembly 
    5055  
    5056 224 atoms have alternate locations. Control/examine alternate locations with
    5057 Altloc Explorer [start tool...] or the altlocs command. 
    5058 
    5059 > select add #19
    5060 
    5061 7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 4 models selected 
    5062 
    5063 > style sel stick
    5064 
    5065 Changed 7633 atom styles 
    5066 
    5067 > hide sel atoms
    5068 
    5069 > show sel cartoons
    5070 
    5071 > matchmaker #19/A to #12/A pairing ss
    5072 
    5073 Parameters 
    5074 --- 
    5075 Chain pairing | ss 
    5076 Alignment algorithm | Needleman-Wunsch 
    5077 Similarity matrix | BLOSUM-62 
    5078 SS fraction | 0.3 
    5079 Gap open (HH/SS/other) | 18/18/6 
    5080 Gap extend | 1 
    5081 SS matrix |  |  | H | S | O 
    5082 ---|---|---|--- 
    5083 H | 6 | -9 | -6 
    5084 S |  | 6 | -6 
    5085 O |  |  | 4 
    5086 Iteration cutoff | 2 
    5087  
    5088 Matchmaker 3ts8, chain A (#12) with 3d0a, chain A (#19), sequence alignment
    5089 score = 917.5 
    5090 RMSD between 185 pruned atom pairs is 0.571 angstroms; (across all 196 pairs:
    5091 2.397) 
    5092  
    5093 
    5094 > hide #!12 models
    5095 
    5096 > show #!12 models
    5097 
    5098 > show #!1 models
    5099 
    5100 > show #!2 models
    5101 
    5102 > show #!3 models
    5103 
    5104 > show #!4 models
    5105 
    5106 > show #!5 models
    5107 
    5108 > show #!6 models
    5109 
    5110 > show #!7 models
    5111 
    5112 > show #!8 models
    5113 
    5114 > show #!9 models
    5115 
    5116 > show #!10 models
    5117 
    5118 > show #!11 models
    5119 
    5120 > show #!13 models
    5121 
    5122 > show #!14 models
    5123 
    5124 > show #!16 models
    5125 
    5126 > show #!15 models
    5127 
    5128 > show #!17 models
    5129 
    5130 > show #!18 models
    5131 
    5132 > select clear
    5133 
    5134 > select add #1
    5135 
    5136 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected 
    5137 
    5138 > select subtract #1
    5139 
    5140 Nothing selected 
    5141 
    5142 > hide #!3 models
    5143 
    5144 > hide #!2 models
    5145 
    5146 > hide #!4 models
    5147 
    5148 > hide #!5 models
    5149 
    5150 > hide #!6 models
    5151 
    5152 > hide #!7 models
    5153 
    5154 > hide #!8 models
    5155 
    5156 > hide #!9 models
    5157 
    5158 > hide #!10 models
    5159 
    5160 > hide #!11 models
    5161 
    5162 > hide #!12 models
    5163 
    5164 > hide #!13 models
    5165 
    5166 > hide #!14 models
    5167 
    5168 > hide #!15 models
    5169 
    5170 > hide #!16 models
    5171 
    5172 > hide #!17 models
    5173 
    5174 > hide #!18 models
    5175 
    5176 > hide #!19 models
    5177 
    5178 > show #!12 models
    5179 
    5180 > hide #!12 models
    5181 
    5182 > ui tool show "Show Sequence Viewer"
    5183 
    5184 > sequence chain #1/B
    5185 
    5186 Alignment identifier is 1/B 
    5187 
    5188 > select add #1
    5189 
    5190 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected 
    5191 
    5192 > show sel surfaces
    5193 
    5194 Cell requested for row 12 is out of bounds for table with 21 rows! Resizing
    5195 table model. 
    5196 
    5197 > hide sel surfaces
    5198 
    5199 > select subtract #1.4
    5200 
    5201 4306 atoms, 4092 bonds, 51 pseudobonds, 820 residues, 8 models selected 
    5202 
    5203 > select subtract #1.7
    5204 
    5205 3871 atoms, 3602 bonds, 8 pseudobonds, 799 residues, 6 models selected 
    5206 
    5207 > select subtract #1.6
    5208 
    5209 3451 atoms, 3134 bonds, 8 pseudobonds, 778 residues, 5 models selected 
    5210 
    5211 > hide sel cartoons
    5212 
    5213 > select add #1
    5214 
    5215 5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 5 models selected 
    5216 
    5217 > select subtract #1
    5218 
    5219 5 models selected 
    5220 
    5221 > select add #1.7
    5222 
    5223 435 atoms, 21 residues, 1 model selected 
    5224 
    5225 > select add #1.6
    5226 
    5227 855 atoms, 42 residues, 2 models selected 
    5228 
    5229 > select add #1.4
    5230 
    5231 2377 atoms, 236 residues, 3 models selected 
    5232 
    5233 > hide sel cartoons
    5234 
    5235 > show sel atoms
    5236 
    5237 > select clear
    5238 
    5239 > select
    5240 > #1/B:110-112,124-127,132-135,141-146,156-163,195-197,204-207,214-219,230-236,251-258,264-274
    5241 
    5242 530 atoms, 532 bonds, 64 residues, 1 model selected 
    5243 
    5244 > select #1/B:220
    5245 
    5246 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5247 
    5248 > select #1/B:220
    5249 
    5250 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5251 
    5252 > save "/Users/kompa012/Desktop/P53/Before mutation.cxs"
    5253 
    5254 > ui tool show Rotamers
    5255 
    5256 > swapaa interactive sel SER rotLib Dunbrack
    5257 
    5258 1tup #1/B TYR 220: phi -77.3, psi 125.7 trans 
    5259 Changed 9 bond radii 
    5260 
    5261 > swapaa interactive sel SER rotLib Dynameomics
    5262 
    5263 1tup #!1/B TYR 220: phi -77.3, psi 125.7 trans 
    5264 Changed 9 bond radii 
    5265 
    5266 > hide sel atoms
    5267 
    5268 > show sel atoms
    5269 
    5270 > style sel stick
    5271 
    5272 Changed 12 atom styles 
    5273 
    5274 > style sel stick
    5275 
    5276 Changed 12 atom styles 
    5277 
    5278 > style sel ball
    5279 
    5280 Changed 12 atom styles 
    5281 
    5282 > style sel stick
    5283 
    5284 Changed 12 atom styles 
    5285 
    5286 > style (#!1 & sel) ringFill thin
    5287 
    5288 Changed 1 residue ring style 
    5289 
    5290 > style (#!1 & sel) stick
    5291 
    5292 Changed 12 atom styles 
    5293 
    5294 > style (#!1 & sel) ringFill off
    5295 
    5296 Changed 1 residue ring style 
    5297 
    5298 > color (#!1 & sel) byhetero
    5299 
    5300 > select add #1.8
    5301 
    5302 24 atoms, 21 bonds, 4 residues, 6 models selected 
    5303 
    5304 > select subtract #1.4
    5305 
    5306 12 atoms, 9 bonds, 3 residues, 5 models selected 
    5307 
    5308 > select add #1.9
    5309 
    5310 24 atoms, 18 bonds, 6 residues, 8 models selected 
    5311 
    5312 > close #1.8-9
    5313 
    5314 > select #1/B:220@CA
    5315 
    5316 1 atom, 1 residue, 1 model selected 
    5317 
    5318 > select #1/B:220@CA
    5319 
    5320 1 atom, 1 residue, 1 model selected 
    5321 
    5322 > select #1/B:220
    5323 
    5324 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5325 
    5326 > select #1/B:220
    5327 
    5328 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5329 
    5330 > swapaa interactive sel SER rotLib Richardson.common
    5331 
    5332 1tup #1/B TYR 220: phi -77.3, psi 125.7 trans 
    5333 Changed 9 bond radii 
    5334 
    5335 > hide sel atoms
    5336 
    5337 > select #!1/B:220
    5338 
    5339 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5340 
    5341 > select #!1/B:220
    5342 
    5343 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5344 
    5345 > select #!1/B:220
    5346 
    5347 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5348 
    5349 > select #!1/B:220
    5350 
    5351 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5352 
    5353 > select #!1/B:220
    5354 
    5355 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5356 
    5357 > select #!1/B:220
    5358 
    5359 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5360 
    5361 > swapaa interactive sel TYR rotLib Richardson.common
    5362 
    5363 1tup #!1/B TYR 220: phi -77.3, psi 125.7 trans 
    5364 Changed 40 bond radii 
    5365 
    5366 > select add #1.9
    5367 
    5368 52 atoms, 52 bonds, 5 residues, 7 models selected 
    5369 
    5370 > select add #1.8
    5371 
    5372 64 atoms, 61 bonds, 8 residues, 11 models selected 
    5373 
    5374 > close #1.8-9
    5375 
    5376 > select #1/B:220
    5377 
    5378 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5379 
    5380 > select #1/B:220
    5381 
    5382 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5383 
    5384 > swapaa interactive sel TYR rotLib Richardson.mode
    5385 
    5386 1tup #1/B TYR 220: phi -77.3, psi 125.7 trans 
    5387 Changed 40 bond radii 
    5388 
    5389 > close #1.8
    5390 
    5391 > swapaa interactive sel SER rotLib Richardson.mode
    5392 
    5393 1tup #1/B TYR 220: phi -77.3, psi 125.7 trans 
    5394 Changed 9 bond radii 
    5395 
    5396 > hide #1.8.3 models
    5397 
    5398 > hide #1.8.2 models
    5399 
    5400 > close #1.8
    5401 
    5402 > swapaa interactive sel SER rotLib Dunbrack
    5403 
    5404 1tup #1/B TYR 220: phi -77.3, psi 125.7 trans 
    5405 Changed 9 bond radii 
    5406 
    5407 > show sel atoms
    5408 
    5409 > hide sel atoms
    5410 
    5411 > show sel atoms
    5412 
    5413 > hide #1.8.3 models
    5414 
    5415 > hide #1.8.2 models
    5416 
    5417 > hide sel atoms
    5418 
    5419 > show sel atoms
    5420 
    5421 > hide sel atoms
    5422 
    5423 > select #!1/B:220@CD2
    5424 
    5425 1 atom, 1 residue, 1 model selected 
    5426 
    5427 > hide sel atoms
    5428 
    5429 > select #!1/B:220@CG
    5430 
    5431 1 atom, 1 residue, 1 model selected 
    5432 
    5433 > hide sel atoms
    5434 
    5435 > select #!1/B:220@CZ
    5436 
    5437 1 atom, 1 residue, 1 model selected 
    5438 
    5439 > hide sel atoms
    5440 
    5441 > select #!1/B:220@CE2
    5442 
    5443 1 atom, 1 residue, 1 model selected 
    5444 
    5445 > hide sel atoms
    5446 
    5447 > select #!1/B:220@OH
    5448 
    5449 1 atom, 1 residue, 1 model selected 
    5450 
    5451 > hide sel atoms
    5452 
    5453 > select #!1/B:220@CE1
    5454 
    5455 1 atom, 1 residue, 1 model selected 
    5456 
    5457 > hide sel atoms
    5458 
    5459 > select #!1/B:220@CD1
    5460 
    5461 1 atom, 1 residue, 1 model selected 
    5462 
    5463 > hide sel atoms
    5464 
    5465 > style sel ball
    5466 
    5467 Changed 0 atom styles 
    5468 
    5469 > style sel ball
    5470 
    5471 Changed 0 atom styles 
    5472 
    5473 > style sel sphere
    5474 
    5475 Changed 0 atom styles 
    5476 
    5477 > style sel sphere
    5478 
    5479 Changed 0 atom styles 
    5480 
    5481 > select add #1.8.1
    5482 
    5483 4 atoms, 3 bonds, 1 residue, 1 model selected 
    5484 
    5485 > style sel sphere
    5486 
    5487 Changed 4 atom styles 
    5488 
    5489 > style sel ball
    5490 
    5491 Changed 4 atom styles 
    5492 
    5493 > style sel stick
    5494 
    5495 Changed 4 atom styles 
    5496 
    5497 > select clear
    5498 
    5499 > select add #1.8.1
    5500 
    5501 4 atoms, 3 bonds, 1 residue, 1 model selected 
    5502 
    5503 > style sel sphere
    5504 
    5505 Changed 4 atom styles 
    5506 
    5507 > select subtract #1.8.1
    5508 
    5509 Nothing selected 
    5510 
    5511 > select add #1.8.1
    5512 
    5513 4 atoms, 3 bonds, 1 residue, 1 model selected 
    5514 
    5515 > show #1.8.2 models
    5516 
    5517 > select add #1.8.2
    5518 
    5519 8 atoms, 6 bonds, 2 residues, 2 models selected 
    5520 
    5521 > style sel stick
    5522 
    5523 Changed 8 atom styles 
    5524 
    5525 > show #1.8.3 models
    5526 
    5527 > select add #1.8
    5528 
    5529 12 atoms, 9 bonds, 3 residues, 4 models selected 
    5530 
    5531 > select subtract #1.8
    5532 
    5533 Nothing selected 
    5534 
    5535 > hide #!1.8 models
    5536 
    5537 > select #!1/B:220
    5538 
    5539 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5540 
    5541 > select #!1/B:220
    5542 
    5543 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5544 
    5545 > show sel atoms
    5546 
    5547 > select #1/B:282
    5548 
    5549 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5550 
    5551 > select #1/B:282
    5552 
    5553 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5554 
    5555 > color (#!1 & sel) byhetero
    5556 
    5557 > select #1/B:280-281
    5558 
    5559 19 atoms, 18 bonds, 2 residues, 1 model selected 
    5560 
    5561 > select #1/B:280-284
    5562 
    5563 48 atoms, 47 bonds, 5 residues, 1 model selected 
    5564 
    5565 > select subtract #1.4
    5566 
    5567 1 model selected 
    5568 
    5569 > select add #1.3
    5570 
    5571 1535 atoms, 196 residues, 1 model selected 
    5572 
    5573 > show sel cartoons
    5574 
    5575 > select #1/A:282
    5576 
    5577 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5578 
    5579 > show sel atoms
    5580 
    5581 > hide sel atoms
    5582 
    5583 > select subtract #1.3
    5584 
    5585 1 model selected 
    5586 
    5587 > select add #1.3
    5588 
    5589 1535 atoms, 196 residues, 1 model selected 
    5590 
    5591 > hide sel cartoons
    5592 
    5593 > select add #1.5
    5594 
    5595 3064 atoms, 391 residues, 2 models selected 
    5596 
    5597 > show sel cartoons
    5598 
    5599 > select subtract #1.5
    5600 
    5601 1535 atoms, 196 residues, 3 models selected 
    5602 
    5603 > hide sel cartoons
    5604 
    5605 > select #1/C:282
    5606 
    5607 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5608 
    5609 > show sel atoms
    5610 
    5611 > hide sel atoms
    5612 
    5613 > select subtract #1.5
    5614 
    5615 1 model selected 
    5616 
    5617 > select add #1.5
    5618 
    5619 1529 atoms, 195 residues, 1 model selected 
    5620 
    5621 > hide sel cartoons
    5622 
    5623 > select add #1.3
    5624 
    5625 3064 atoms, 391 residues, 2 models selected 
    5626 
    5627 > select subtract #1.3
    5628 
    5629 1529 atoms, 195 residues, 3 models selected 
    5630 
    5631 > select add #1.4
    5632 
    5633 3051 atoms, 389 residues, 2 models selected 
    5634 
    5635 > select subtract #1.5
    5636 
    5637 1522 atoms, 194 residues, 3 models selected 
    5638 
    5639 > show sel cartoons
    5640 
    5641 > select clear
    5642 
    5643 > select #1/B:282
    5644 
    5645 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5646 
    5647 > select #1/B:282
    5648 
    5649 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5650 
    5651 > swapaa interactive sel GLN rotLib Dunbrack
    5652 
    5653 1tup #1/B ARG 282: phi -80.7, psi -38.2 trans 
    5654 Changed 648 bond radii 
    5655 
    5656 > select add #1.8.108
    5657 
    5658 18 atoms, 16 bonds, 2 residues, 3 models selected 
    5659 
    5660 > select add #1.8.107
    5661 
    5662 25 atoms, 22 bonds, 3 residues, 4 models selected 
    5663 
    5664 > select add #1.8.106
    5665 
    5666 32 atoms, 28 bonds, 4 residues, 5 models selected 
    5667 
    5668 > select add #1.8.105
    5669 
    5670 39 atoms, 34 bonds, 5 residues, 6 models selected 
    5671 
    5672 > select add #1.8.104
    5673 
    5674 46 atoms, 40 bonds, 6 residues, 7 models selected 
    5675 
    5676 > select add #1.8.103
    5677 
    5678 53 atoms, 46 bonds, 7 residues, 8 models selected 
    5679 
    5680 > select add #1.8.102
    5681 
    5682 60 atoms, 52 bonds, 8 residues, 9 models selected 
    5683 
    5684 > select add #1.8.101
    5685 
    5686 67 atoms, 58 bonds, 9 residues, 10 models selected 
    5687 
    5688 > select add #1.8
    5689 
    5690 767 atoms, 658 bonds, 109 residues, 111 models selected 
    5691 
    5692 > select subtract #1.8
    5693 
    5694 11 atoms, 10 bonds, 1 residue, 2 models selected 
    5695 
    5696 > select add #1.8
    5697 
    5698 767 atoms, 658 bonds, 109 residues, 111 models selected 
    5699 
    5700 > select subtract #1.8.39
    5701 
    5702 760 atoms, 652 bonds, 108 residues, 110 models selected 
    5703 
    5704 > select subtract #1.8.38
    5705 
    5706 753 atoms, 646 bonds, 107 residues, 109 models selected 
    5707 
    5708 > select add #1.8.38
    5709 
    5710 760 atoms, 652 bonds, 108 residues, 110 models selected 
    5711 
    5712 > select subtract #1.8.40
    5713 
    5714 753 atoms, 646 bonds, 107 residues, 109 models selected 
    5715 
    5716 > select add #1.8.40
    5717 
    5718 760 atoms, 652 bonds, 108 residues, 110 models selected 
    5719 
    5720 > hide sel atoms
    5721 
    5722 > select #!1/B:282-283
    5723 
    5724 22 atoms, 21 bonds, 2 residues, 1 model selected 
    5725 
    5726 > select #!1/B:282-283
    5727 
    5728 22 atoms, 21 bonds, 2 residues, 1 model selected 
    5729 
    5730 > select #!1/B:282
    5731 
    5732 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5733 
    5734 > select #!1/B:282
    5735 
    5736 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5737 
    5738 > show sel atoms
    5739 
    5740 > select add #1.8.40
    5741 
    5742 18 atoms, 16 bonds, 2 residues, 3 models selected 
    5743 
    5744 > show sel atoms
    5745 
    5746 > select add #1.8.41
    5747 
    5748 25 atoms, 22 bonds, 3 residues, 4 models selected 
    5749 
    5750 > show sel atoms
    5751 
    5752 > select subtract #1.8.40
    5753 
    5754 18 atoms, 16 bonds, 2 residues, 3 models selected 
    5755 
    5756 > select add #1.8.40
    5757 
    5758 25 atoms, 22 bonds, 3 residues, 4 models selected 
    5759 
    5760 > select subtract #1.8.41
    5761 
    5762 18 atoms, 16 bonds, 2 residues, 3 models selected 
    5763 
    5764 > hide sel atoms
    5765 
    5766 > select add #1.8
    5767 
    5768 767 atoms, 658 bonds, 109 residues, 111 models selected 
    5769 
    5770 > hide sel atoms
    5771 
    5772 > select #!1/B:282-289
    5773 
    5774 72 atoms, 71 bonds, 8 residues, 1 model selected 
    5775 
    5776 > select #!1/B:282-289
    5777 
    5778 72 atoms, 71 bonds, 8 residues, 1 model selected 
    5779 
    5780 > select #!1/B:282
    5781 
    5782 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5783 
    5784 > select #!1/B:282
    5785 
    5786 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5787 
    5788 > show sel atoms
    5789 
    5790 > select #!1/B:220
    5791 
    5792 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5793 
    5794 > select #!1/B:220
    5795 
    5796 12 atoms, 12 bonds, 1 residue, 1 model selected 
    5797 
    5798 > swapaa interactive sel CYS rotLib Dunbrack
    5799 
    5800 1tup #!1/B TYR 220: phi -77.3, psi 125.7 trans 
    5801 Changed 9 bond radii 
    5802 
    5803 > select add #1
    5804 
    5805 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 117 models selected 
    5806 
    5807 > select subtract #1
    5808 
    5809 5 models selected 
    5810 
    5811 > hide #!1 models
    5812 
    5813 > show #!1 models
    5814 
    5815 > show #!2 models
    5816 
    5817 > select add #2
    5818 
    5819 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected 
    5820 
    5821 > show sel atoms
    5822 
    5823 > select clear
    5824 
    5825 > show #!3 models
    5826 
    5827 > show #!4 models
    5828 
    5829 > show #!5 models
    5830 
    5831 > show #!6 models
    5832 
    5833 > show #!7 models
    5834 
    5835 > show #!8 models
    5836 
    5837 > show #!9 models
    5838 
    5839 > show #!10 models
    5840 
    5841 > show #!12 models
    5842 
    5843 > show #!11 models
    5844 
    5845 > show #!19 models
    5846 
    5847 > show #!18 models
    5848 
    5849 > show #!17 models
    5850 
    5851 > show #!16 models
    5852 
    5853 > show #!15 models
    5854 
    5855 > show #!14 models
    5856 
    5857 > show #!13 models
    5858 
    5859 > select add #1
    5860 
    5861 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 116 models selected 
    5862 
    5863 > select subtract #1
    5864 
    5865 5 models selected 
    5866 
    5867 > select add #3
    5868 
    5869 7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 3 models selected 
    5870 
    5871 > select add #4
    5872 
    5873 15128 atoms, 14594 bonds, 131 pseudobonds, 2688 residues, 6 models selected 
    5874 
    5875 > select add #5
    5876 
    5877 22909 atoms, 21901 bonds, 201 pseudobonds, 4243 residues, 17 models selected 
    5878 
    5879 > select add #6
    5880 
    5881 24841 atoms, 23736 bonds, 205 pseudobonds, 4609 residues, 27 models selected 
    5882 
    5883 > select add #7
    5884 
    5885 33434 atoms, 32548 bonds, 278 pseudobonds, 5670 residues, 30 models selected 
    5886 
    5887 > select add #8
    5888 
    5889 41522 atoms, 39905 bonds, 359 pseudobonds, 7483 residues, 33 models selected 
    5890 
    5891 > select add #10
    5892 
    5893 43694 atoms, 41785 bonds, 364 pseudobonds, 8045 residues, 36 models selected 
    5894 
    5895 > select add #9
    5896 
    5897 45643 atoms, 43622 bonds, 369 pseudobonds, 8425 residues, 39 models selected 
    5898 
    5899 > select add #11
    5900 
    5901 53618 atoms, 51008 bonds, 432 pseudobonds, 10103 residues, 42 models selected 
    5902 
    5903 > select add #12
    5904 
    5905 62239 atoms, 59808 bonds, 503 pseudobonds, 11200 residues, 45 models selected 
    5906 
    5907 > select add #13
    5908 
    5909 69826 atoms, 67106 bonds, 567 pseudobonds, 12565 residues, 48 models selected 
    5910 
    5911 > select add #14
    5912 
    5913 71919 atoms, 68920 bonds, 572 pseudobonds, 13112 residues, 51 models selected 
    5914 
    5915 > select add #15
    5916 
    5917 74028 atoms, 70747 bonds, 577 pseudobonds, 13663 residues, 54 models selected 
    5918 
    5919 > select add #16
    5920 
    5921 77725 atoms, 74246 bonds, 587 pseudobonds, 14388 residues, 57 models selected 
    5922 
    5923 > select add #17
    5924 
    5925 86402 atoms, 83046 bonds, 664 pseudobonds, 15541 residues, 60 models selected 
    5926 
    5927 > select add #18
    5928 
    5929 94858 atoms, 91786 bonds, 723 pseudobonds, 16521 residues, 63 models selected 
    5930 
    5931 > select add #19
    5932 
    5933 102491 atoms, 98898 bonds, 804 pseudobonds, 18099 residues, 67 models selected 
    5934 
    5935 > show sel atoms
    5936 
    5937 > select clear
    5938 
    5939 > select #!1/B:282
    5940 
    5941 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5942 
    5943 > select #!1/B:282
    5944 
    5945 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5946 
    5947 > select #!1/B:248
    5948 
    5949 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5950 
    5951 > select #!1/B:248
    5952 
    5953 11 atoms, 10 bonds, 1 residue, 1 model selected 
    5954 
    5955 > hide #!13 models
    5956 
    5957 > hide #!14 models
    5958 
    5959 > hide #!15 models
    5960 
    5961 > hide #!16 models
    5962 
    5963 > hide #!17 models
    5964 
    5965 > hide #!18 models
    5966 
    5967 > hide #!19 models
    5968 
    5969 > hide #!11 models
    5970 
    5971 > hide #!10 models
    5972 
    5973 > hide #!9 models
    5974 
    5975 > hide #!8 models
    5976 
    5977 > hide #!7 models
    5978 
    5979 > hide #!6 models
    5980 
    5981 > hide #!5 models
    5982 
    5983 > hide #!4 models
    5984 
    5985 > hide #!3 models
    5986 
    5987 > hide #!2 models
    5988 
    5989 > hide #!12 models
    5990 
    5991 > show #!12 models
    5992 
    5993 > select add #12
    5994 
    5995 8632 atoms, 8810 bonds, 71 pseudobonds, 1098 residues, 5 models selected 
    5996 
    5997 > hide sel cartoons
    5998 
    5999 > select #!1/B:248
    6000 
    6001 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6002 
    6003 > select #!1/B:248
    6004 
    6005 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6006 
    6007 > ui mousemode right distance
    6008 
    6009 > distance #!1/B:248@NH2 #12/L:35@N2
    6010 
    6011 Distance between 1tup #!1/B ARG 248 NH2 and 3ts8 #12/L DG 35 N2: 5.304Å 
    6012 
    6013 > distance #12/A:248@NH2 #!1/F:1113@N2
    6014 
    6015 Distance between 3ts8 #12/A ARG 248 NH2 and 1tup #!1/F DG 1113 N2: 5.414Å 
    6016 
    6017 > hide #!12 models
    6018 
    6019 > select add #1
    6020 
    6021 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 117 models selected 
    6022 
    6023 > select O
    6024 
    6025 30159 atoms, 21045 residues, 127 models selected 
    6026 
    6027 > show (#1.8.1-108#!1 & sel) target ab
    6028 
    6029 > ui mousemode right select
    6030 
    6031 > select clear
    6032 
    6033 > select #!1/B:248
    6034 
    6035 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6036 
    6037 > select #!1/B:248
    6038 
    6039 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6040 
    6041 > show #!12 models
    6042 
    6043 > hide #!1 models
    6044 
    6045 > select #12/A:248@CB
    6046 
    6047 1 atom, 1 residue, 1 model selected 
    6048 
    6049 > select #12/A:248@CA
    6050 
    6051 1 atom, 1 residue, 1 model selected 
    6052 
    6053 > select #12/A:248@CA
    6054 
    6055 1 atom, 1 residue, 1 model selected 
    6056 
    6057 > show #!1 models
    6058 
    6059 > hide #!1 models
    6060 
    6061 > select #12/A:248@CA
    6062 
    6063 1 atom, 1 residue, 1 model selected 
    6064 
    6065 > select #12/A:248@CA
    6066 
    6067 1 atom, 1 residue, 1 model selected 
    6068 
    6069 > select #12/C:283@NH2
    6070 
    6071 1 atom, 1 residue, 1 model selected 
    6072 Drag select of 1 atoms, 1 bonds 
    6073 
    6074 > ui tool show "Show Sequence Viewer"
    6075 
    6076 > sequence chain #12/A
    6077 
    6078 Alignment identifier is 12/A 
    6079 
    6080 > select #12/A:248-249
    6081 
    6082 22 atoms, 21 bonds, 2 residues, 1 model selected 
    6083 
    6084 > select #12/A:248-249
    6085 
    6086 22 atoms, 21 bonds, 2 residues, 1 model selected 
    6087 
    6088 > select #12/A:248
    6089 
    6090 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6091 
    6092 > select #12/A:248
    6093 
    6094 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6095 
    6096 > select add #12
    6097 
    6098 8621 atoms, 8800 bonds, 71 pseudobonds, 1097 residues, 3 models selected 
    6099 
    6100 > select clear
    6101 
    6102 > select O
    6103 
    6104 30159 atoms, 21045 residues, 127 models selected 
    6105 
    6106 > show (#!12 & sel) target ab
    6107 
    6108 > select clear
    6109 
    6110 > show #!1 models
    6111 
    6112 > select add #20
    6113 
    6114 2 pseudobonds, 2 models selected 
    6115 
    6116 > close #20
    6117 
    6118 > select #12/A:248
    6119 
    6120 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6121 
    6122 > select #12/A:248
    6123 
    6124 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6125 
    6126 > hide #!12 models
    6127 
    6128 > show #!12 models
    6129 
    6130 > hide #!1 models
    6131 
    6132 > hide #!12 models
    6133 
    6134 > show #!1 models
    6135 
    6136 > show #!12 models
    6137 
    6138 > hide #!1 models
    6139 
    6140 > show #!1 models
    6141 
    6142 > hide #!12 models
    6143 
    6144 > show #!2 models
    6145 
    6146 > show #!3 models
    6147 
    6148 > hide #!1 models
    6149 
    6150 > show #!1 models
    6151 
    6152 > hide #!2 models
    6153 
    6154 > hide #!3 models
    6155 
    6156 > select #!1/B:248
    6157 
    6158 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6159 
    6160 > select #!1/B:248
    6161 
    6162 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6163 
    6164 > show #!19 models
    6165 
    6166 > show #!18 models
    6167 
    6168 > show #!17 models
    6169 
    6170 > show #!16 models
    6171 
    6172 > show #!15 models
    6173 
    6174 > show #!14 models
    6175 
    6176 > show #!13 models
    6177 
    6178 > hide #!13 models
    6179 
    6180 > hide #!14 models
    6181 
    6182 > hide #!15 models
    6183 
    6184 > hide #!16 models
    6185 
    6186 > hide #!17 models
    6187 
    6188 > hide #!18 models
    6189 
    6190 > hide #!19 models
    6191 
    6192 > hide #!1 models
    6193 
    6194 > show #!1 models
    6195 
    6196 > select add #1
    6197 
    6198 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 117 models selected 
    6199 
    6200 > show sel cartoons
    6201 
    6202 > show #!2 models
    6203 
    6204 > show #!3 models
    6205 
    6206 > hide #!2 models
    6207 
    6208 > select clear
    6209 
    6210 > select #!1/B:248
    6211 
    6212 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6213 
    6214 > select #!1/B:248
    6215 
    6216 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6217 
    6218 > show #!19 models
    6219 
    6220 > show #!18 models
    6221 
    6222 > hide #!1 models
    6223 
    6224 > hide #!18 models
    6225 
    6226 > hide #!19 models
    6227 
    6228 > show #!19 models
    6229 
    6230 > show #!18 models
    6231 
    6232 > show #!17 models
    6233 
    6234 > hide #!3 models
    6235 
    6236 > show #!16 models
    6237 
    6238 > hide #!17 models
    6239 
    6240 > hide #!18 models
    6241 
    6242 > hide #!19 models
    6243 
    6244 > select add #16
    6245 
    6246 3708 atoms, 3509 bonds, 10 pseudobonds, 726 residues, 5 models selected 
    6247 
    6248 > style sel & #!16 stick
    6249 
    6250 Changed 3697 atom styles 
    6251 
    6252 > hide sel & #!16 cartoons
    6253 
    6254 > nucleotides sel & #!16 atoms
    6255 
    6256 > style nucleic & sel & #!16 stick
    6257 
    6258 Changed 410 atom styles 
    6259 
    6260 > show #!15 models
    6261 
    6262 > hide #!16 models
    6263 
    6264 > select add #15
    6265 
    6266 5817 atoms, 5336 bonds, 15 pseudobonds, 1277 residues, 8 models selected 
    6267 
    6268 > select subtract #16
    6269 
    6270 2120 atoms, 1837 bonds, 5 pseudobonds, 552 residues, 5 models selected 
    6271 
    6272 > nucleotides sel & #!15 atoms
    6273 
    6274 > style nucleic & sel & #!15 stick
    6275 
    6276 Changed 225 atom styles 
    6277 
    6278 > hide sel & #!15 cartoons
    6279 
    6280 > show #!16 models
    6281 
    6282 > show #!14 models
    6283 
    6284 > select add #14
    6285 
    6286 4213 atoms, 3651 bonds, 10 pseudobonds, 1099 residues, 8 models selected 
    6287 
    6288 > select subtract #15
    6289 
    6290 2104 atoms, 1824 bonds, 5 pseudobonds, 548 residues, 5 models selected 
    6291 
    6292 > nucleotides sel & #!14 atoms
    6293 
    6294 > style nucleic & sel & #!14 stick
    6295 
    6296 Changed 225 atom styles 
    6297 
    6298 > hide sel & #!14 cartoons
    6299 
    6300 > show #!13 models
    6301 
    6302 > select subtract #14
    6303 
    6304 11 atoms, 10 bonds, 1 residue, 2 models selected 
    6305 
    6306 > select add #13
    6307 
    6308 7598 atoms, 7308 bonds, 64 pseudobonds, 1366 residues, 5 models selected 
    6309 
    6310 > hide sel & #!13 cartoons
    6311 
    6312 > hide #!14 models
    6313 
    6314 > hide #!15 models
    6315 
    6316 > hide #!16 models
    6317 
    6318 > show #!12 models
    6319 
    6320 > hide #!13 models
    6321 
    6322 > show #!11 models
    6323 
    6324 > show #!10 models
    6325 
    6326 > show #!9 models
    6327 
    6328 > show #!8 models
    6329 
    6330 > show #!7 models
    6331 
    6332 > show #!6 models
    6333 
    6334 > select add #12
    6335 
    6336 16219 atoms, 16108 bonds, 135 pseudobonds, 2463 residues, 8 models selected 
    6337 
    6338 > select subtract #13
    6339 
    6340 8632 atoms, 8810 bonds, 71 pseudobonds, 1098 residues, 5 models selected 
    6341 
    6342 > select add #11
    6343 
    6344 16607 atoms, 16196 bonds, 134 pseudobonds, 2776 residues, 8 models selected 
    6345 
    6346 > select add #10
    6347 
    6348 18779 atoms, 18076 bonds, 139 pseudobonds, 3338 residues, 11 models selected 
    6349 
    6350 > select add #9
    6351 
    6352 20728 atoms, 19913 bonds, 144 pseudobonds, 3718 residues, 14 models selected 
    6353 
    6354 > select add #8
    6355 
    6356 28816 atoms, 27270 bonds, 225 pseudobonds, 5531 residues, 17 models selected 
    6357 
    6358 > select add #6
    6359 
    6360 30748 atoms, 29105 bonds, 229 pseudobonds, 5897 residues, 19 models selected 
    6361 
    6362 > select add #7
    6363 
    6364 39341 atoms, 37917 bonds, 302 pseudobonds, 6958 residues, 22 models selected 
    6365 
    6366 > nucleotides sel & #!6-12 atoms
    6367 
    6368 > style nucleic & sel & #!6-12 stick
    6369 
    6370 Changed 4560 atom styles 
    6371 
    6372 > hide sel & #!6-12 cartoons
    6373 
    6374 > hide #!6 models
    6375 
    6376 > show #!19 models
    6377 
    6378 > show #!18 models
    6379 
    6380 > show #!17 models
    6381 
    6382 > show #!16 models
    6383 
    6384 > show #!15 models
    6385 
    6386 > show #!14 models
    6387 
    6388 > show #!13 models
    6389 
    6390 > select add #13
    6391 
    6392 46928 atoms, 45215 bonds, 366 pseudobonds, 8323 residues, 25 models selected 
    6393 
    6394 > select add #14
    6395 
    6396 49021 atoms, 47029 bonds, 371 pseudobonds, 8870 residues, 28 models selected 
    6397 
    6398 > select add #15
    6399 
    6400 51130 atoms, 48856 bonds, 376 pseudobonds, 9421 residues, 31 models selected 
    6401 
    6402 > select add #16
    6403 
    6404 54827 atoms, 52355 bonds, 386 pseudobonds, 10146 residues, 34 models selected 
    6405 
    6406 > select add #17
    6407 
    6408 63504 atoms, 61155 bonds, 463 pseudobonds, 11299 residues, 37 models selected 
    6409 
    6410 > select add #18
    6411 
    6412 71960 atoms, 69895 bonds, 522 pseudobonds, 12279 residues, 40 models selected 
    6413 
    6414 > select add #19
    6415 
    6416 79593 atoms, 77007 bonds, 603 pseudobonds, 13857 residues, 44 models selected 
    6417 
    6418 > hide sel & #!7-19 cartoons
    6419 
    6420 > nucleotides sel & #!7-19 atoms
    6421 
    6422 > style nucleic & sel & #!7-19 stick
    6423 
    6424 Changed 9010 atom styles 
    6425 
    6426 > show #!6 models
    6427 
    6428 > select subtract #6
    6429 
    6430 77661 atoms, 75172 bonds, 599 pseudobonds, 13491 residues, 42 models selected 
    6431 
    6432 > show #!5 models
    6433 
    6434 > show #!4 models
    6435 
    6436 > show #!3 models
    6437 
    6438 > show #!2 models
    6439 
    6440 > show #!1 models
    6441 
    6442 > select add #2
    6443 
    6444 85871 atoms, 82580 bonds, 677 pseudobonds, 15387 residues, 45 models selected 
    6445 
    6446 > select add #1
    6447 
    6448 92456 atoms, 88876 bonds, 732 pseudobonds, 16511 residues, 168 models selected 
    6449 
    6450 > select add #3
    6451 
    6452 99549 atoms, 96189 bonds, 789 pseudobonds, 17366 residues, 175 models selected 
    6453 
    6454 > select add #4
    6455 
    6456 107584 atoms, 103470 bonds, 863 pseudobonds, 19199 residues, 178 models
    6457 selected 
    6458 
    6459 > select add #5
    6460 
    6461 115365 atoms, 110777 bonds, 933 pseudobonds, 20754 residues, 189 models
    6462 selected 
    6463 
    6464 > select add #6
    6465 
    6466 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 199 models
    6467 selected 
    6468 
    6469 > select subtract #7
    6470 
    6471 108704 atoms, 103800 bonds, 864 pseudobonds, 20059 residues, 196 models
    6472 selected 
    6473 
    6474 > select add #7
    6475 
    6476 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 199 models
    6477 selected 
    6478 
    6479 > hide #!7 models
    6480 
    6481 > select subtract #7
    6482 
    6483 108704 atoms, 103800 bonds, 864 pseudobonds, 20059 residues, 196 models
    6484 selected 
    6485 
    6486 > hide #!8 models
    6487 
    6488 > show #!8 models
    6489 
    6490 > show #!7 models
    6491 
    6492 > select add #7
    6493 
    6494 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 199 models
    6495 selected 
    6496 
    6497 > hide sel cartoons
    6498 
    6499 > nucleotides sel atoms
    6500 
    6501 > style nucleic & sel stick
    6502 
    6503 Changed 13700 atom styles 
    6504 
    6505 > hide #!10 models
    6506 
    6507 > hide #!8 models
    6508 
    6509 > show #!8 models
    6510 
    6511 > hide #!8 models
    6512 
    6513 > show #!10 models
    6514 
    6515 > hide #!10 models
    6516 
    6517 > hide #!1 models
    6518 
    6519 > hide #!4 models
    6520 
    6521 > hide #!11 models
    6522 
    6523 > hide #!5 models
    6524 
    6525 > hide #!7 models
    6526 
    6527 > hide #!17 models
    6528 
    6529 > hide #!9 models
    6530 
    6531 > hide #!12 models
    6532 
    6533 > show sel & #!2-3,6,13-16,18-19 surfaces
    6534 
    6535 > hide sel & #!2-3,6,13-16,18-19 surfaces
    6536 
    6537 > hide #!19 models
    6538 
    6539 > show #!19 models
    6540 
    6541 > hide #!19 models
    6542 
    6543 > hide #!18 models
    6544 
    6545 > hide #!16 models
    6546 
    6547 > hide #!15 models
    6548 
    6549 > hide #!14 models
    6550 
    6551 > hide #!13 models
    6552 
    6553 > hide #!6 models
    6554 
    6555 > hide #!3 models
    6556 
    6557 > select clear
    6558 
    6559 > select add #2
    6560 
    6561 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected 
    6562 
    6563 > select subtract #2.10
    6564 
    6565 7967 atoms, 7136 bonds, 44 pseudobonds, 1884 residues, 11 models selected 
    6566 
    6567 > select subtract #2.9
    6568 
    6569 7724 atoms, 6864 bonds, 44 pseudobonds, 1872 residues, 10 models selected 
    6570 
    6571 > select subtract #2.8
    6572 
    6573 7481 atoms, 6592 bonds, 16 pseudobonds, 1860 residues, 8 models selected 
    6574 
    6575 > select subtract #2.7
    6576 
    6577 7238 atoms, 6320 bonds, 16 pseudobonds, 1848 residues, 7 models selected 
    6578 
    6579 > select add #2.9
    6580 
    6581 7481 atoms, 6320 bonds, 16 pseudobonds, 1860 residues, 6 models selected 
    6582 
    6583 > select subtract #2.9
    6584 
    6585 7238 atoms, 6320 bonds, 16 pseudobonds, 1848 residues, 7 models selected 
    6586 
    6587 > select subtract #2.5
    6588 
    6589 5709 atoms, 4756 bonds, 12 pseudobonds, 1653 residues, 6 models selected 
    6590 
    6591 > select add #2.5
    6592 
    6593 7238 atoms, 4756 bonds, 12 pseudobonds, 1848 residues, 5 models selected 
    6594 
    6595 > select subtract #2.3
    6596 
    6597 5686 atoms, 3169 bonds, 8 pseudobonds, 1649 residues, 6 models selected 
    6598 
    6599 > hide sel atoms
    6600 
    6601 > select add #2.10
    6602 
    6603 5929 atoms, 3169 bonds, 8 pseudobonds, 1661 residues, 5 models selected 
    6604 
    6605 > select add #2.9
    6606 
    6607 6172 atoms, 3169 bonds, 8 pseudobonds, 1673 residues, 6 models selected 
    6608 
    6609 > select subtract #2.6
    6610 
    6611 4618 atoms, 1580 bonds, 4 pseudobonds, 1475 residues, 7 models selected 
    6612 
    6613 > select subtract #2.5
    6614 
    6615 3089 atoms, 1580 bonds, 4 pseudobonds, 1280 residues, 6 models selected 
    6616 
    6617 > select subtract #2.4
    6618 
    6619 1544 atoms, 1082 residues, 4 models selected 
    6620 
    6621 > hide sel atoms
    6622 
    6623 > select add #1
    6624 
    6625 8140 atoms, 6306 bonds, 55 pseudobonds, 2207 residues, 119 models selected 
    6626 
    6627 > select subtract #1
    6628 
    6629 1544 atoms, 1082 residues, 8 models selected 
    6630 
    6631 > show #!1 models
    6632 
    6633 > hide #!1 models
    6634 
    6635 > hide #!2 models
    6636 
    6637 > select add #2
    6638 
    6639 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 5 models selected 
    6640 
    6641 > select subtract #2
    6642 
    6643 8 models selected 
    6644 
    6645 > show #!3 models
    6646 
    6647 > select add #3
    6648 
    6649 7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 3 models selected 
    6650 
    6651 > show #!1 models
    6652 
    6653 > hide #!1 models
    6654 
    6655 > select subtract #3.8
    6656 
    6657 6666 atoms, 6835 bonds, 16 pseudobonds, 834 residues, 8 models selected 
    6658 
    6659 > select subtract #3.7
    6660 
    6661 6238 atoms, 6354 bonds, 16 pseudobonds, 813 residues, 7 models selected 
    6662 
    6663 > select subtract #3.3
    6664 
    6665 4686 atoms, 4767 bonds, 12 pseudobonds, 616 residues, 6 models selected 
    6666 
    6667 > hide sel atoms
    6668 
    6669 > show #!2 models
    6670 
    6671 > hide #!3 models
    6672 
    6673 > hide #!2 models
    6674 
    6675 > show #!3 models
    6676 
    6677 > hide #!3 models
    6678 
    6679 > select add #3
    6680 
    6681 7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 6 models selected 
    6682 
    6683 > select subtract #3
    6684 
    6685 6 models selected 
    6686 
    6687 Cell requested for row 3 is out of bounds for table with 27 rows! Resizing
    6688 table model. 
    6689 
    6690 > show #!4 models
    6691 
    6692 > select add #4
    6693 
    6694 8035 atoms, 7281 bonds, 74 pseudobonds, 1833 residues, 3 models selected 
    6695 
    6696 > select subtract #4.10
    6697 
    6698 7792 atoms, 7009 bonds, 42 pseudobonds, 1821 residues, 11 models selected 
    6699 
    6700 > select add #4.10
    6701 
    6702 8035 atoms, 7009 bonds, 42 pseudobonds, 1833 residues, 10 models selected 
    6703 
    6704 > select subtract #4.10
    6705 
    6706 7792 atoms, 7009 bonds, 42 pseudobonds, 1821 residues, 11 models selected 
    6707 
    6708 > select subtract #4.9
    6709 
    6710 7549 atoms, 6737 bonds, 42 pseudobonds, 1809 residues, 10 models selected 
    6711 
    6712 > select subtract #4.8
    6713 
    6714 7325 atoms, 6486 bonds, 16 pseudobonds, 1798 residues, 8 models selected 
    6715 
    6716 > select subtract #4.7
    6717 
    6718 7123 atoms, 6260 bonds, 16 pseudobonds, 1788 residues, 7 models selected 
    6719 
    6720 > select subtract #4.3
    6721 
    6722 5572 atoms, 4674 bonds, 12 pseudobonds, 1589 residues, 6 models selected 
    6723 
    6724 > hide sel atoms
    6725 
    6726 > show #!3 models
    6727 
    6728 > hide #!3 models
    6729 
    6730 > show #!2 models
    6731 
    6732 > hide #!2 models
    6733 
    6734 > show #!1 models
    6735 
    6736 > hide #!1 models
    6737 
    6738 > show #!1 models
    6739 
    6740 > show #!2 models
    6741 
    6742 > show #!3 models
    6743 
    6744 > select add #4
    6745 
    6746 8035 atoms, 7281 bonds, 74 pseudobonds, 1833 residues, 6 models selected 
    6747 
    6748 > select subtract #4
    6749 
    6750 8 models selected 
    6751 
    6752 > select add #4.10
    6753 
    6754 243 atoms, 12 residues, 1 model selected 
    6755 
    6756 > select add #4.9
    6757 
    6758 486 atoms, 24 residues, 2 models selected 
    6759 
    6760 > hide sel atoms
    6761 
    6762 > select add #4
    6763 
    6764 8035 atoms, 7281 bonds, 74 pseudobonds, 1833 residues, 5 models selected 
    6765 
    6766 > select subtract #4
    6767 
    6768 8 models selected 
    6769 
    6770 > hide #!3 models
    6771 
    6772 > hide #!2 models
    6773 
    6774 > hide #!1 models
    6775 
    6776 > show #!5 models
    6777 
    6778 > hide #!4 models
    6779 
    6780 > select add #5.10
    6781 
    6782 223 atoms, 11 residues, 1 model selected 
    6783 
    6784 > select add #5.9
    6785 
    6786 466 atoms, 23 residues, 2 models selected 
    6787 
    6788 > select add #5.6
    6789 
    6790 2002 atoms, 221 residues, 3 models selected 
    6791 
    6792 > select add #5.5
    6793 
    6794 3537 atoms, 417 residues, 4 models selected 
    6795 
    6796 > select add #5.4
    6797 
    6798 5089 atoms, 616 residues, 5 models selected 
    6799 
    6800 > hide sel atoms
    6801 
    6802 > show #!4 models
    6803 
    6804 > hide #!4 models
    6805 
    6806 > select add #5
    6807 
    6808 7781 atoms, 7307 bonds, 70 pseudobonds, 1555 residues, 8 models selected 
    6809 
    6810 > select subtract #5
    6811 
    6812 8 models selected 
    6813 
    6814 > show #!6 models
    6815 
    6816 > hide #!5 models
    6817 
    6818 > show #!7 models
    6819 
    6820 > hide #!6 models
    6821 
    6822 > select add #7
    6823 
    6824 8593 atoms, 8812 bonds, 73 pseudobonds, 1061 residues, 3 models selected 
    6825 
    6826 > show sel surfaces
    6827 
    6828 > hide sel surfaces
    6829 
    6830 > select subtract #7
    6831 
    6832 6 models selected 
    6833 
    6834 > select add #7.8
    6835 
    6836 535 atoms, 26 residues, 1 model selected 
    6837 
    6838 > select add #7.7
    6839 
    6840 1060 atoms, 52 residues, 2 models selected 
    6841 
    6842 > select subtract #7.7
    6843 
    6844 535 atoms, 26 residues, 3 models selected 
    6845 
    6846 > select subtract #7.8
    6847 
    6848 1 model selected 
    6849 
    6850 > select add #7.6
    6851 
    6852 1865 atoms, 234 residues, 1 model selected 
    6853 
    6854 > select add #7.5
    6855 
    6856 3730 atoms, 468 residues, 2 models selected 
    6857 
    6858 > select add #7.4
    6859 
    6860 5595 atoms, 702 residues, 3 models selected 
    6861 
    6862 > hide sel atoms
    6863 
    6864 > show #!6 models
    6865 
    6866 > hide #!6 models
    6867 
    6868 > select add #7
    6869 
    6870 8593 atoms, 8812 bonds, 73 pseudobonds, 1061 residues, 6 models selected 
    6871 
    6872 > select subtract #7
    6873 
    6874 6 models selected 
    6875 
    6876 Cell requested for row 7 is out of bounds for table with 27 rows! Resizing
    6877 table model. 
    6878 
    6879 > show #!8 models
    6880 
    6881 > hide #!7 models
    6882 
    6883 > select add #8
    6884 
    6885 8088 atoms, 7357 bonds, 81 pseudobonds, 1813 residues, 3 models selected 
    6886 
    6887 > select add #9
    6888 
    6889 10037 atoms, 9194 bonds, 86 pseudobonds, 2193 residues, 6 models selected 
    6890 
    6891 > select add #10
    6892 
    6893 12209 atoms, 11074 bonds, 91 pseudobonds, 2755 residues, 9 models selected 
    6894 
    6895 > select add #11
    6896 
    6897 20184 atoms, 18460 bonds, 154 pseudobonds, 4433 residues, 12 models selected 
    6898 
    6899 > show sel & #!8 surfaces
    6900 
    6901 > hide sel & #!8 surfaces
    6902 
    6903 > select subtract #9
    6904 
    6905 18235 atoms, 16623 bonds, 149 pseudobonds, 4053 residues, 17 models selected 
    6906 
    6907 > select subtract #10
    6908 
    6909 16063 atoms, 14743 bonds, 144 pseudobonds, 3491 residues, 14 models selected 
    6910 
    6911 > select subtract #11
    6912 
    6913 8088 atoms, 7357 bonds, 81 pseudobonds, 1813 residues, 11 models selected 
    6914 
    6915 > select subtract #8.10
    6916 
    6917 7845 atoms, 7085 bonds, 47 pseudobonds, 1801 residues, 11 models selected 
    6918 
    6919 > select subtract #8.9
    6920 
    6921 7602 atoms, 6813 bonds, 47 pseudobonds, 1789 residues, 10 models selected 
    6922 
    6923 > select subtract #8.6
    6924 
    6925 6083 atoms, 5260 bonds, 43 pseudobonds, 1593 residues, 9 models selected 
    6926 
    6927 > select subtract #8.5
    6928 
    6929 4569 atoms, 3711 bonds, 39 pseudobonds, 1398 residues, 8 models selected 
    6930 
    6931 > select subtract #8.4
    6932 
    6933 3028 atoms, 2135 bonds, 35 pseudobonds, 1200 residues, 7 models selected 
    6934 
    6935 > hide sel atoms
    6936 
    6937 > select subtract #8.3
    6938 
    6939 1483 atoms, 555 bonds, 31 pseudobonds, 1003 residues, 5 models selected 
    6940 
    6941 > select add #8.4
    6942 
    6943 3024 atoms, 555 bonds, 31 pseudobonds, 1201 residues, 4 models selected 
    6944 
    6945 > select add #8.5
    6946 
    6947 4538 atoms, 555 bonds, 31 pseudobonds, 1396 residues, 5 models selected 
    6948 
    6949 > select add #8.6
    6950 
    6951 6057 atoms, 555 bonds, 31 pseudobonds, 1592 residues, 6 models selected 
    6952 
    6953 > hide sel atoms
    6954 
    6955 > select add #8.3
    6956 
    6957 7602 atoms, 555 bonds, 31 pseudobonds, 1789 residues, 7 models selected 
    6958 
    6959 > select subtract #8.4
    6960 
    6961 6061 atoms, 555 bonds, 31 pseudobonds, 1591 residues, 8 models selected 
    6962 
    6963 > select subtract #8.5
    6964 
    6965 4547 atoms, 555 bonds, 31 pseudobonds, 1396 residues, 7 models selected 
    6966 
    6967 > select subtract #8.6
    6968 
    6969 3028 atoms, 555 bonds, 31 pseudobonds, 1200 residues, 6 models selected 
    6970 
    6971 > select subtract #8.7
    6972 
    6973 2807 atoms, 308 bonds, 1189 residues, 4 models selected 
    6974 
    6975 > select subtract #8.8
    6976 
    6977 2580 atoms, 54 bonds, 1178 residues, 3 models selected 
    6978 
    6979 > show sel atoms
    6980 
    6981 > show #!7 models
    6982 
    6983 > hide #!7 models
    6984 
    6985 > select add #8.10
    6986 
    6987 2823 atoms, 54 bonds, 1190 residues, 2 models selected 
    6988 
    6989 > select add #8.9
    6990 
    6991 3066 atoms, 54 bonds, 1202 residues, 3 models selected 
    6992 
    6993 > select subtract #8.3
    6994 
    6995 1521 atoms, 54 bonds, 1005 residues, 4 models selected 
    6996 
    6997 > hide sel atoms
    6998 
    6999 > select add #8.8
    7000 
    7001 1748 atoms, 54 bonds, 1016 residues, 3 models selected 
    7002 
    7003 > select add #8.7
    7004 
    7005 1969 atoms, 54 bonds, 1027 residues, 4 models selected 
    7006 
    7007 > select subtract #8.9
    7008 
    7009 1726 atoms, 54 bonds, 1015 residues, 5 models selected 
    7010 
    7011 > select subtract #8.10
    7012 
    7013 1483 atoms, 54 bonds, 1003 residues, 4 models selected 
    7014 
    7015 > show sel atoms
    7016 
    7017 > select clear
    7018 
    7019 > hide #!8 models
    7020 
    7021 > show #!10 models
    7022 
    7023 > show #!9 models
    7024 
    7025 > show #!8 models
    7026 
    7027 > hide #!8 models
    7028 
    7029 > hide #!9 models
    7030 
    7031 > hide #!10 models
    7032 
    7033 > show #!11 models
    7034 
    7035 > select add #11
    7036 
    7037 7975 atoms, 7386 bonds, 63 pseudobonds, 1678 residues, 3 models selected 
    7038 
    7039 > show sel surfaces
    7040 
    7041 > hide sel surfaces
    7042 
    7043 > show sel surfaces
    7044 
    7045 > hide sel surfaces
    7046 
    7047 > select subtract #11.8
    7048 
    7049 7548 atoms, 6909 bonds, 16 pseudobonds, 1657 residues, 8 models selected 
    7050 
    7051 > select add #11.8
    7052 
    7053 7975 atoms, 6909 bonds, 16 pseudobonds, 1678 residues, 7 models selected 
    7054 
    7055 > select subtract #11.3
    7056 
    7057 6404 atoms, 5302 bonds, 12 pseudobonds, 1478 residues, 8 models selected 
    7058 
    7059 > select add #11.3
    7060 
    7061 7975 atoms, 5302 bonds, 12 pseudobonds, 1678 residues, 7 models selected 
    7062 
    7063 > select subtract #11.3
    7064 
    7065 6404 atoms, 5302 bonds, 12 pseudobonds, 1478 residues, 8 models selected 
    7066 
    7067 > select subtract #11.8
    7068 
    7069 5977 atoms, 5302 bonds, 12 pseudobonds, 1457 residues, 7 models selected 
    7070 
    7071 > select subtract #11.7
    7072 
    7073 5549 atoms, 4821 bonds, 12 pseudobonds, 1436 residues, 6 models selected 
    7074 
    7075 > hide sel atoms
    7076 
    7077 > show #!10 models
    7078 
    7079 > hide #!10 models
    7080 
    7081 > select add #11
    7082 
    7083 7975 atoms, 7386 bonds, 63 pseudobonds, 1678 residues, 6 models selected 
    7084 
    7085 > select subtract #11
    7086 
    7087 6 models selected 
    7088 
    7089 > show #!12 models
    7090 
    7091 > hide #!11 models
    7092 
    7093 > select add #12
    7094 
    7095 8621 atoms, 8800 bonds, 71 pseudobonds, 1097 residues, 3 models selected 
    7096 
    7097 > show sel surfaces
    7098 
    7099 > hide sel surfaces
    7100 
    7101 > select subtract #12.3
    7102 
    7103 6758 atoms, 6897 bonds, 67 pseudobonds, 863 residues, 9 models selected 
    7104 
    7105 > select subtract #12.8
    7106 
    7107 6232 atoms, 6310 bonds, 12 pseudobonds, 837 residues, 7 models selected 
    7108 
    7109 > select subtract #12.7
    7110 
    7111 5698 atoms, 5709 bonds, 12 pseudobonds, 811 residues, 6 models selected 
    7112 
    7113 > hide sel atoms
    7114 
    7115 > show #!11 models
    7116 
    7117 > hide #!11 models
    7118 
    7119 > show #!11 models
    7120 
    7121 > hide #!11 models
    7122 
    7123 > hide #!12 models
    7124 
    7125 > show #!13 models
    7126 
    7127 > select add #12
    7128 
    7129 8621 atoms, 8800 bonds, 71 pseudobonds, 1097 residues, 6 models selected 
    7130 
    7131 > select subtract #12
    7132 
    7133 6 models selected 
    7134 
    7135 > select add #13
    7136 
    7137 7587 atoms, 7298 bonds, 64 pseudobonds, 1365 residues, 3 models selected 
    7138 
    7139 > select subtract #13.3
    7140 
    7141 6016 atoms, 5691 bonds, 60 pseudobonds, 1165 residues, 9 models selected 
    7142 
    7143 > select subtract #13.8
    7144 
    7145 5628 atoms, 5256 bonds, 12 pseudobonds, 1146 residues, 7 models selected 
    7146 
    7147 > select subtract #13.7
    7148 
    7149 5240 atoms, 4821 bonds, 12 pseudobonds, 1127 residues, 6 models selected 
    7150 
    7151 > hide sel atoms
    7152 
    7153 > select add #13
    7154 
    7155 7587 atoms, 7298 bonds, 64 pseudobonds, 1365 residues, 6 models selected 
    7156 
    7157 > select subtract #13
    7158 
    7159 6 models selected 
    7160 
    7161 > show #!14 models
    7162 
    7163 > hide #!13 models
    7164 
    7165 > show #!15 models
    7166 
    7167 > hide #!14 models
    7168 
    7169 > show #!16 models
    7170 
    7171 > hide #!15 models
    7172 
    7173 > select add #16
    7174 
    7175 3697 atoms, 3499 bonds, 10 pseudobonds, 725 residues, 3 models selected 
    7176 
    7177 > select subtract #16.3
    7178 
    7179 2211 atoms, 1979 bonds, 5 pseudobonds, 530 residues, 6 models selected 
    7180 
    7181 > select subtract #16.5
    7182 
    7183 1801 atoms, 1520 bonds, 5 pseudobonds, 510 residues, 5 models selected 
    7184 
    7185 > hide sel atoms
    7186 
    7187 > select add #16
    7188 
    7189 3697 atoms, 3499 bonds, 10 pseudobonds, 725 residues, 4 models selected 
    7190 
    7191 > select subtract #16
    7192 
    7193 3 models selected 
    7194 
    7195 > show #!17 models
    7196 
    7197 > hide #!16 models
    7198 
    7199 > select add #17
    7200 
    7201 8677 atoms, 8800 bonds, 77 pseudobonds, 1153 residues, 3 models selected 
    7202 
    7203 > show sel surfaces
    7204 
    7205 > hide sel surfaces
    7206 
    7207 > select subtract #17.3
    7208 
    7209 6814 atoms, 6897 bonds, 73 pseudobonds, 919 residues, 9 models selected 
    7210 
    7211 > select subtract #17.8
    7212 
    7213 6281 atoms, 6299 bonds, 12 pseudobonds, 893 residues, 7 models selected 
    7214 
    7215 > select subtract #17.7
    7216 
    7217 5754 atoms, 5709 bonds, 12 pseudobonds, 867 residues, 6 models selected 
    7218 
    7219 > hide sel atoms
    7220 
    7221 > select add #17
    7222 
    7223 8677 atoms, 8800 bonds, 77 pseudobonds, 1153 residues, 6 models selected 
    7224 
    7225 > select subtract #17
    7226 
    7227 6 models selected 
    7228 
    7229 Cell requested for row 17 is out of bounds for table with 27 rows! Resizing
    7230 table model. 
    7231 
    7232 > show #!18 models
    7233 
    7234 > hide #!17 models
    7235 
    7236 > select add #18
    7237 
    7238 8456 atoms, 8740 bonds, 59 pseudobonds, 980 residues, 3 models selected 
    7239 
    7240 > select subtract #18.3
    7241 
    7242 6608 atoms, 6852 bonds, 55 pseudobonds, 749 residues, 9 models selected 
    7243 
    7244 > select subtract #18.8
    7245 
    7246 6075 atoms, 6254 bonds, 12 pseudobonds, 723 residues, 7 models selected 
    7247 
    7248 > select subtract #18.7
    7249 
    7250 5548 atoms, 5664 bonds, 12 pseudobonds, 697 residues, 6 models selected 
    7251 
    7252 > hide sel atoms
    7253 
    7254 > hide #!18 models
    7255 
    7256 > select add #18
    7257 
    7258 8456 atoms, 8740 bonds, 59 pseudobonds, 980 residues, 6 models selected 
    7259 
    7260 > select subtract #18
    7261 
    7262 6 models selected 
    7263 
    7264 > show #!19 models
    7265 
    7266 > select add #19
    7267 
    7268 7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 4 models selected 
    7269 
    7270 > select subtract #19.11
    7271 
    7272 7406 atoms, 6860 bonds, 46 pseudobonds, 1566 residues, 12 models selected 
    7273 
    7274 > select subtract #19.10
    7275 
    7276 7163 atoms, 6588 bonds, 46 pseudobonds, 1554 residues, 11 models selected 
    7277 
    7278 > select subtract #19.4
    7279 
    7280 5649 atoms, 5040 bonds, 42 pseudobonds, 1358 residues, 10 models selected 
    7281 
    7282 > select add #19.10
    7283 
    7284 5892 atoms, 5040 bonds, 42 pseudobonds, 1370 residues, 9 models selected 
    7285 
    7286 > select add #19.11
    7287 
    7288 6119 atoms, 5040 bonds, 42 pseudobonds, 1382 residues, 10 models selected 
    7289 
    7290 > select subtract #19.9
    7291 
    7292 5903 atoms, 4802 bonds, 12 pseudobonds, 1371 residues, 9 models selected 
    7293 
    7294 > select subtract #19.8
    7295 
    7296 5690 atoms, 4566 bonds, 12 pseudobonds, 1359 residues, 8 models selected 
    7297 
    7298 > hide sel atoms
    7299 
    7300 > select add #19
    7301 
    7302 7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 9 models selected 
    7303 
    7304 > select subtract #19
    7305 
    7306 8 models selected 
    7307 
    7308 > show #!1 models
    7309 
    7310 > show #!2 models
    7311 
    7312 > show #!3 models
    7313 
    7314 > show #!4 models
    7315 
    7316 > show #!5 models
    7317 
    7318 > show #!6 models
    7319 
    7320 > show #!8 models
    7321 
    7322 > show #!7 models
    7323 
    7324 > show #!9 models
    7325 
    7326 > show #!10 models
    7327 
    7328 > show #!11 models
    7329 
    7330 > show #!12 models
    7331 
    7332 > show #!13 models
    7333 
    7334 > show #!14 models
    7335 
    7336 > show #!15 models
    7337 
    7338 > show #!16 models
    7339 
    7340 > show #!17 models
    7341 
    7342 > show #!18 models
    7343 
    7344 > select
    7345 > #!1/B:110-112,124-127,132-135,141-146,156-163,195-197,204-207,214-219,230-236,251-258,264-274
    7346 
    7347 530 atoms, 532 bonds, 64 residues, 1 model selected 
    7348 
    7349 > select #!1/B:220
    7350 
    7351 12 atoms, 12 bonds, 1 residue, 1 model selected 
    7352 
    7353 > select #!1/B:220
    7354 
    7355 12 atoms, 12 bonds, 1 residue, 1 model selected 
    7356 
    7357 > select O
    7358 
    7359 30159 atoms, 21045 residues, 127 models selected 
    7360 
    7361 > hide sel atoms
    7362 
    7363 > show sel atoms
    7364 
    7365 > select add #1
    7366 
    7367 35149 atoms, 6306 bonds, 55 pseudobonds, 21051 residues, 230 models selected 
    7368 
    7369 > select add #2
    7370 
    7371 40862 atoms, 13714 bonds, 133 pseudobonds, 21058 residues, 232 models selected 
    7372 
    7373 > select add #3
    7374 
    7375 46517 atoms, 21027 bonds, 190 pseudobonds, 21062 residues, 234 models selected 
    7376 
    7377 > select add #4
    7378 
    7379 52139 atoms, 28308 bonds, 264 pseudobonds, 21070 residues, 236 models selected 
    7380 
    7381 > select add #5
    7382 
    7383 57787 atoms, 35615 bonds, 334 pseudobonds, 21078 residues, 238 models selected 
    7384 
    7385 > select add #6
    7386 
    7387 59208 atoms, 37450 bonds, 338 pseudobonds, 21079 residues, 239 models selected 
    7388 
    7389 > select add #7
    7390 
    7391 66012 atoms, 46262 bonds, 411 pseudobonds, 21083 residues, 241 models selected 
    7392 
    7393 > select add #8
    7394 
    7395 71687 atoms, 53619 bonds, 492 pseudobonds, 21087 residues, 243 models selected 
    7396 
    7397 > select add #9
    7398 
    7399 73111 atoms, 55456 bonds, 497 pseudobonds, 21088 residues, 245 models selected 
    7400 
    7401 > select add #10
    7402 
    7403 74561 atoms, 57336 bonds, 502 pseudobonds, 21089 residues, 247 models selected 
    7404 
    7405 > select add #11
    7406 
    7407 80272 atoms, 64722 bonds, 565 pseudobonds, 21093 residues, 249 models selected 
    7408 
    7409 > select add #12
    7410 
    7411 87064 atoms, 73522 bonds, 636 pseudobonds, 21097 residues, 251 models selected 
    7412 
    7413 > select add #13
    7414 
    7415 92720 atoms, 80820 bonds, 700 pseudobonds, 21101 residues, 253 models selected 
    7416 
    7417 > select add #14
    7418 
    7419 94122 atoms, 82634 bonds, 705 pseudobonds, 21102 residues, 255 models selected 
    7420 
    7421 > select add #15
    7422 
    7423 95535 atoms, 84461 bonds, 710 pseudobonds, 21104 residues, 257 models selected 
    7424 
    7425 > select add #16
    7426 
    7427 98255 atoms, 87960 bonds, 720 pseudobonds, 21108 residues, 259 models selected 
    7428 
    7429 > select add #17
    7430 
    7431 105047 atoms, 96760 bonds, 797 pseudobonds, 21112 residues, 261 models
    7432 selected 
    7433 
    7434 > select add #18
    7435 
    7436 111803 atoms, 105500 bonds, 856 pseudobonds, 21116 residues, 263 models
    7437 selected 
    7438 
    7439 > select add #19
    7440 
    7441 117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 266 models
    7442 selected 
    7443 
    7444 > show sel atoms
    7445 
    7446 > select subtract #1
    7447 
    7448 110701 atoms, 106306 bonds, 882 pseudobonds, 19995 residues, 150 models
    7449 selected 
    7450 
    7451 > select subtract #2
    7452 
    7453 102491 atoms, 98898 bonds, 804 pseudobonds, 18099 residues, 142 models
    7454 selected 
    7455 
    7456 > select subtract #3
    7457 
    7458 95398 atoms, 91585 bonds, 747 pseudobonds, 17244 residues, 131 models selected 
    7459 
    7460 > select subtract #4
    7461 
    7462 87363 atoms, 84304 bonds, 673 pseudobonds, 15411 residues, 122 models selected 
    7463 
    7464 > select subtract #5
    7465 
    7466 79582 atoms, 76997 bonds, 603 pseudobonds, 13856 residues, 111 models selected 
    7467 
    7468 > select subtract #6
    7469 
    7470 77650 atoms, 75162 bonds, 599 pseudobonds, 13490 residues, 101 models selected 
    7471 
    7472 > select subtract #7
    7473 
    7474 69057 atoms, 66350 bonds, 526 pseudobonds, 12429 residues, 96 models selected 
    7475 
    7476 > select subtract #8
    7477 
    7478 60969 atoms, 58993 bonds, 445 pseudobonds, 10616 residues, 87 models selected 
    7479 
    7480 > select subtract #9
    7481 
    7482 59020 atoms, 57156 bonds, 440 pseudobonds, 10236 residues, 76 models selected 
    7483 
    7484 > select subtract #10
    7485 
    7486 56848 atoms, 55276 bonds, 435 pseudobonds, 9674 residues, 73 models selected 
    7487 
    7488 > select subtract #11
    7489 
    7490 48873 atoms, 47890 bonds, 372 pseudobonds, 7996 residues, 70 models selected 
    7491 
    7492 > select subtract #12
    7493 
    7494 40252 atoms, 39090 bonds, 301 pseudobonds, 6899 residues, 61 models selected 
    7495 
    7496 > select subtract #13
    7497 
    7498 32665 atoms, 31792 bonds, 237 pseudobonds, 5534 residues, 52 models selected 
    7499 
    7500 > select subtract #14
    7501 
    7502 30572 atoms, 29978 bonds, 232 pseudobonds, 4987 residues, 43 models selected 
    7503 
    7504 > select subtract #15
    7505 
    7506 28463 atoms, 28151 bonds, 227 pseudobonds, 4436 residues, 38 models selected 
    7507 
    7508 > select subtract #16
    7509 
    7510 24766 atoms, 24652 bonds, 217 pseudobonds, 3711 residues, 33 models selected 
    7511 
    7512 > select subtract #17
    7513 
    7514 16089 atoms, 15852 bonds, 140 pseudobonds, 2558 residues, 27 models selected 
    7515 
    7516 > select subtract #18
    7517 
    7518 7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 18 models selected 
    7519 
    7520 > select subtract #19
    7521 
    7522 8 models selected 
    7523 
    7524 > select add #1.2
    7525 
    7526 12 pseudobonds, 1 model selected 
    7527 
    7528 > select subtract #1.2
    7529 
    7530 Nothing selected 
    7531 
    7532 > select add #1.1
    7533 
    7534 43 pseudobonds, 1 model selected 
    7535 
    7536 > select add #2.3
    7537 
    7538 1552 atoms, 43 pseudobonds, 199 residues, 2 models selected 
    7539 
    7540 > select subtract #2.3
    7541 
    7542 43 pseudobonds, 2 models selected 
    7543 
    7544 > hide #!1 models
    7545 
    7546 > select add #1
    7547 
    7548 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 116 models selected 
    7549 
    7550 > select subtract #1
    7551 
    7552 5 models selected 
    7553 
    7554 > hide #!19 models
    7555 
    7556 > hide #!18 models
    7557 
    7558 > hide #!17 models
    7559 
    7560 > hide #!16 models
    7561 
    7562 > hide #!15 models
    7563 
    7564 > hide #!13 models
    7565 
    7566 > hide #!12 models
    7567 
    7568 > hide #!11 models
    7569 
    7570 > hide #!14 models
    7571 
    7572 > hide #!10 models
    7573 
    7574 > hide #!9 models
    7575 
    7576 > hide #!8 models
    7577 
    7578 > hide #!7 models
    7579 
    7580 > hide #!6 models
    7581 
    7582 > hide #!5 models
    7583 
    7584 > hide #!4 models
    7585 
    7586 > hide #!3 models
    7587 
    7588 > show #!1 models
    7589 
    7590 > hide #!2 models
    7591 
    7592 > show #!2 models
    7593 
    7594 > hide #!2 models
    7595 
    7596 > select add #1.2
    7597 
    7598 12 pseudobonds, 1 model selected 
    7599 
    7600 > select subtract #1.2
    7601 
    7602 Nothing selected 
    7603 
    7604 > select add #1.1
    7605 
    7606 43 pseudobonds, 1 model selected 
    7607 
    7608 > select subtract #1.1
    7609 
    7610 Nothing selected 
    7611 
    7612 > select add #1.3
    7613 
    7614 1535 atoms, 196 residues, 1 model selected 
    7615 
    7616 > select add #1.5
    7617 
    7618 3064 atoms, 391 residues, 2 models selected 
    7619 
    7620 > select add #1.6
    7621 
    7622 3484 atoms, 412 residues, 3 models selected 
    7623 
    7624 > select add #1.7
    7625 
    7626 3919 atoms, 433 residues, 4 models selected 
    7627 
    7628 > select subtract #1.7
    7629 
    7630 3484 atoms, 412 residues, 5 models selected 
    7631 
    7632 > select subtract #1.6
    7633 
    7634 3064 atoms, 391 residues, 4 models selected 
    7635 
    7636 > hide sel atoms
    7637 
    7638 Drag select of 46 atoms 
    7639 Drag select of 72 atoms 
    7640 
    7641 > hide sel atoms
    7642 
    7643 Drag select of 2 atoms 
    7644 
    7645 > hide sel atoms
    7646 
    7647 Drag select of 1 atoms 
    7648 
    7649 > hide sel atoms
    7650 
    7651 Drag select of 2 atoms 
    7652 
    7653 > hide sel atoms
    7654 
    7655 Drag select of 81 atoms 
    7656 
    7657 > hide sel atoms
    7658 
    7659 Drag select of 35 atoms 
    7660 
    7661 > hide sel atoms
    7662 
    7663 Drag select of 1 atoms 
    7664 
    7665 > hide sel atoms
    7666 
    7667 > select add #1
    7668 
    7669 6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 116 models selected 
    7670 
    7671 > select subtract #1
    7672 
    7673 5 models selected 
    7674 
    7675 Cell requested for row 0 is out of bounds for table with 28 rows! Resizing
    7676 table model. 
    7677 
    7678 > show #!2 models
    7679 
    7680 > hide #!1 models
    7681 
    7682 > select add #2
    7683 
    7684 8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected 
    7685 
    7686 > select subtract #2.10
    7687 
    7688 7967 atoms, 7136 bonds, 44 pseudobonds, 1884 residues, 11 models selected 
    7689 
    7690 > select add #2.10
    7691 
    7692 8210 atoms, 7136 bonds, 44 pseudobonds, 1896 residues, 10 models selected 
    7693 
    7694 > select subtract #2.8
    7695 
    7696 7967 atoms, 6864 bonds, 16 pseudobonds, 1884 residues, 10 models selected 
    7697 
    7698 > select subtract #2.7
    7699 
    7700 7724 atoms, 6592 bonds, 16 pseudobonds, 1872 residues, 9 models selected 
    7701 
    7702 > select subtract #2.6
    7703 
    7704 6170 atoms, 5003 bonds, 12 pseudobonds, 1674 residues, 8 models selected 
    7705 
    7706 > select subtract #2.5
    7707 
    7708 4641 atoms, 3439 bonds, 8 pseudobonds, 1479 residues, 7 models selected 
    7709 
    7710 > select subtract #2.4
    7711 
    7712 3096 atoms, 1859 bonds, 4 pseudobonds, 1281 residues, 6 models selected 
    7713 
    7714 > hide sel atoms
    7715 
    7716 > select add #2.8
    7717 
    7718 3339 atoms, 1859 bonds, 4 pseudobonds, 1293 residues, 5 models selected 
    7719 
    7720 > select add #2.7
    7721 
    7722 3582 atoms, 1859 bonds, 4 pseudobonds, 1305 residues, 6 models selected 
    7723 
    7724 > select add #2.6
    7725 
    7726 5136 atoms, 1859 bonds, 4 pseudobonds, 1503 residues, 7 models selected 
    7727 
    7728 > select add #2.5
    7729 
    7730 6665 atoms, 1859 bonds, 4 pseudobonds, 1698 residues, 8 models selected 
    7731 
    7732 > select add #2.4
    7733 
    7734 8210 atoms, 1859 bonds, 4 pseudobonds, 1896 residues, 9 models selected 
    7735 
    7736 > show #!1 models
    7737 
    7738 > select subtract #2.3
    7739 
    7740 6658 atoms, 272 bonds, 1697 residues, 9 models selected 
    7741 
    7742 > select add #2.3
    7743 
    7744 8210 atoms, 272 bonds, 1896 residues, 8 models selected 
    7745 
    7746 > select subtract #2.4
    7747 
    7748 6665 atoms, 272 bonds, 1698 residues, 9 models selected 
     384[deleted to fit within ticket limits]
    7749385
    7750386> select add #2.4