print.core. bio3d 2.3-0

Usage

"print"(x, vol = NULL, ...)

Arguments

x: a list object obtained with the function core.find.
vol: the maximal cumulative volume value at which core positions are detailed.
...: additional arguments to ‘print’.

Description

Print method for core.find objects.

Value

atom: atom indices of core positions
xyz: xyz indices of core positions
resno: residue numbers of core positions

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Note

The produced plot.core function can be useful for deciding on the core/non-core boundary.

Examples

##-- Generate a small kinesin alignment and read corresponding structures pdbfiles <- get.pdb(c("1bg2","2ncd","1i6i","1i5s"), URLonly=TRUE) pdbs <- pdbaln(pdbfiles)

Reading PDB files: http://www.rcsb.org/pdb/files/1bg2.pdb http://www.rcsb.org/pdb/files/2ncd.pdb http://www.rcsb.org/pdb/files/1i6i.pdb http://www.rcsb.org/pdb/files/1i5s.pdb .. PDB has ALT records, taking A only, rm.alt=TRUE . PDB has ALT records, taking A only, rm.alt=TRUE . Extracting sequences pdb/seq: 1 name: http://www.rcsb.org/pdb/files/1bg2.pdb pdb/seq: 2 name: http://www.rcsb.org/pdb/files/2ncd.pdb pdb/seq: 3 name: http://www.rcsb.org/pdb/files/1i6i.pdb PDB has ALT records, taking A only, rm.alt=TRUE pdb/seq: 4 name: http://www.rcsb.org/pdb/files/1i5s.pdb PDB has ALT records, taking A only, rm.alt=TRUE

##-- Find 'core' positions core <- core.find(pdbs)

core size 293 of 294 vol = 699.925 core size 292 of 294 vol = 596.377 core size 291 of 294 vol = 526.367 core size 290 of 294 vol = 461.809 core size 289 of 294 vol = 398.743 core size 288 of 294 vol = 338.511 core size 287 of 294 vol = 284.55 core size 286 of 294 vol = 245.99 core size 285 of 294 vol = 209.855 core size 284 of 294 vol = 181.912 core size 283 of 294 vol = 174.392 core size 282 of 294 vol = 164.476 core size 281 of 294 vol = 156.414 core size 280 of 294 vol = 146.519 core size 279 of 294 vol = 138.917 core size 278 of 294 vol = 130.52 core size 277 of 294 vol = 123.34 core size 276 of 294 vol = 118.842 core size 275 of 294 vol = 113.597 core size 274 of 294 vol = 107.865 core size 273 of 294 vol = 103.215 core size 272 of 294 vol = 97.239 core size 271 of 294 vol = 92.829 core size 270 of 294 vol = 87.717 core size 269 of 294 vol = 84.086 core size 268 of 294 vol = 80.571 core size 267 of 294 vol = 77.329 core size 266 of 294 vol = 75.464 core size 265 of 294 vol = 72.27 core size 264 of 294 vol = 70.298 core size 263 of 294 vol = 67.809 core size 262 of 294 vol = 64.211 core size 261 of 294 vol = 61.395 core size 260 of 294 vol = 59.047 core size 259 of 294 vol = 57.234 core size 258 of 294 vol = 55.442 core size 257 of 294 vol = 53.374 core size 256 of 294 vol = 50.983 core size 255 of 294 vol = 48.827 core size 254 of 294 vol = 47.141 core size 253 of 294 vol = 45.141 core size 252 of 294 vol = 43.701 core size 251 of 294 vol = 43.009 core size 250 of 294 vol = 42.575 core size 249 of 294 vol = 40.857 core size 248 of 294 vol = 39.521 core size 247 of 294 vol = 38.055 core size 246 of 294 vol = 36.383 core size 245 of 294 vol = 34.777 core size 244 of 294 vol = 33.234 core size 243 of 294 vol = 31.942 core size 242 of 294 vol = 30.77 core size 241 of 294 vol = 29.364 core size 240 of 294 vol = 28.579 core size 239 of 294 vol = 27.857 core size 238 of 294 vol = 26.662 core size 237 of 294 vol = 25.791 core size 236 of 294 vol = 25.126 core size 235 of 294 vol = 24.758 core size 234 of 294 vol = 24.072 core size 233 of 294 vol = 22.984 core size 232 of 294 vol = 22.483 core size 231 of 294 vol = 21.414 core size 230 of 294 vol = 20.533 core size 229 of 294 vol = 19.881 core size 228 of 294 vol = 19.328 core size 227 of 294 vol = 18.594 core size 226 of 294 vol = 17.918 core size 225 of 294 vol = 17.824 core size 224 of 294 vol = 17.519 core size 223 of 294 vol = 16.291 core size 222 of 294 vol = 15.704 core size 221 of 294 vol = 15.036 core size 220 of 294 vol = 14.852 core size 219 of 294 vol = 14.298 core size 218 of 294 vol = 13.536 core size 217 of 294 vol = 12.802 core size 216 of 294 vol = 12.249 core size 215 of 294 vol = 11.663 core size 214 of 294 vol = 11.121 core size 213 of 294 vol = 10.52 core size 212 of 294 vol = 10.379 core size 211 of 294 vol = 10.062 core size 210 of 294 vol = 9.795 core size 209 of 294 vol = 9.539 core size 208 of 294 vol = 9.176 core size 207 of 294 vol = 9.299 core size 206 of 294 vol = 8.77 core size 205 of 294 vol = 8.437 core size 204 of 294 vol = 8.153 core size 203 of 294 vol = 7.771 core size 202 of 294 vol = 7.517 core size 201 of 294 vol = 7.312 core size 200 of 294 vol = 7.091 core size 199 of 294 vol = 6.829 core size 198 of 294 vol = 6.458 core size 197 of 294 vol = 6.261 core size 196 of 294 vol = 6.101 core size 195 of 294 vol = 5.734 core size 194 of 294 vol = 5.563 core size 193 of 294 vol = 5.372 core size 192 of 294 vol = 5.228 core size 191 of 294 vol = 5.153 core size 190 of 294 vol = 5.03 core size 189 of 294 vol = 4.917 core size 188 of 294 vol = 4.85 core size 187 of 294 vol = 4.744 core size 186 of 294 vol = 4.613 core size 185 of 294 vol = 4.478 core size 184 of 294 vol = 4.39 core size 183 of 294 vol = 4.275 core size 182 of 294 vol = 4.149 core size 181 of 294 vol = 4.034 core size 180 of 294 vol = 3.944 core size 179 of 294 vol = 3.876 core size 178 of 294 vol = 3.753 core size 177 of 294 vol = 3.753 core size 176 of 294 vol = 3.621 core size 175 of 294 vol = 3.457 core size 174 of 294 vol = 3.349 core size 173 of 294 vol = 3.119 core size 172 of 294 vol = 2.994 core size 171 of 294 vol = 2.875 core size 170 of 294 vol = 2.736 core size 169 of 294 vol = 2.681 core size 168 of 294 vol = 2.591 core size 167 of 294 vol = 2.535 core size 166 of 294 vol = 2.475 core size 165 of 294 vol = 2.43 core size 164 of 294 vol = 2.383 core size 163 of 294 vol = 2.351 core size 162 of 294 vol = 2.193 core size 161 of 294 vol = 2.134 core size 160 of 294 vol = 2.086 core size 159 of 294 vol = 2.042 core size 158 of 294 vol = 1.952 core size 157 of 294 vol = 1.908 core size 156 of 294 vol = 1.854 core size 155 of 294 vol = 1.814 core size 154 of 294 vol = 1.761 core size 153 of 294 vol = 1.729 core size 152 of 294 vol = 1.672 core size 151 of 294 vol = 1.631 core size 150 of 294 vol = 1.589 core size 149 of 294 vol = 1.537 core size 148 of 294 vol = 1.509 core size 147 of 294 vol = 1.496 core size 146 of 294 vol = 1.474 core size 145 of 294 vol = 1.449 core size 144 of 294 vol = 1.365 core size 143 of 294 vol = 1.33 core size 142 of 294 vol = 1.303 core size 141 of 294 vol = 1.268 core size 140 of 294 vol = 1.268 core size 139 of 294 vol = 1.24 core size 138 of 294 vol = 1.231 core size 137 of 294 vol = 1.214 core size 136 of 294 vol = 1.119 core size 135 of 294 vol = 1.112 core size 134 of 294 vol = 1.102 core size 133 of 294 vol = 1.078 core size 132 of 294 vol = 1.043 core size 131 of 294 vol = 1.018 core size 130 of 294 vol = 0.969 core size 129 of 294 vol = 0.938 core size 128 of 294 vol = 0.93 core size 127 of 294 vol = 0.903 core size 126 of 294 vol = 0.882 core size 125 of 294 vol = 0.873 core size 124 of 294 vol = 0.86 core size 123 of 294 vol = 0.851 core size 122 of 294 vol = 0.833 core size 121 of 294 vol = 0.824 core size 120 of 294 vol = 0.803 core size 119 of 294 vol = 0.78 core size 118 of 294 vol = 0.756 core size 117 of 294 vol = 0.763 core size 116 of 294 vol = 0.712 core size 115 of 294 vol = 0.704 core size 114 of 294 vol = 0.697 core size 113 of 294 vol = 0.665 core size 112 of 294 vol = 0.656 core size 111 of 294 vol = 0.64 core size 110 of 294 vol = 0.632 core size 109 of 294 vol = 0.608 core size 108 of 294 vol = 0.594 core size 107 of 294 vol = 0.584 core size 106 of 294 vol = 0.528 core size 105 of 294 vol = 0.526 core size 104 of 294 vol = 0.516 core size 103 of 294 vol = 0.534 core size 102 of 294 vol = 0.517 core size 101 of 294 vol = 0.485 FINISHED: Min vol ( 0.5 ) reached

plot(core) ##-- Fit on these relatively invarient subset of positions core.inds <- print(core, vol=0.5)

# 102 positions (cumulative volume <= 0.5 Angstrom^3) start end length 1 9 16 8 2 34 34 1 3 36 36 1 4 51 53 3 5 57 59 3 6 61 62 2 7 67 67 1 8 70 70 1 9 72 72 1 10 74 74 1 11 78 78 1 12 80 95 16 13 97 97 1 14 104 104 1 15 106 118 13 16 129 129 1 17 132 134 3 18 136 137 2 19 168 168 1 20 172 173 2 21 179 179 1 22 181 181 1 23 183 183 1 24 205 210 6 25 212 213 2 26 225 225 1 27 228 236 9 28 284 284 1 29 294 294 1 30 296 303 8 31 306 306 1 32 308 309 2 33 311 313 3 34 315 316 2

print(core, vol=0.7)

# 115 positions (cumulative volume <= 0.7 Angstrom^3) start end length 1 9 16 8 2 34 34 1 3 36 36 1 4 51 53 3 5 57 59 3 6 61 62 2 7 67 67 1 8 70 70 1 9 72 72 1 10 74 74 1 11 78 95 18 12 97 97 1 13 104 104 1 14 106 119 14 15 129 130 2 16 132 137 6 17 144 144 1 18 166 166 1 19 168 169 2 20 171 173 3 21 175 175 1 22 179 179 1 23 181 181 1 24 183 183 1 25 204 210 7 26 212 213 2 27 225 226 2 28 228 236 9 29 283 284 2 30 287 287 1 31 294 294 1 32 296 303 8 33 306 306 1 34 308 309 2 35 311 313 3 36 315 316 2

print(core, vol=1.0)

# 131 positions (cumulative volume <= 1 Angstrom^3) start end length 1 9 16 8 2 34 34 1 3 36 36 1 4 38 38 1 5 48 49 2 6 51 53 3 7 57 62 6 8 67 67 1 9 69 70 2 10 72 74 3 11 78 95 18 12 97 97 1 13 104 104 1 14 106 119 14 15 129 137 9 16 139 139 1 17 142 142 1 18 144 145 2 19 166 166 1 20 168 173 6 21 175 175 1 22 179 179 1 23 181 181 1 24 183 183 1 25 203 210 8 26 212 213 2 27 225 236 12 28 283 284 2 29 287 287 1 30 294 294 1 31 296 304 9 32 306 306 1 33 308 313 6 34 315 316 2 35 318 318 1

Author

Barry Grant

Printing Core Positions and Returning Indices