WHAT IF has the capability to run the program DSSP (written by Kabsch and
Sander, see the appendices for a further description and acknowledgments)
without you having to do anything but typing SHOHST.
The DSSP determinations of secondary structure are used
by WHAT IF in many options. If you do not know the DSSP
principles, I suggest you read the article, but in short: No code means random
coil; H means normal helix. 3 means 3-10 helix; T means turn, and
E mean extended.
In case you don't have a DSSP lisence, WHAT IF will determine the secondary
structure itself. However, DSSP does this better...
Since WHAT IF already knew about secondary structure before I knew about
DSSP, there is a renaming of secondary structure codes going from DSSP to
WHAT IF.
DSSP-H,I -> WHAT IF-H
DSSP-G -> WHAT IF-3
DSSP-E -> WHAT IF-S
DSSP-B,T -> WHAT IF-T
DSSP-S is neglected by WHAT IF.
Sorry for this....
This command will list the sequence at the screen in one-letter code. It will
also for every amino acid show what its secondary structure is. If the
secondary structure has not been calculated yet, it will automatically
issue the call to DSSP first. This option evaluates secondary structure,
it will NOT predict it!
The command WIFHST does the same as SHOHST. The only difference is that
WIFHST does not even look at DSSP, it will always use the emulator.
The command SHOSSS will cause WHAT IF to prompt you for a residue range.
For this range the secondary structure will shown similar as SHOHST does.
Every residue involved in symmetry contacts will be labeled with an asterix.
Every residue that is clearly solvent accessible will be labeled with
a capital A.
If you made some changes in the molecule, WHAT IF can not determine itself
if it is time to call DSSP again for a new secondary structure evaluation.
The command SHOHST will therefore display the old evaluation results. You
can force WHAT IF to call DSSP again with the command INIHST followed
by SHOHST.
The hidden command ALLHEL will convert all secondary structure
values in H (helix). This option should be used after SHOHST. It only changes
what WHAT IF thinks that the structure looks like, and does not change anything
in the structure.
The hidden command ALLCOI will convert all secondary structure
values in ' ' (helix). This option should be used after SHOHST. It only changes
what WHAT IF thinks that the structure looks like, and does not change anything
in the structure.
The hidden command ALCOIL is an alternative spelling for ALLCOI.
The hidden command EDTHST will cause WHAT IF to prompt you for a residue range.
For every residue in this range you will see the local sequence and secondary
structure determination. You will residue by residue be prompted for the
new secondary structure determination. This option should be used after the
SHOHST command. It only changes
what WHAT IF thinks that the structure looks like, and does not change anything
in the structure.
The command SUMHST will cause WHAT IF to prompt you for a range. If not yet done,
the secondary structure will be determined for this range. The percentage helix,
strand, etc., in this range will be calculated.
DSSP and the WHAT IF based DSSP emulator do not give the same results. The command
CHKDSP will ask you for a range of database proteins. For every protein in this
range the DSSP determined secondary structure will be shown, followed by the
determination by the emulator. The third line of secondary structure output is
a desparate and hopelessly failed attempt to make the emulator output
look like the DSSP output using a small neural network.
Per structure a small table with the frequency of all DSSP-emulator determination
permutations is given. If the two were to agree, all off-diagonal elements
in this table should always be zero.
The command GETDSP will prompt you for a DSSP file. The coordinates (alpha
carbons only) will be read from this file as if it was a PDB file holding
only alpha carbon coordinates.
We are working on a small neural network that optimises the secondary
structure determinations. It does not work yet, but this is one
of the options involved.
The WHAT IF internal database of about 300 proteins has the
secondary structure stored for every residue. WHAT IF reduces
this to a 4-state determination using the conversion table:
DSSP H,I -> WHAT IF H
DSSP G -> WHAT IF 3
DSSP E -> WHAT IF S
DSSP B,T -> WHAT IF T
DSSP S is neglected by WHAT IF.
The command ORGDSP regenerates the original values. Be aware that
not all options will function properly after this option. This
holds especially for statistics on secondary structure.
The command NEWHST is an alternative spelling for INIHST.