Torsion calculation for PDBs with duplicated resno
Issue #534
resolved
I tried to calculate phi, psi angles based on torsion.pdb function.
There are some PDBs that have duplicated resno. Example: PDB: 1ACX, resno: 63
test <- get.pdb("1ACX")
pdb <- read.pdb("./1ACX.pdb")
tor <- torsion.pdb(pdb)
View(tor$tbl)
Please use "insert" column to distinguish between them (63 and 63A). Otherwise, those 2 cases are merged into one and the phi/psi angles are different than for example from DSSP (see attachment).
My suggestion: Change
res.data <- colpaste(pdb$atom,c("resno","chain"))
to
res.data <- colpaste(pdb$atom,c("resno","chain", "insert", "resid"))
It would also be nice if you add in the output "tbl" data frame a column "res.list" (so it would be easier to identify residues to which the angles were calculated).
Comments (5)
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assigned issue to
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assigned issue to
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- changed component to ToDo
- changed version to v2.3 [devel]
- marked as minor
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Should be fixed by this commit.
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- changed status to resolved
Fixed
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Hi Tomasz,
Thanks for the suggestion. Will add these soon.