dssp(...)"dssp"(pdb, exefile = "dssp", resno=TRUE, full=FALSE, verbose=FALSE, ...)"dssp"(pdbs, ...)"dssp"(xyz, pdb, ...)stride(pdb, exefile = "stride", resno=TRUE)"print"(x, ...)
"pdb", obtained from
read.pdb. "pdbs" (obtained with
pdbaln or read.fasta.pdb). "xyz", obtained from
read.ncdf, read.dcd,
read.crd. sse object obtained from dssp.pdb or
stride. Secondary structure assignment according to the method of Kabsch and Sander (DSSP) or the method of Frishman and Argos (STRIDE).
This function calls the ‘DSSP’ or ‘STRIDE’ program to define secondary structure and psi and phi torsion angles.
dssp Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
‘DSSP’ is the work of Kabsch and Sander: Kabsch and Sander (1983) Biopolymers. 12, 2577--2637.
For information on obtaining ‘DSSP’, see: http://swift.cmbi.ru.nl/gv/dssp/.
‘STRIDE’ is the work of Frishman and Argos: Frishman and Argos (1995) Proteins. 3, 566--579.
For information on obtaining the ‘STRIDE’ program, see: http://webclu.bio.wzw.tum.de/stride/, or copy it from an installation of VMD.
A system call is made to the ‘DSSP’ or ‘STRIDE’ program, which must be installed on your system and in the search path for executables. See http://thegrantlab.org/bio3d/tutorials/installing-bio3d for instructions of how to install these programs.
For the hbonds list component the column names can be
used as a convenient means of data access, namely:
Bridge pair 1 “BP1”,
Bridge pair 2 “BP2”,
Backbone H-bond (NH-->O) “NH-O.1”,
H-bond energy of NH-->O “E1”,
Backbone H-bond (O-->NH) “O-HN.1”,
H-bond energy of O-->NH “E2”,
Backbone H-bond (NH-->O) “NH-O.2”,
H-bond energy of NH-->O “E3”,
Backbone H-bond (O-->NH) “O-HN.2”,
H-bond energy of O-->NH “E4”.
If ‘resno=TRUE’ the following additional columns are included: Chain ID of resno “BP1”: “ChainBP1”, Chain ID of resno “BP2”: “ChainBP2”, Chain ID of resno “O-HN.1”: “Chain1”, Chain ID of resno “NH-O.2”: “Chain2”, Chain ID of resno “O-HN.1”: “Chain3”, Chain ID of resno “NH-O.2”: “Chain4”.
##- PDB example # Read a PDB file pdb <- read.pdb("1bg2")Note: Accessing on-line PDB filesse <- dssp(pdb)Warning message: Non-protein residues detected in input PDB: MG, ACT, ADP, HOHsse2 <- stride(pdb) ## Short summary sseCall: dssp.pdb(pdb = pdb) Class: sse Helices: 13 20-25 (A) 58-65 (A) 67-74 (A) 91-95 (A) 107-122 (A) 176-189 (A) 197-203 (A) 256-269 (A) 281-285 (A) 309-320 (A) 277-279 (A) 286-288 (A) 306-308 (A) Sheets: 14 8-15 (A) 32-34 (A) 38-41 (A) 44-47 (A) 50-52 (A) 79-84 (A) 126-138 (A) 141-144 (A) 155-157 (A) 163-165 (A) 171-173 (A) 205-216 (A) 222-231 (A) 295-302 (A) Turns: 20 26-26 (A) 35-37 (A) 42-43 (A) 54-55 (A) 66-66 (A) 75-76 (A) 87-88 (A) 96-96 (A) 99-100 (A) 102-104 (A) 139-140 (A) 148-149 (A) 159-160 (A) 166-167 (A) 190-193 (A) 217-219 (A) 246-247 (A) 270-271 (A) 289-289 (A) 321-321 (A) Output is provided in residue numberssse2Call: stride(pdb = pdb) Class: sse Helices: 11 20-25 (A) 58-75 (A) 91-96 (A) 107-122 (A) 176-190 (A) 197-203 (A) 256-270 (A) 281-286 (A) 309-321 (A) 277-279 (A) 306-308 (A) Sheets: 14 9-15 (A) 32-34 (A) 38-41 (A) 44-47 (A) 50-52 (A) 79-84 (A) 126-138 (A) 141-144 (A) 154-157 (A) 163-166 (A) 171-173 (A) 205-216 (A) 222-231 (A) 295-302 (A) Turns: 18 3-8 (A) 35-37 (A) 42-43 (A) 48-49 (A) 53-56 (A) 86-89 (A) 98-104 (A) 123-125 (A) 139-140 (A) 145-152 (A) 158-161 (A) 167-168 (A) 191-196 (A) 217-220 (A) 237-240 (A) 245-249 (A) 272-276 (A) 287-294 (A) Output is provided in residue numbers# Helix data sse$helix$start 1 2 3 4 5 6 7 8 9 10 11 12 13 20 58 67 91 107 176 197 256 281 309 277 286 306 $end 1 2 3 4 5 6 7 8 9 10 11 12 13 25 65 74 95 122 189 203 269 285 320 279 288 308 $length 1 2 3 4 5 6 7 8 9 10 11 12 13 6 8 8 5 16 14 7 14 5 12 3 3 3 $chain 1 2 3 4 5 6 7 8 9 10 11 12 13 "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" $type 1 2 3 4 5 6 7 8 9 10 11 12 13 "H" "H" "H" "H" "H" "H" "H" "H" "H" "H" "G" "G" "G"# Precent SSE content sum(sse$helix$length)/sum(pdb$calpha) * 100[1] 32.19814sum(sse$sheet$length)/sum(pdb$calpha) * 100[1] 26.00619##- PDBs example aln <- read.fasta( system.file("examples/kif1a.fa",package="bio3d") ) pdbs <- read.fasta.pdb( aln )pdb/seq: 1 name: http://www.rcsb.org/pdb/files/1bg2.pdb pdb/seq: 2 name: http://www.rcsb.org/pdb/files/1i6i.pdb PDB has ALT records, taking A only, rm.alt=TRUE pdb/seq: 3 name: http://www.rcsb.org/pdb/files/1i5s.pdb PDB has ALT records, taking A only, rm.alt=TRUE pdb/seq: 4 name: http://www.rcsb.org/pdb/files/2ncd.pdb## Aligned PDB defined secondary structure pdbs$sse[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] http://www.rcsb.org/pdb/files/1bg2.pdb "E" "E" "E" "E" "E" "E" "E" "E" http://www.rcsb.org/pdb/files/1i6i.pdb "E" " " "E" "E" "E" "E" "E" "E" http://www.rcsb.org/pdb/files/1i5s.pdb " " "E" "E" "E" "E" "E" "E" "E" http://www.rcsb.org/pdb/files/2ncd.pdb " " " " " " " " "E" "E" "E" " " [,9] [,10] [,11] [,12] [,13] [,14] [,15] http://www.rcsb.org/pdb/files/1bg2.pdb " " " " " " " " "H" "H" "H" http://www.rcsb.org/pdb/files/1i6i.pdb " " " " " " "H" "H" "H" "H" http://www.rcsb.org/pdb/files/1i5s.pdb " " " " " " "H" "H" "H" "H" http://www.rcsb.org/pdb/files/2ncd.pdb " " " " " " " " "H" "H" "H" [,16] [,17] [,18] [,19] [,20] [,21] http://www.rcsb.org/pdb/files/1bg2.pdb "H" "H" "H" " " " " " " http://www.rcsb.org/pdb/files/1i6i.pdb "H" "H" "H" " " " " " " http://www.rcsb.org/pdb/files/1i5s.pdb "H" "H" "H" " " " " " " http://www.rcsb.org/pdb/files/2ncd.pdb " " " " " " " " " " NA [,22] [,23] [,24] [,25] [,26] [,27] http://www.rcsb.org/pdb/files/1bg2.pdb " " " " " " "E" "E" "E" http://www.rcsb.org/pdb/files/1i6i.pdb " " " " "E" "E" "E" "E" http://www.rcsb.org/pdb/files/1i5s.pdb " " " " "E" "E" "E" "E" http://www.rcsb.org/pdb/files/2ncd.pdb " " "E" "E" "E" "E" "E" [,28] [,29] [,30] [,31] [,32] [,33] http://www.rcsb.org/pdb/files/1bg2.pdb " " " " " " "E" "E" NA http://www.rcsb.org/pdb/files/1i6i.pdb " " " " "E" "E" "E" NA http://www.rcsb.org/pdb/files/1i5s.pdb " " " " "E" "E" "E" NA http://www.rcsb.org/pdb/files/2ncd.pdb " " " " " " "E" "E" "E" [,34] [,35] [,36] [,37] [,38] [,39] http://www.rcsb.org/pdb/files/1bg2.pdb NA NA NA "E" "E" " " http://www.rcsb.org/pdb/files/1i6i.pdb NA NA NA "E" " " " " http://www.rcsb.org/pdb/files/1i5s.pdb NA NA NA "E" " " " " http://www.rcsb.org/pdb/files/2ncd.pdb "E" "E" " " " " " " "H" [,40] [,41] [,42] [,43] [,44] [,45] http://www.rcsb.org/pdb/files/1bg2.pdb " " "E" NA NA NA NA http://www.rcsb.org/pdb/files/1i6i.pdb " " " " " " " " " " " " http://www.rcsb.org/pdb/files/1i5s.pdb " " " " " " " " " " " " http://www.rcsb.org/pdb/files/2ncd.pdb "H" "H" "H" "H" "H" " " [,46] [,47] [,48] [,49] [,50] [,51] http://www.rcsb.org/pdb/files/1bg2.pdb NA NA NA "E" "E" "E" http://www.rcsb.org/pdb/files/1i6i.pdb " " " " "E" "E" "E" "E" http://www.rcsb.org/pdb/files/1i5s.pdb " " " " "E" "E" "E" "E" http://www.rcsb.org/pdb/files/2ncd.pdb " " " " " " "E" "E" "E" [,52] [,53] [,54] [,55] [,56] [,57] http://www.rcsb.org/pdb/files/1bg2.pdb " " " " "E" "E" "E" " " http://www.rcsb.org/pdb/files/1i6i.pdb " " " " "E" "E" "E" "E" http://www.rcsb.org/pdb/files/1i5s.pdb " " " " "E" "E" "E" "E" http://www.rcsb.org/pdb/files/2ncd.pdb " " " " "E" "E" "E" " " [,58] [,59] [,60] [,61] [,62] [,63] http://www.rcsb.org/pdb/files/1bg2.pdb " " " " NA NA NA NA http://www.rcsb.org/pdb/files/1i6i.pdb " " " " " " " " " " " " http://www.rcsb.org/pdb/files/1i5s.pdb " " " " " " " " " " " " http://www.rcsb.org/pdb/files/2ncd.pdb " " " " NA NA NA NA [,64] [,65] [,66] [,67] [,68] [,69] http://www.rcsb.org/pdb/files/1bg2.pdb NA NA NA NA " " " " http://www.rcsb.org/pdb/files/1i6i.pdb " " " " " " " " " " "H" http://www.rcsb.org/pdb/files/1i5s.pdb " " " " " " " " " " "H" http://www.rcsb.org/pdb/files/2ncd.pdb NA NA NA NA " " " " [,70] [,71] [,72] [,73] [,74] [,75] http://www.rcsb.org/pdb/files/1bg2.pdb "H" "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/1i6i.pdb "H" "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/1i5s.pdb "H" "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/2ncd.pdb "H" "H" "H" "H" "H" NA [,76] [,77] [,78] [,79] [,80] [,81] http://www.rcsb.org/pdb/files/1bg2.pdb "H" "H" " " "H" "H" "H" http://www.rcsb.org/pdb/files/1i6i.pdb "H" "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/1i5s.pdb "H" "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/2ncd.pdb "H" "H" " " "H" "H" "H" [,82] [,83] [,84] [,85] [,86] [,87] http://www.rcsb.org/pdb/files/1bg2.pdb "H" "H" "H" "H" "H" " " http://www.rcsb.org/pdb/files/1i6i.pdb "H" "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/1i5s.pdb "H" "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/2ncd.pdb "H" "H" "H" "H" "H" "H" [,88] [,89] [,90] [,91] [,92] [,93] http://www.rcsb.org/pdb/files/1bg2.pdb " " " " " " "E" "E" "E" http://www.rcsb.org/pdb/files/1i6i.pdb "H" " " " " "E" "E" "E" http://www.rcsb.org/pdb/files/1i5s.pdb " " " " " " "E" "E" "E" http://www.rcsb.org/pdb/files/2ncd.pdb " " " " "E" "E" "E" "E" [,94] [,95] [,96] [,97] [,98] [,99] http://www.rcsb.org/pdb/files/1bg2.pdb "E" "E" "E" " " " " " " http://www.rcsb.org/pdb/files/1i6i.pdb "E" "E" "E" "E" " " " " http://www.rcsb.org/pdb/files/1i5s.pdb "E" "E" "E" "E" " " " " http://www.rcsb.org/pdb/files/2ncd.pdb "E" "E" " " " " " " " " [,100] [,101] [,102] [,103] [,104] http://www.rcsb.org/pdb/files/1bg2.pdb " " " " " " "H" "H" http://www.rcsb.org/pdb/files/1i6i.pdb " " " " "H" "H" "H" http://www.rcsb.org/pdb/files/1i5s.pdb " " " " "H" "H" "H" http://www.rcsb.org/pdb/files/2ncd.pdb " " " " " " "H" "H" [,105] [,106] [,107] [,108] [,109] http://www.rcsb.org/pdb/files/1bg2.pdb "H" "H" "H" " " " " http://www.rcsb.org/pdb/files/1i6i.pdb "H" "H" "H" "H" " " http://www.rcsb.org/pdb/files/1i5s.pdb "H" "H" "H" "H" " " http://www.rcsb.org/pdb/files/2ncd.pdb "H" "H" "H" " " " " [,110] [,111] [,112] [,113] [,114] http://www.rcsb.org/pdb/files/1bg2.pdb " " " " " " " " " " http://www.rcsb.org/pdb/files/1i6i.pdb " " " " " " " " NA http://www.rcsb.org/pdb/files/1i5s.pdb " " " " " " " " NA http://www.rcsb.org/pdb/files/2ncd.pdb " " NA NA NA " " [,115] [,116] [,117] [,118] [,119] http://www.rcsb.org/pdb/files/1bg2.pdb " " " " " " " " "H" http://www.rcsb.org/pdb/files/1i6i.pdb " " " " " " "H" "H" http://www.rcsb.org/pdb/files/1i5s.pdb " " " " " " "H" "H" http://www.rcsb.org/pdb/files/2ncd.pdb " " " " " " " " "H" [,120] [,121] [,122] [,123] [,124] http://www.rcsb.org/pdb/files/1bg2.pdb "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/1i6i.pdb "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/1i5s.pdb "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/2ncd.pdb "H" "H" "H" "H" "H" [,125] [,126] [,127] [,128] [,129] http://www.rcsb.org/pdb/files/1bg2.pdb "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/1i6i.pdb "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/1i5s.pdb "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/2ncd.pdb "H" "H" "H" "H" "H" [,130] [,131] [,132] [,133] [,134] http://www.rcsb.org/pdb/files/1bg2.pdb "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/1i6i.pdb "H" "H" "H" "H" " " http://www.rcsb.org/pdb/files/1i5s.pdb "H" "H" "H" "H" " " http://www.rcsb.org/pdb/files/2ncd.pdb "H" "H" "H" "H" "H" [,135] [,136] [,137] [,138] [,139] http://www.rcsb.org/pdb/files/1bg2.pdb " " " " " " "E" NA http://www.rcsb.org/pdb/files/1i6i.pdb " " " " " " " " "E" http://www.rcsb.org/pdb/files/1i5s.pdb " " " " " " " " "E" http://www.rcsb.org/pdb/files/2ncd.pdb "H" "H" "H" " " " " [,140] [,141] [,142] [,143] [,144] http://www.rcsb.org/pdb/files/1bg2.pdb "E" "E" "E" "E" "E" http://www.rcsb.org/pdb/files/1i6i.pdb "E" "E" "E" "E" "E" http://www.rcsb.org/pdb/files/1i5s.pdb "E" "E" "E" "E" "E" http://www.rcsb.org/pdb/files/2ncd.pdb "E" "E" "E" "E" "E" [,145] [,146] [,147] [,148] [,149] http://www.rcsb.org/pdb/files/1bg2.pdb "E" "E" "E" "E" "E" http://www.rcsb.org/pdb/files/1i6i.pdb "E" "E" "E" "E" "E" http://www.rcsb.org/pdb/files/1i5s.pdb "E" "E" "E" "E" "E" http://www.rcsb.org/pdb/files/2ncd.pdb "E" "E" "E" "E" "E" [,150] [,151] [,152] [,153] [,154] http://www.rcsb.org/pdb/files/1bg2.pdb "E" "E" " " " " "E" http://www.rcsb.org/pdb/files/1i6i.pdb "E" "E" " " " " "E" http://www.rcsb.org/pdb/files/1i5s.pdb "E" "E" " " " " "E" http://www.rcsb.org/pdb/files/2ncd.pdb "E" " " " " " " " " [,155] [,156] [,157] [,158] [,159] http://www.rcsb.org/pdb/files/1bg2.pdb "E" "E" "E" " " " " http://www.rcsb.org/pdb/files/1i6i.pdb "E" "E" "E" " " " " http://www.rcsb.org/pdb/files/1i5s.pdb "E" "E" "E" " " " " http://www.rcsb.org/pdb/files/2ncd.pdb "E" "E" "E" " " " " [,160] [,161] [,162] [,163] [,164] http://www.rcsb.org/pdb/files/1bg2.pdb NA " " " " " " " " http://www.rcsb.org/pdb/files/1i6i.pdb NA " " " " " " " " http://www.rcsb.org/pdb/files/1i5s.pdb NA " " " " " " " " http://www.rcsb.org/pdb/files/2ncd.pdb " " " " " " " " " " [,165] [,166] [,167] [,168] [,169] http://www.rcsb.org/pdb/files/1bg2.pdb " " NA " " " " " " http://www.rcsb.org/pdb/files/1i6i.pdb " " " " " " " " " " http://www.rcsb.org/pdb/files/1i5s.pdb " " " " " " " " " " http://www.rcsb.org/pdb/files/2ncd.pdb " " " " " " "E" "E" [,170] [,171] [,172] [,173] [,174] http://www.rcsb.org/pdb/files/1bg2.pdb "E" "E" "E" " " " " http://www.rcsb.org/pdb/files/1i6i.pdb "E" "E" "E" "E" " " http://www.rcsb.org/pdb/files/1i5s.pdb "E" "E" "E" "E" " " http://www.rcsb.org/pdb/files/2ncd.pdb "E" " " " " " " " " [,175] [,176] [,177] [,178] [,179] http://www.rcsb.org/pdb/files/1bg2.pdb " " " " " " "E" "E" http://www.rcsb.org/pdb/files/1i6i.pdb " " " " "E" "E" "E" http://www.rcsb.org/pdb/files/1i5s.pdb " " " " "E" "E" "E" http://www.rcsb.org/pdb/files/2ncd.pdb " " " " " " "E" "E" [,180] [,181] [,182] [,183] [,184] http://www.rcsb.org/pdb/files/1bg2.pdb "E" " " " " " " " " http://www.rcsb.org/pdb/files/1i6i.pdb "E" " " " " " " " " http://www.rcsb.org/pdb/files/1i5s.pdb "E" " " " " " " " " http://www.rcsb.org/pdb/files/2ncd.pdb "E" " " " " " " " " [,185] [,186] [,187] [,188] [,189] http://www.rcsb.org/pdb/files/1bg2.pdb " " "E" "E" "E" " " http://www.rcsb.org/pdb/files/1i6i.pdb " " "E" "E" " " " " http://www.rcsb.org/pdb/files/1i5s.pdb " " "E" "E" "E" " " http://www.rcsb.org/pdb/files/2ncd.pdb " " "E" "E" "E" " " [,190] [,191] [,192] [,193] [,194] http://www.rcsb.org/pdb/files/1bg2.pdb " " "H" "H" "H" "H" http://www.rcsb.org/pdb/files/1i6i.pdb "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/1i5s.pdb "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/2ncd.pdb " " "H" "H" "H" "H" [,195] [,196] [,197] [,198] [,199] http://www.rcsb.org/pdb/files/1bg2.pdb "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/1i6i.pdb "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/1i5s.pdb "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/2ncd.pdb "H" "H" "H" "H" "H" [,200] [,201] [,202] [,203] [,204] http://www.rcsb.org/pdb/files/1bg2.pdb "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/1i6i.pdb "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/1i5s.pdb "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/2ncd.pdb "H" "H" "H" "H" "H" [,205] [,206] [,207] [,208] [,209] http://www.rcsb.org/pdb/files/1bg2.pdb "H" "H" " " " " " " 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[,336] [,337] [,338] [,339] http://www.rcsb.org/pdb/files/1bg2.pdb "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/1i6i.pdb "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/1i5s.pdb "H" "H" "H" "H" "H" http://www.rcsb.org/pdb/files/2ncd.pdb "H" "H" "H" "H" "H" [,340] [,341] [,342] [,343] [,344] http://www.rcsb.org/pdb/files/1bg2.pdb "H" " " " " " " " " http://www.rcsb.org/pdb/files/1i6i.pdb "H" "H" "H" " " " " http://www.rcsb.org/pdb/files/1i5s.pdb "H" "H" "H" NA NA http://www.rcsb.org/pdb/files/2ncd.pdb "H" "H" " " " " " "## Aligned DSSP defined secondary structure sse <- dssp(pdbs)Warning message: Non-protein residues detected in input PDB: MG, ACT, ADP, HOHPDB has ALT records, taking A only, rm.alt=TRUEWarning message: Non-protein residues detected in input PDB: MG, ACP, TRS, HOHPDB has ALT records, taking A only, rm.alt=TRUEWarning message: Non-protein residues detected in input PDB: MG, ADP, HOH Warning message: Non-protein residues detected in input PDB: SO4, ADP, HOH##- XYZ Trajectory pdb <- read.pdb("2mda", multi=TRUE)Note: Accessing on-line PDB filedssp.xyz(pdb$xyz, pdb)65_A_NA 66_A_NA 67_A_NA 68_A_NA 69_A_NA 70_A_NA 71_A_NA 72_A_NA 73_A_NA sse " " " " " " "T" "T" "S" "S" " " " " sse " " " " " " "S" "S" " " " " " " " " sse " " " " " " "S" "S" " " " " " " " " sse " " " " " " "S" "S" " " "S" "S" " " sse " " " " " " "S" "S" " " " " "S" " " sse " " " " " " "S" "S" " " "S" "S" " " sse " " " " " " "S" "S" " " "S" "S" " " sse " " " " " " "S" "S" " " " " " " " " sse " " " " " " "T" "T" " " " " " " "S" sse " " " " " " "T" "T" "S" "S" "S" " " 74_A_NA 75_A_NA 76_A_NA 77_A_NA 78_A_NA 79_A_NA 80_A_NA 81_A_NA 82_A_NA sse " " "E" "E" "E" "T" "T" "E" "E" "E" sse " " " " "E" "E" "T" "T" "E" "E" "E" sse " " " " " " "B" "T" "T" "E" "E" "E" sse " " "E" "E" "E" "T" "T" "E" "E" "E" sse " " "E" "E" "E" "T" "T" "E" "E" "E" sse " " "E" "E" "S" "S" "S" "E" "E" "E" sse " " "E" "E" "E" "T" "T" "E" "E" "E" sse " " " " " " "B" "T" "T" "E" "E" "E" sse " " "E" "E" "S" "S" "S" "E" "E" "E" sse " " "E" "E" "E" "T" "T" "E" "E" "E" 83_A_NA 84_A_NA 85_A_NA 86_A_NA 87_A_NA 88_A_NA 89_A_NA 90_A_NA 91_A_NA sse "E" "E" "B" " " " " " " " " " " "S" sse "E" "E" " " " " " " " " " " " " "T" sse "E" "E" " " "E" "E" " " " " "S" "S" sse "E" "E" " " "B" " " " " " " " " "S" sse "E" "E" " " "B" " " " " " " " " "S" sse "E" "E" "B" " " " " " " " " " " "S" sse "E" "E" "E" "E" " " " " " " "S" "S" sse "E" "E" "E" "E" " " " " " " "S" "S" sse "E" "E" "B" " " " " " " " " "S" "S" sse "E" "E" "E" "E" " " " " " " "S" "S" 92_A_NA 93_A_NA 94_A_NA 95_A_NA 96_A_NA 97_A_NA 98_A_NA 99_A_NA 100_A_NA sse "S" "S" " " " " "T" "T" "H" "H" "H" sse "T" " " " " " " " " " " "H" "H" "H" sse "S" " " " " " " "T" "T" "H" "H" "H" sse "S" "S" " " " " " " " " "H" "H" "H" sse "S" "S" "S" " " " " " " "H" "H" "H" sse "S" "S" " " " " " " "H" "H" "H" "H" sse " " "S" " " " " " " " " "H" "H" "H" sse "S" " " " " " " " " " " "H" "H" "H" sse "S" "S" " " " " " " " " "H" "H" "H" sse "S" "S" " " " " " " "H" "H" "H" "H" 101_A_NA 102_A_NA 103_A_NA 104_A_NA 105_A_NA 106_A_NA 107_A_NA 108_A_NA sse "H" "H" "H" "H" "H" "H" "T" "T" sse "H" "H" "H" "H" "H" "H" "T" "T" sse "H" "H" "H" "H" "H" "H" "T" "T" sse "H" "H" "H" "H" "H" "H" "T" "T" sse "H" "H" "H" "H" "H" "H" "T" "T" sse "H" "H" "H" "H" "H" "H" "T" "T" sse "H" "H" "H" "H" "H" "H" "T" "T" sse "H" "H" "H" "H" "H" "H" "T" "T" sse "H" "H" "H" "H" "H" "H" "T" "T" sse "H" "H" "H" "H" "H" "H" "T" "T" 109_A_NA 110_A_NA 111_A_NA 112_A_NA 113_A_NA 114_A_NA 115_A_NA 116_A_NA sse " " "E" "E" "E" "E" "E" "E" "E" sse " " "E" "E" "S" " " " " "B" " " sse " " "E" "E" "E" "E" "E" "E" "E" sse " " "E" "E" "E" "E" "E" "E" "E" sse " " "E" "E" "E" "E" "E" "E" "E" sse " " "E" "E" "E" "E" "E" "E" "E" sse " " "E" "E" "E" "E" "E" "E" "E" sse " " "E" "E" "E" "E" "E" "E" "E" sse " " "E" "E" "E" "E" "E" "E" "E" sse " " "E" "E" "E" "E" "E" "E" "E" 117_A_NA 118_A_NA 119_A_NA 120_A_NA 121_A_NA 122_A_NA 123_A_NA 124_A_NA sse " " " " "S" "S" "S" "S" " " " " sse "S" "B" " " " " "S" "S" "S" "S" sse "E" "E" " " " " "S" "S" "S" "S" sse "B" "S" " " " " "S" "S" "S" " " sse "B" " " " " " " " " "S" "S" " " sse "E" " " " " " " "T" "T" "T" "S" sse " " " " " " " " "S" "S" "S" " " sse "E" " " " " " " "S" "S" " " "S" sse "E" " " " " " " "S" "S" "S" "S" sse "E" " " " " " " "S" "S" " " "S" 125_A_NA 126_A_NA 127_A_NA 128_A_NA 129_A_NA 130_A_NA 131_A_NA 132_A_NA sse "S" "S" " " " " " " " " " " " " sse "S" "S" "S" " " "B" " " " " " " sse "S" "S" "S" " " "E" "E" "E" "E" sse "S" "S" "S" " " " " "B" " " " " sse "S" "S" "S" " " " " "B" " " " " sse "S" "S" "S" " " " " "E" "E" "E" sse "S" "S" " " " " " " " " " " "E" sse "S" "S" "S" " " " " "E" "E" "E" sse "S" "S" "S" " " " " "E" "E" "E" sse "S" "S" "S" "S" " " "E" "E" "E" 133_A_NA 134_A_NA 135_A_NA 136_A_NA 137_A_NA 138_A_NA 139_A_NA 140_A_NA sse "E" "E" "E" "E" "E" "E" "T" "T" sse " " "E" "E" "E" "E" "E" "H" "H" sse "E" "E" "E" "E" "E" "E" "H" "H" sse "E" "E" "E" "E" "E" "E" "H" "H" sse "E" "E" "E" "E" "E" "E" "T" "T" sse "E" "E" "E" "E" "E" "E" "H" "H" sse "E" "E" "E" "E" "E" "E" "H" "H" sse "E" "E" "E" "E" "E" "E" "T" "T" sse "E" "E" "E" "E" "E" "E" "H" "H" sse "E" "E" "E" "E" "E" " " "H" "H" 141_A_NA 142_A_NA 143_A_NA 144_A_NA 145_A_NA 146_A_NA 147_A_NA 148_A_NA sse "H" "H" "H" "H" "H" "H" "H" "H" sse "H" "H" "H" "H" "H" "H" "H" "H" sse "H" "H" "H" "H" "H" "H" "H" "H" sse "H" "H" "H" "H" "H" "H" "H" "H" sse "H" "H" "H" "H" "H" "H" "H" "H" sse "H" "H" "H" "H" "H" "H" "H" "H" sse "H" "H" "H" "H" "H" "H" "H" "H" sse "H" "H" "H" "H" "H" "H" "H" "H" sse "H" "H" "H" "H" "H" "H" "H" "H" sse "H" "H" "H" "H" "H" "H" "H" "H" 149_A_NA 150_A_NA 151_A_NA 152_A_NA 153_A_NA 154_A_NA 155_A_NA 156_A_NA sse "H" "H" "T" "T" " " "S" "S" " " sse "H" "T" "T" "T" " " "S" "S" " " sse "H" "H" "H" "H" " " "S" "S" "E" sse "H" "H" "H" "H" "S" " " "S" " " sse "H" "H" "H" "H" "S" " " "S" " " sse "H" "H" "H" "H" " " "S" "S" " " sse "H" "T" "T" "T" " " " " "S" " " sse "H" "H" "H" "H" " " "S" "S" " " sse "H" "T" "T" "T" " " " " "S" " " sse "H" "H" "H" "H" "S" "S" "S" " " 157_A_NA 158_A_NA 159_A_NA 65_B_NA 66_B_NA 67_B_NA 68_B_NA 69_B_NA 70_B_NA sse " " "B" " " " " " " " " "T" "T" "S" sse " " " " " " " " " " " " "S" "S" " " sse "E" " " " " " " " " " " "S" "S" " " sse "B" " " " " " " " " " " "S" "S" " " sse "B" " " " " " " " " " " "S" "S" " " sse " " "B" " " " " " " " " "S" "S" " " sse " " "B" " " " " " " " " "S" "S" " " sse "E" "E" " " " " " " " " "S" "S" " " sse " " "B" " " " " " " " " "T" "T" " " sse "E" "E" " " " " " " " " "T" "T" "S" 71_B_NA 72_B_NA 73_B_NA 74_B_NA 75_B_NA 76_B_NA 77_B_NA 78_B_NA 79_B_NA sse "S" " " " " " " "E" "E" "E" "T" "T" sse " " " " " " " " " " "E" "E" "T" "T" sse " " " " " " " " " " " " "B" "T" "T" sse "S" "S" " " " " "E" "E" "E" "T" "T" sse " " "S" " " " " "E" "E" "E" "T" "T" sse "S" "S" " " " " "E" "E" "S" "S" "S" sse "S" "S" " " " " "E" "E" "E" "T" "T" sse " " " " " " " " " " " " "B" "T" "T" sse " " " " "S" " " "E" "E" "S" "S" "S" sse "S" "S" " " " " "E" "E" "E" "T" "T" 80_B_NA 81_B_NA 82_B_NA 83_B_NA 84_B_NA 85_B_NA 86_B_NA 87_B_NA 88_B_NA sse "E" "E" "E" "E" "E" "B" " " " " " " sse "E" "E" "E" "E" "E" " " " " " " " " sse "E" "E" "E" "E" "E" " " "E" "E" " " sse "E" "E" "E" "E" "E" " " "B" " " " " sse "E" "E" "E" "E" "E" " " "B" " " " " sse "E" "E" "E" "E" "E" "B" " " " " " " sse "E" "E" "E" "E" "E" "E" "E" " " " " sse "E" "E" "E" "E" "E" "E" "E" " " " " sse "E" "E" "E" "E" "E" "B" " " " " " " sse "E" "E" "E" "E" "E" "E" "E" " " " " 89_B_NA 90_B_NA 91_B_NA 92_B_NA 93_B_NA 94_B_NA 95_B_NA 96_B_NA 97_B_NA sse " " " " "S" "S" "S" " " " " "T" "T" sse " " " " "T" "T" " " " " " " " " " " sse " " "S" "S" "S" " " " " " " "T" "T" sse " " " " "S" "S" "S" " " " " " " " " sse " " " " "S" "S" "S" "S" " " " " " " sse " " " " "S" "S" "S" " " " " " " "H" sse " " "S" "S" " " "S" " " " " " " " " sse " " "S" "S" "S" " " " " " " " " " " sse " " "S" "S" "S" "S" " " " " " " " " sse " " "S" "S" "S" "S" " " " " " " "H" 98_B_NA 99_B_NA 100_B_NA 101_B_NA 102_B_NA 103_B_NA 104_B_NA 105_B_NA sse "H" "H" "H" "H" "H" "H" "H" "H" sse "H" "H" "H" "H" "H" "H" "H" "H" sse "H" "H" "H" "H" "H" "H" "H" "H" sse "H" "H" "H" "H" "H" "H" "H" "H" sse "H" "H" "H" "H" "H" "H" "H" "H" sse "H" "H" "H" "H" "H" "H" "H" "H" sse "H" "H" "H" "H" "H" "H" "H" "H" sse "H" "H" "H" "H" "H" "H" "H" "H" sse "H" "H" "H" "H" "H" "H" "H" "H" sse "H" "H" "H" "H" "H" "H" "H" "H" 106_B_NA 107_B_NA 108_B_NA 109_B_NA 110_B_NA 111_B_NA 112_B_NA 113_B_NA sse "H" "T" "T" " " "E" "E" "E" "E" sse "H" "T" "T" " " "E" "E" "S" " " sse "H" "T" "T" " " "E" "E" "E" "E" sse "H" "T" "T" " " "E" "E" "E" "E" sse "H" "T" "T" " " "E" "E" "E" "E" sse "H" "T" "T" " " "E" "E" "E" "E" sse "H" "T" "T" " " "E" "E" "E" "E" sse "H" "T" "T" " " "E" "E" "E" "E" sse "H" "T" "T" " " "E" "E" "E" "E" sse "H" "T" "T" " " "E" "E" "E" "E" 114_B_NA 115_B_NA 116_B_NA 117_B_NA 118_B_NA 119_B_NA 120_B_NA 121_B_NA sse "E" "E" "E" " " " " "S" "S" "S" sse " " "B" " " "S" "B" " " " " "S" sse "E" "E" "E" "E" "E" " " " " "S" sse "E" "E" "E" "B" "S" " " " " "S" sse "E" "E" "E" "B" " " " " " " " " sse "E" "E" "E" "E" " " " " " " "T" sse "E" "E" "E" "E" " " " " " " "S" sse "E" "E" "E" "E" " " " " " " "S" sse "E" "E" "E" "E" " " " " " " "S" sse "E" "E" "E" "E" " " " " " " "S" 122_B_NA 123_B_NA 124_B_NA 125_B_NA 126_B_NA 127_B_NA 128_B_NA 129_B_NA sse "S" " " " " "S" "S" " " " " " " sse "S" "S" "S" "S" "S" "S" " " "B" sse "S" "S" "S" "S" "S" "S" " " "E" sse "S" "S" " " "S" "S" "S" " " " " sse "S" "S" " " "S" "S" "S" " " " " sse "T" "T" "S" "S" "S" "S" " " " " sse "S" "S" " " "S" "S" " " " " " " sse "S" " " "S" "S" "S" "S" " " " " sse "S" "S" "S" "S" "S" "S" " " " " sse "S" " " "S" "S" "S" "S" "S" " " 130_B_NA 131_B_NA 132_B_NA 133_B_NA 134_B_NA 135_B_NA 136_B_NA 137_B_NA sse " " " " " " "E" "E" "E" "E" "E" sse " " " " " " " " "E" "E" "E" "E" sse "E" "E" "E" "E" "E" "E" "E" "E" sse "B" " " " " "E" "E" "E" "E" "E" sse "B" " " " " "E" "E" "E" "E" "E" sse "E" "E" "E" "E" "E" "E" "E" "E" sse "E" "E" "E" "E" "E" "E" "E" "E" sse "E" "E" "E" "E" "E" "E" "E" "E" sse "E" "E" "E" "E" "E" "E" "E" "E" sse "E" "E" "E" "E" "E" "E" "E" "E" 138_B_NA 139_B_NA 140_B_NA 141_B_NA 142_B_NA 143_B_NA 144_B_NA 145_B_NA sse "E" "T" "T" "H" "H" "H" "H" "H" sse "E" "H" "H" "H" "H" "H" "H" "H" sse "E" "H" "H" "H" "H" "H" "H" "H" sse "E" "H" "H" "H" "H" "H" "H" "H" sse "E" "T" "T" "H" "H" "H" "H" "H" sse "E" "H" "H" "H" "H" "H" "H" "H" sse "E" "H" "H" "H" "H" "H" "H" "H" sse "E" "T" "T" "H" "H" "H" "H" "H" sse "E" "H" "H" "H" "H" "H" "H" "H" sse " " "H" "H" "H" "H" "H" "H" "H" 146_B_NA 147_B_NA 148_B_NA 149_B_NA 150_B_NA 151_B_NA 152_B_NA 153_B_NA sse "H" "H" "H" "H" "H" "T" "T" " " sse "H" "H" "H" "H" "T" "T" "T" " " sse "H" "H" "H" "H" "H" "H" "H" " " sse "H" "H" "H" "H" "H" "H" "H" "S" sse "H" "H" "H" "H" "H" "H" "H" "S" sse "H" "H" "H" "H" "H" "H" "H" " " sse "H" "H" "H" "H" "T" "T" "T" " " sse "H" "H" "H" "H" "H" "H" "H" " " sse "H" "H" "H" "H" "T" "T" "T" " " sse "H" "H" "H" "H" "H" "H" "H" "S" 154_B_NA 155_B_NA 156_B_NA 157_B_NA 158_B_NA 159_B_NA sse "S" "S" " " " " "B" " " sse "S" "S" " " " " " " " " sse "S" "S" "E" "E" " " " " sse " " "S" " " "B" " " " " sse " " "S" " " "B" " " " " sse "S" "S" " " " " "B" " " sse " " "S" " " " " "B" " " sse "S" "S" " " "E" "E" " " sse " " "S" " " " " "B" " " sse "S" "S" " " "E" "E" " "## Note. for large MD trajectories you may want to skip some frames, e.g. xyz <- rbind(pdb$xyz, pdb$xyz) ## dummy trajectory frames <- seq(1, to=nrow(xyz), by=4) ## frame numbers to examine ss <- dssp.xyz(xyz[frames, ], pdb) ## matrix of sse frame x residue
read.pdb,
torsion.pdb, torsion.xyz,
plot.bio3d,
read.ncdf, read.dcd,
read.prmtop, read.crd,