Identification of Invariant Core Positions

Usage

core.find(...)


"core.find"(pdbs, shortcut = FALSE, rm.island = FALSE, verbose = TRUE, stop.at = 15, stop.vol = 0.5, write.pdbs = FALSE, outpath="core_pruned", ncore = 1, nseg.scale = 1, ...)


"core.find"(xyz, ...)


"core.find"(pdb, verbose=TRUE, ...)

Arguments

pdbs
a numeric matrix of aligned C-alpha xyz Cartesian coordinates. For example an alignment data structure obtained with read.fasta.pdb or pdbaln.
shortcut
if TRUE, remove more than one position at a time.
rm.island
remove isolated fragments of less than three residues.
verbose
logical, if TRUE a “core\_pruned” directory containing ‘core structures’ for each iteraction is written to the current directory.
stop.at
minimal core size at which iterations should be stopped.
stop.vol
minimal core volume at which iterations should be stopped.
write.pdbs
logical, if TRUE core coordinate files, containing only core positions for each iteration, are written to a location specified by outpath.
outpath
character string specifying the output directory when write.pdbs is TRUE.
ncore
number of CPU cores used to do the calculation. ncore>1 requires package ‘parallel’ installed.
nseg.scale
split input data into specified number of segments prior to running multiple core calculation. See fit.xyz.
xyz
a numeric matrix of xyz Cartesian coordinates, e.g. obtained from read.dcd or read.ncdf.
pdb
an object of type pdb as obtained from function read.pdb with multiple frames (>=4) stored in its xyz component. Note that the function will attempt to identify C-alpha and phosphate atoms (for protein and nucleic acids, respectively) in which the calculation should be based.
...
arguments passed to and from functions.

Description

Perform iterated rounds of structural superposition to identify the most invariant region in an aligned set of protein structures.

Details

This function attempts to iteratively refine an initial structural superposition determined from a multiple alignment. This involves iterated rounds of superposition, where at each round the position(s) displaying the largest differences is(are) excluded from the dataset. The spatial variation at each aligned position is determined from the eigenvalues of their Cartesian coordinates (i.e. the variance of the distribution along its three principal directions). Inspired by the work of Gerstein et al. (1991, 1995), an ellipsoid of variance is determined from the eigenvalues, and its volume is taken as a measure of structural variation at a given position.

Optional “core PDB files” containing core positions, upon which superposition is based, can be written to a location specified by outpath by setting write.pdbs=TRUE. These files are useful for examining the core filtering process by visualising them in a graphics program.

Value

Returns a list of class "core" with the following components:
volume
total core volume at each fitting iteration/round.

length
core length at each round.

resno
residue number of core residues at each round (taken from the first aligned structure) or, alternatively, the numeric index of core residues at each round.

step.inds
atom indices of core atoms at each round.

atom
atom indices of core positions in the last round.

xyz
xyz indices of core positions in the last round.

c1A.atom
atom indices of core positions with a total volume under 1 Angstrom\^3.

c1A.xyz
xyz indices of core positions with a total volume under 1 Angstrom\^3.

c1A.resno
residue numbers of core positions with a total volume under 1 Angstrom\^3.

c0.5A.atom
atom indices of core positions with a total volume under 0.5 Angstrom\^3.

c0.5A.xyz
xyz indices of core positions with a total volume under 0.5 Angstrom\^3.

c0.5A.resno
residue numbers of core positions with a total volume under 0.5 Angstrom\^3.

References

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

Gerstein and Altman (1995) J. Mol. Biol. 251, 161--175.

Gerstein and Chothia (1991) J. Mol. Biol. 220, 133--149.

Note

The relevance of the ‘core positions’ identified by this procedure is dependent upon the number of input structures and their diversity.

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=1)
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



xyz <- pdbfit(pdbs, core.inds, outpath="corefit_structures")



   PDB has ALT records, taking A only, rm.alt=TRUE
   PDB has ALT records, taking A only, rm.alt=TRUE




##-- Compare to fitting on all equivalent positions
xyz2 <- pdbfit(pdbs)

## Note that overall RMSD will be higher but RMSF will
##  be lower in core regions, which may equate to a
##  'better fit' for certain applications
gaps <- gap.inspect(pdbs$xyz)
rmsd(xyz[,gaps$f.inds])


Warning message:
No indices provided, using the 294 non NA positions


      [,1]  [,2]  [,3]  [,4]
[1,] 0.000 3.583 3.390 3.116
[2,] 3.583 0.000 3.787 3.599
[3,] 3.390 3.787 0.000 2.351
[4,] 3.116 3.599 2.351 0.000



rmsd(xyz2[,gaps$f.inds])


Warning message:
No indices provided, using the 294 non NA positions


      [,1]  [,2]  [,3]  [,4]
[1,] 0.000 3.570 3.297 3.089
[2,] 3.570 0.000 3.696 3.579
[3,] 3.297 3.696 0.000 2.222
[4,] 3.089 3.579 2.222 0.000




plot(rmsf(xyz[,gaps$f.inds]), typ="l", col="blue", ylim=c(0,9))



points(rmsf(xyz2[,gaps$f.inds]), typ="l", col="red")






##-- Run core.find() on a multimodel PDB file
pdb <- read.pdb('1d1d', multi=TRUE)



  Note: Accessing on-line PDB file



core <- core.find(pdb)




 ..      220 atom(s) from 'string' selection 
 ..      220 atom(s) in final combined selection 


 ..        0 atom(s) from 'string' selection 
 ..        0 atom(s) from 'elety' selection 
 ..        0 atom(s) in final combined selection 

 Union of selects
 *  Selected a total of: 220 atoms  *
 core size 219 of 220  vol = 80028.92 
 core size 218 of 220  vol = 78588.22 
 core size 217 of 220  vol = 76410.13 
 core size 216 of 220  vol = 74091.53 
 core size 215 of 220  vol = 72626.57 
 core size 214 of 220  vol = 70791.32 
 core size 213 of 220  vol = 69224.37 
 core size 212 of 220  vol = 67861.81 
 core size 211 of 220  vol = 66479.53 
 core size 210 of 220  vol = 64913.15 
 core size 209 of 220  vol = 63452.38 
 core size 208 of 220  vol = 62054.96 
 core size 207 of 220  vol = 60965.03 
 core size 206 of 220  vol = 59532.15 
 core size 205 of 220  vol = 58123.13 
 core size 204 of 220  vol = 56913.48 
 core size 203 of 220  vol = 56013.92 
 core size 202 of 220  vol = 54824.84 
 core size 201 of 220  vol = 53692.84 
 core size 200 of 220  vol = 51976.8 
 core size 199 of 220  vol = 50319.93 
 core size 198 of 220  vol = 49132.73 
 core size 197 of 220  vol = 48361.34 
 core size 196 of 220  vol = 47276.21 
 core size 195 of 220  vol = 46269.85 
 core size 194 of 220  vol = 45136.55 
 core size 193 of 220  vol = 44072.71 
 core size 192 of 220  vol = 43323.08 
 core size 191 of 220  vol = 42364.85 
 core size 190 of 220  vol = 41325.58 
 core size 189 of 220  vol = 40658.42 
 core size 188 of 220  vol = 39536.91 
 core size 187 of 220  vol = 38598.77 
 core size 186 of 220  vol = 37659.78 
 core size 185 of 220  vol = 36891.51 
 core size 184 of 220  vol = 36240.27 
 core size 183 of 220  vol = 35560.02 
 core size 182 of 220  vol = 34684.24 
 core size 181 of 220  vol = 33889.36 
 core size 180 of 220  vol = 33212.81 
 core size 179 of 220  vol = 32233.6 
 core size 178 of 220  vol = 31223.56 
 core size 177 of 220  vol = 30556.8 
 core size 176 of 220  vol = 29908.46 
 core size 175 of 220  vol = 29253.3 
 core size 174 of 220  vol = 28070.19 
 core size 173 of 220  vol = 27319.49 
 core size 172 of 220  vol = 26595.86 
 core size 171 of 220  vol = 25931.99 
 core size 170 of 220  vol = 25254.61 
 core size 169 of 220  vol = 24538.45 
 core size 168 of 220  vol = 24041.35 
 core size 167 of 220  vol = 23064.07 
 core size 166 of 220  vol = 22528.61 
 core size 165 of 220  vol = 22040.96 
 core size 164 of 220  vol = 21487.35 
 core size 163 of 220  vol = 20773.03 
 core size 162 of 220  vol = 20172.09 
 core size 161 of 220  vol = 19541.43 
 core size 160 of 220  vol = 19063.78 
 core size 159 of 220  vol = 18534.67 
 core size 158 of 220  vol = 18075.66 
 core size 157 of 220  vol = 17488.76 
 core size 156 of 220  vol = 17003.33 
 core size 155 of 220  vol = 16423.39 
 core size 154 of 220  vol = 15648.52 
 core size 153 of 220  vol = 14945.91 
 core size 152 of 220  vol = 13975.75 
 core size 151 of 220  vol = 13291.79 
 core size 150 of 220  vol = 12455.54 
 core size 149 of 220  vol = 11440.64 
 core size 148 of 220  vol = 10332.09 
 core size 147 of 220  vol = 9491.928 
 core size 146 of 220  vol = 8548.282 
 core size 145 of 220  vol = 7373.966 
 core size 144 of 220  vol = 6194.034 
 core size 143 of 220  vol = 4856.297 
 core size 142 of 220  vol = 3238.08 
 core size 141 of 220  vol = 1915.693 
 core size 140 of 220  vol = 1059.597 
 core size 139 of 220  vol = 599.305 
 core size 138 of 220  vol = 383.745 
 core size 137 of 220  vol = 256.211 
 core size 136 of 220  vol = 158.747 
 core size 135 of 220  vol = 107.812 
 core size 134 of 220  vol = 88.012 
 core size 133 of 220  vol = 69.301 
 core size 132 of 220  vol = 55.639 
 core size 131 of 220  vol = 44.668 
 core size 130 of 220  vol = 33.939 
 core size 129 of 220  vol = 26.558 
 core size 128 of 220  vol = 24.122 
 core size 127 of 220  vol = 22.316 
 core size 126 of 220  vol = 21.486 
 core size 125 of 220  vol = 20.677 
 core size 124 of 220  vol = 19.789 
 core size 123 of 220  vol = 18.956 
 core size 122 of 220  vol = 18.03 
 core size 121 of 220  vol = 17.241 
 core size 120 of 220  vol = 16.465 
 core size 119 of 220  vol = 15.771 
 core size 118 of 220  vol = 15.084 
 core size 117 of 220  vol = 14.441 
 core size 116 of 220  vol = 13.958 
 core size 115 of 220  vol = 13.364 
 core size 114 of 220  vol = 12.795 
 core size 113 of 220  vol = 12.228 
 core size 112 of 220  vol = 11.703 
 core size 111 of 220  vol = 11.166 
 core size 110 of 220  vol = 10.723 
 core size 109 of 220  vol = 10.251 
 core size 108 of 220  vol = 9.788 
 core size 107 of 220  vol = 9.355 
 core size 106 of 220  vol = 8.913 
 core size 105 of 220  vol = 8.475 
 core size 104 of 220  vol = 8.113 
 core size 103 of 220  vol = 7.737 
 core size 102 of 220  vol = 7.436 
 core size 101 of 220  vol = 7.024 
 core size 100 of 220  vol = 6.712 
 core size 99 of 220  vol = 6.403 
 core size 98 of 220  vol = 6.11 
 core size 97 of 220  vol = 5.777 
 core size 96 of 220  vol = 5.467 
 core size 95 of 220  vol = 5.087 
 core size 94 of 220  vol = 4.73 
 core size 93 of 220  vol = 4.44 
 core size 92 of 220  vol = 4.139 
 core size 91 of 220  vol = 3.814 
 core size 90 of 220  vol = 3.544 
 core size 89 of 220  vol = 3.336 
 core size 88 of 220  vol = 3.17 
 core size 87 of 220  vol = 2.99 
 core size 86 of 220  vol = 2.81 
 core size 85 of 220  vol = 2.613 
 core size 84 of 220  vol = 2.436 
 core size 83 of 220  vol = 2.269 
 core size 82 of 220  vol = 2.124 
 core size 81 of 220  vol = 1.999 
 core size 80 of 220  vol = 1.899 
 core size 79 of 220  vol = 1.8 
 core size 78 of 220  vol = 1.726 
 core size 77 of 220  vol = 1.662 
 core size 76 of 220  vol = 1.578 
 core size 75 of 220  vol = 1.511 
 core size 74 of 220  vol = 1.451 
 core size 73 of 220  vol = 1.394 
 core size 72 of 220  vol = 1.337 
 core size 71 of 220  vol = 1.289 
 core size 70 of 220  vol = 1.239 
 core size 69 of 220  vol = 1.186 
 core size 68 of 220  vol = 1.137 
 core size 67 of 220  vol = 1.094 
 core size 66 of 220  vol = 1.044 
 core size 65 of 220  vol = 0.995 
 core size 64 of 220  vol = 0.947 
 core size 63 of 220  vol = 0.9 
 core size 62 of 220  vol = 0.858 
 core size 61 of 220  vol = 0.81 
 core size 60 of 220  vol = 0.767 
 core size 59 of 220  vol = 0.733 
 core size 58 of 220  vol = 0.697 
 core size 57 of 220  vol = 0.659 
 core size 56 of 220  vol = 0.628 
 core size 55 of 220  vol = 0.601 
 core size 54 of 220  vol = 0.563 
 core size 53 of 220  vol = 0.527 
 core size 52 of 220  vol = 0.491 
 FINISHED: Min vol ( 0.5 ) reached




##-- Run core.find() on a trajectory
trtfile <- system.file("examples/hivp.dcd", package="bio3d")
trj <- read.dcd(trtfile)



 NATOM = 198 
 NFRAME= 117 
 ISTART= 0 
 last  = 117 
 nstep = 117 
 nfile = 117 
 NSAVE = 1 
 NDEGF = 0 
 version 24 
Reading (x100)
  |======================================================================| 100%




## Read the starting PDB file to determine atom correspondence
pdbfile <- system.file("examples/hivp.pdb", package="bio3d")
pdb <- read.pdb(pdbfile)

## select calpha coords from a manageable number of frames
ca.ind <- atom.select(pdb, "calpha")$xyz
frames <- seq(1, nrow(trj), by=10)

core <- core.find( trj[frames, ca.ind], write.pdbs=TRUE )



 core size 197 of 198  vol = 379.113 
 core size 196 of 198  vol = 359.625 
 core size 195 of 198  vol = 342.013 
 core size 194 of 198  vol = 327.636 
 core size 193 of 198  vol = 314.284 
 core size 192 of 198  vol = 302.926 
 core size 191 of 198  vol = 291.664 
 core size 190 of 198  vol = 280.909 
 core size 189 of 198  vol = 270.866 
 core size 188 of 198  vol = 261.247 
 core size 187 of 198  vol = 252.37 
 core size 186 of 198  vol = 243.948 
 core size 185 of 198  vol = 235.569 
 core size 184 of 198  vol = 227.501 
 core size 183 of 198  vol = 220.684 
 core size 182 of 198  vol = 213.842 
 core size 181 of 198  vol = 206.979 
 core size 180 of 198  vol = 200.46 
 core size 179 of 198  vol = 194.523 
 core size 178 of 198  vol = 189.055 
 core size 177 of 198  vol = 183.923 
 core size 176 of 198  vol = 178.328 
 core size 175 of 198  vol = 173.85 
 core size 174 of 198  vol = 169.616 
 core size 173 of 198  vol = 164.985 
 core size 172 of 198  vol = 160.923 
 core size 171 of 198  vol = 156.433 
 core size 170 of 198  vol = 152.544 
 core size 169 of 198  vol = 148.882 
 core size 168 of 198  vol = 144.709 
 core size 167 of 198  vol = 141.148 
 core size 166 of 198  vol = 137.941 
 core size 165 of 198  vol = 134.225 
 core size 164 of 198  vol = 130.687 
 core size 163 of 198  vol = 127.211 
 core size 162 of 198  vol = 124.155 
 core size 161 of 198  vol = 121.213 
 core size 160 of 198  vol = 118.4 
 core size 159 of 198  vol = 116.104 
 core size 158 of 198  vol = 113.746 
 core size 157 of 198  vol = 111.249 
 core size 156 of 198  vol = 108.6 
 core size 155 of 198  vol = 106.528 
 core size 154 of 198  vol = 104.057 
 core size 153 of 198  vol = 102.063 
 core size 152 of 198  vol = 100.064 
 core size 151 of 198  vol = 97.77 
 core size 150 of 198  vol = 95.843 
 core size 149 of 198  vol = 94.004 
 core size 148 of 198  vol = 92.017 
 core size 147 of 198  vol = 90.19 
 core size 146 of 198  vol = 88.477 
 core size 145 of 198  vol = 86.675 
 core size 144 of 198  vol = 84.823 
 core size 143 of 198  vol = 83.159 
 core size 142 of 198  vol = 81.642 
 core size 141 of 198  vol = 80.064 
 core size 140 of 198  vol = 78.276 
 core size 139 of 198  vol = 76.764 
 core size 138 of 198  vol = 75.33 
 core size 137 of 198  vol = 73.963 
 core size 136 of 198  vol = 72.652 
 core size 135 of 198  vol = 71.334 
 core size 134 of 198  vol = 69.968 
 core size 133 of 198  vol = 68.612 
 core size 132 of 198  vol = 66.996 
 core size 131 of 198  vol = 65.66 
 core size 130 of 198  vol = 64.271 
 core size 129 of 198  vol = 62.969 
 core size 128 of 198  vol = 61.783 
 core size 127 of 198  vol = 60.592 
 core size 126 of 198  vol = 59.539 
 core size 125 of 198  vol = 58.411 
 core size 124 of 198  vol = 57.264 
 core size 123 of 198  vol = 56.185 
 core size 122 of 198  vol = 55.117 
 core size 121 of 198  vol = 54.052 
 core size 120 of 198  vol = 52.987 
 core size 119 of 198  vol = 51.928 
 core size 118 of 198  vol = 50.868 
 core size 117 of 198  vol = 49.942 
 core size 116 of 198  vol = 48.97 
 core size 115 of 198  vol = 47.903 
 core size 114 of 198  vol = 46.909 
 core size 113 of 198  vol = 45.909 
 core size 112 of 198  vol = 44.944 
 core size 111 of 198  vol = 43.991 
 core size 110 of 198  vol = 43.068 
 core size 109 of 198  vol = 42.121 
 core size 108 of 198  vol = 41.071 
 core size 107 of 198  vol = 40.146 
 core size 106 of 198  vol = 39.336 
 core size 105 of 198  vol = 38.507 
 core size 104 of 198  vol = 37.752 
 core size 103 of 198  vol = 36.972 
 core size 102 of 198  vol = 36.345 
 core size 101 of 198  vol = 35.598 
 core size 100 of 198  vol = 34.916 
 core size 99 of 198  vol = 34.26 
 core size 98 of 198  vol = 33.578 
 core size 97 of 198  vol = 32.882 
 core size 96 of 198  vol = 32.107 
 core size 95 of 198  vol = 31.456 
 core size 94 of 198  vol = 30.663 
 core size 93 of 198  vol = 30.01 
 core size 92 of 198  vol = 29.393 
 core size 91 of 198  vol = 28.798 
 core size 90 of 198  vol = 28.159 
 core size 89 of 198  vol = 27.491 
 core size 88 of 198  vol = 26.833 
 core size 87 of 198  vol = 26.209 
 core size 86 of 198  vol = 25.625 
 core size 85 of 198  vol = 25.025 
 core size 84 of 198  vol = 24.448 
 core size 83 of 198  vol = 23.778 
 core size 82 of 198  vol = 23.211 
 core size 81 of 198  vol = 22.589 
 core size 80 of 198  vol = 22.006 
 core size 79 of 198  vol = 21.436 
 core size 78 of 198  vol = 20.869 
 core size 77 of 198  vol = 20.402 
 core size 76 of 198  vol = 19.866 
 core size 75 of 198  vol = 19.282 
 core size 74 of 198  vol = 18.73 
 core size 73 of 198  vol = 18.261 
 core size 72 of 198  vol = 17.768 
 core size 71 of 198  vol = 17.366 
 core size 70 of 198  vol = 16.903 
 core size 69 of 198  vol = 16.356 
 core size 68 of 198  vol = 15.898 
 core size 67 of 198  vol = 15.478 
 core size 66 of 198  vol = 15.068 
 core size 65 of 198  vol = 14.652 
 core size 64 of 198  vol = 14.184 
 core size 63 of 198  vol = 13.798 
 core size 62 of 198  vol = 13.391 
 core size 61 of 198  vol = 12.968 
 core size 60 of 198  vol = 12.587 
 core size 59 of 198  vol = 12.139 
 core size 58 of 198  vol = 11.711 
 core size 57 of 198  vol = 11.329 
 core size 56 of 198  vol = 10.93 
 core size 55 of 198  vol = 10.555 
 core size 54 of 198  vol = 10.143 
 core size 53 of 198  vol = 9.74 
 core size 52 of 198  vol = 9.289 
 core size 51 of 198  vol = 8.917 
 core size 50 of 198  vol = 8.587 
 core size 49 of 198  vol = 8.248 
 core size 48 of 198  vol = 7.925 
 core size 47 of 198  vol = 7.618 
 core size 46 of 198  vol = 7.365 
 core size 45 of 198  vol = 7.027 
 core size 44 of 198  vol = 6.723 
 core size 43 of 198  vol = 6.461 
 core size 42 of 198  vol = 6.186 
 core size 41 of 198  vol = 5.969 
 core size 40 of 198  vol = 5.771 
 core size 39 of 198  vol = 5.489 
 core size 38 of 198  vol = 5.21 
 core size 37 of 198  vol = 4.932 
 core size 36 of 198  vol = 4.676 
 core size 35 of 198  vol = 4.376 
 core size 34 of 198  vol = 4.145 
 core size 33 of 198  vol = 3.898 
 core size 32 of 198  vol = 3.707 
 core size 31 of 198  vol = 3.458 
 core size 30 of 198  vol = 3.229 
 core size 29 of 198  vol = 3.02 
 core size 28 of 198  vol = 2.834 
 core size 27 of 198  vol = 2.638 
 core size 26 of 198  vol = 2.448 
 core size 25 of 198  vol = 2.269 
 core size 24 of 198  vol = 2.06 
 core size 23 of 198  vol = 1.893 
 core size 22 of 198  vol = 1.698 
 core size 21 of 198  vol = 1.517 
 core size 20 of 198  vol = 1.341 
 core size 19 of 198  vol = 1.218 
 core size 18 of 198  vol = 1.072 
 core size 17 of 198  vol = 0.954 
 core size 16 of 198  vol = 0.822 
 core size 15 of 198  vol = 0.744 




## have a look at the various cores "vmd -m core_pruned/*.pdb"

## Lets use a 6A^3 core cutoff
inds <- print(core, vol=6)



# 42 positions (cumulative volume <= 6 Angstrom^3) 
  start end length
1    23  26      4
2    85  91      7
3    95  95      1
4    99  99      1
5   102 105      4
6   122 133     12
7   174 176      3
8   182 191     10



write.pdb(xyz=pdb$xyz[inds$xyz],resno=pdb$atom[inds$atom,"resno"], file="core.pdb")


##- Fit trj onto starting structure based on core indices
xyz <- fit.xyz( fixed = pdb$xyz,
               mobile = trj,
               fixed.inds  = inds$xyz,
               mobile.inds = inds$xyz)

##write.pdb(pdb=pdb, xyz=xyz, file="new_trj.pdb")
##write.ncdf(xyz, "new_trj.nc")

See also

read.fasta.pdb, plot.core, fit.xyz

Author

Barry Grant