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How to deal with the missing residuals for torsion calculation?
Actually in the pdb file there are some residuals were missed for position information. Such as "1BKS"
pdb <- read.pdb( "1BKS")
xxx <- atom.select(pdb,"backbone",elety=c("N", "CA", "C"),chain = "B")
yyy <- trim.pdb(pdb = pdb,xxx)
zzz <- torsion.pdb(yyy)
head(yyy$atom)
type eleno elety alt resid chain resno insert x y z o b segid elesy charge
1936 ATOM 1937 N <NA> THR B 3 <NA> 56.339 0.537 16.113 1 30.35 <NA> N <NA>
1937 ATOM 1938 CA <NA> THR B 3 <NA> 57.605 0.471 15.380 1 28.60 <NA> C <NA>
1938 ATOM 1939 C <NA> THR B 3 <NA> 58.131 -0.953 15.420 1 30.33 <NA> C <NA>
1943 ATOM 1944 N <NA> LEU B 4 <NA> 58.902 -1.285 14.410 1 30.44 <NA> N <NA>
1944 ATOM 1945 CA <NA> LEU B 4 <NA> 59.513 -2.619 14.283 1 29.04 <NA> C <NA>
1945 ATOM 1946 C <NA> LEU B 4 <NA> 60.675 -2.759 15.259 1 28.93 <NA> C <NA>
The "resno" didn't begin with 1 because they are missed in the pdf file, so the following torsion will not calculate for the first 2 residuals. How can I automatically treated the information of missed residuals as NA in pdb object in R? So that the following result will be the same length of the actual chain.
Comments (3)
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reporter -
Hi Feng,
Sorry for the long waiting. It is an interesting idea to have indications of missing residues explicitly in the 'pdb' object. Bio3D reads a pdb file as is and so adding NAs for non-existing residues could cause some inconsistency. You could first make an alignment between the PDB sequence and the full sequence from e.g. swissprot, find the positions of missing residues, and add NAs in your calculated vectors manually. Let me know if it could help.
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