dssp on pdbs with inserts

[Lars Skjærven]

hmm.. pdb id 1fuj with residue names 63, 63A, 63B:

pdb <- read.pdb("1fuj")
sse <- dssp(pdb)

sse$helix
$start
  1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19  20 
235 235 235 235  56  63  63  63 231  63  63  63 231  56  63  63  63 231  63  63 
 21  22 
 63 231 

[Xinqiu Yao]

This is a residue number problem

# Error
dssp(pdb, verbose=T)
#DSSP could not be created due to an error:
#inconsistent residue types in atom records for residue 22 (ASN != GLY)
#Error in dssp(pdb, verbose = T) : an error occurred

#works
stride(pdb)

# works
dssp(convert.pdb(pdb, type="pdb", renumber=T), ver=T)

[Xinqiu Yao]

Solved the problem by:

1. generate warning and suggest resno=FALSE if resno=TRUE
2. generate correct results if resno=FALSE

sse <- dssp(pdb)
#Warning message:
#In dssp(pdb) :
#  Insertions are found in PDB: Residue numbers may be incorrect.
#                Try again with resno=FALSE

sse <- dssp(pdb, resno=FALSE)
sse$helix
#$start
#  1   2   3   4   5   6   7   8   9  10  11  12  13  14 
#213 434 655 876  43  51 209 272 430 485 493 651 714 872 

#$end
#  1   2   3   4   5   6   7   8   9  10  11  12  13  14 
#220 440 662 882  46  53 212 274 433 487 495 654 716 875 

#$length
# 1  2  3  4  5  6  7  8  9 10 11 12 13 14 
# 8  7  8  7  4  3  4  3  4  3  3  4  3  4 

#$chain
# 1   2   3   4   5   6   7   8   9  10  11  12  13  14 
#"A" "B" "C" "D" "A" "A" "A" "B" "B" "C" "C" "C" "D" "D" 

#$type
#  1   2   3   4   5   6   7   8   9  10  11  12  13  14 
#"H" "H" "H" "H" "G" "G" "G" "G" "G" "G" "G" "G" "G" "G" 

Similar update to stride()