issue with certain PDBs
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Great program. Thanks for your efforts and work.
The code goes awry with some standard PDBs like 7rkf.pdb . The problem is with the dihedral calculation where it calculates the phi, psi's as 360, 360 for a bunch of residues (especially in Chain R) Any standard program like Pymol shows the residues in this chain as a helix - implying that pymol managed to compute the dihedrals correctly.
Correcting this error can hugely increase the utility of this program.
I tried mkdssp on both the mmCIF and the PDB version of 7rkf and see no residues other than the first and last of chain R having a phi/psi of 360.
What version of mkdssp are you using? And which residues do have these 360 degree angles?
Hmm... I am using mkdssp version 4.0.0 2020-12-18 . This is the default with ubuntu apt. Is this the correct version? I'm getting 360s as dihedrals all over. Below is an extract from the output just to indicate phi/psi's in chain A
# RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA
1 26 A D 0 0 218 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 -27.3 138.9 121.2 115.8
2 27 A K 0 0 251 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.971 360.0 360.0 -60.2 360.0 135.3 122.4 116.4
3 ! 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0
4 32 A R 0 0 328 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 135.5 128.2 107.8
5 ! 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0
6 99 A Q 0 0 301 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 145.9 97.1 52.5
7 ! 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0
8 104 A A 0 0 209 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 142.3 96.6 60.8
9 ! 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0
10 139 A Y 0 0 335 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 135.1 111.7 61.3
11 ! 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0
12 149 A D 0 0 265 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 135.5 114.7 71.6
13 ! 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0
14 157 A D 0 0 203 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 150.4 114.7 66.4
15 ! 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0
16 160 A R 0 0 294 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 155.4 113.8 68.3
17 ! 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0
18 164 A L 0 0 282 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 161.6 107.9 72.4
19 ! 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0
20 177 A R 0 0 351 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 140.9 111.2 81.1
21 ! 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0
22 180 A T 0 0 209 2,-0.2 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 139.2 107.0 89.1
23 ! 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0
24 182 A G 0 0 142 0, 0.0 -2,-0.2 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 136.3 106.9 94.1
25 ! 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0
26 189 A D 0 0 265 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 142.8 128.0 100.6
27 ! 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0
28 211 A I 0 0 276 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 122.6 111.1 98.1
29 ! 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0
30 217 A V 0 0 251 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 126.0 121.6 101.0
That's certainly incorrect output. And an out-of-date version of dssp. What Ubuntu version are you using?
the latest - ubuntu 21.10. Thanks for letting me know. I'll just download the code from git and compile. And uninstall the system dssp via apt.
Things work perfectly with the newer version. Thanks for resolving.