dssp.pdbs() unhelpful error msg with CA-only input PDBs

[Barry Grant]

Trying to run dssp() on a pdbs object that contains CA only structures (e.g. as obtained after using mustang() with the cleanpdbs=T option). Gives a very unhelpful message:

> sse<-dssp(pdbs)
Error in dssp.pdb(tmp.pdb, resno = FALSE, full = FALSE, ...) :
  An error occurred while running command
 'dssp /var/folders/69/8y5xz5_s56n19nb1h6mgp3rc0054zz/T//RtmpimejUX/file96c95d95ee2b /var/folders/69/8y5xz5_s56n19nb1h6mgp3rc0054zz/T//RtmpimejUX/file96c91e47790d'

This is because the tmp file which dssp.pdb() is given as input is CA-only.

I propose that there should be a pre-check for this both in dssp.pdbs() and also in dssp.pdb().

[Lars Skjærven]

suggestion for dssp.pdb:

pdb = read.pdb("1hel")
pdb$atom$elety[1:10] = "CA"
sse = dssp(pdb)

Warning message:
In dssp.pdb(pdb) : Residues with missing backbone atoms detected: 1-A, 2-A

pdb = read.pdb("1hel")
pdb$atom$elety = "CA"

Error in dssp.pdb(pdb) : 
  No residues found with a complete set of backbone atoms

see details with commit 1f252bd.

[Xinqiu Yao]

Thanks for the updating! It works well with the example hivp.pdb.