The 3SSP (3-dimensional Superposition of Proteins) menu has many things
in common with the MOTIV option in the SUPPOS menu. The basic ideas
behind 3SSP are described in an article of which you will find a (figureless)
copy at the end of this chapter.
In short, with MAK3SP you will run the
MOTIV option from the SUPPOS menu automatically against all proteins
in the database. This creates a so-called 3SSP file. All other options in the
3SSP menu are involved in the evaluation of these files.
The command MAK3SP can be used to create a so-called 3SSP file. See one
of the appendices for an example of a 3SSP file. WHAT IF expects that
you have exactly one (protein) molecule in the soup upon execution
of MAK3SP. If the soup is empty, you will be prompted for the number
of a database file.
The 3SSP file will get the name MAK.3SSP, unless the soup was empty
when you gave the MAK3SP command, in which case the 3SSP file will
be called ****.3SSP, in which **** stands for the name of the database
protein.
You better run this option as a BATCH job, since it can take up to ten
hours of CPU on a micro VAX.
The 3SSP file holds all final results, including all negative results, and
all alignments. With the SUM3SP command you can reduce this to the bare
minimal list of found significant homologies. You will be prompted for the
name of the 3SSP file.
The 3SSP file holds all final results, including all poor and insignificant
results. With the FILTER command you can reduce this to the bare
minimal list of found significant homologies. You will be prompted for the
name of the 3SSP file. A new 3SSP file will be written out.
The command ORGDSP will cause that the internal secondary structure tables
are overwritten with the original DSSP assignments. WHAT IF normally only
uses S, T, H, 3, and blank for coil. DSSP has a different nomenclature.
There are several ways to graphically evaluate the 3SSP results.
You can display superposed fragments only or whole alpha carbon
traces of the molecules looked at, and you can put these results all
together in a MOL-item, or put them in the movie.
The combination of these possibilities leads to a large set of
options. It is hard to describe what is best or clearest. Just try
a couple...
The command GRA3SP will cause WHAT IF to prompt you for the name of a 3SSP
file. WHAT IF will then extract all aligned fragments from this file and
puts them, superimposed on the mother molecule, in RIDGE. The lower right
dial of the dial box can now be used to dial through the individual hits.
The LED connected to this dial will show the number of the hit.
GRA3SP only shows the homologous fragments. GRW3SP shows the whole
molecules.
The command GRL3SP will cause WHAT IF to prompt you for the name of a 3SSP
file. WHAT IF will then extract all aligned fragments from this file and
puts them, superimposed on the mother molecule, in a mol-item.
GRL3SP only shows the homologous fragments. GRM3SP shows the whole
molecules.
The command GRM3SP will cause WHAT IF to prompt you for the name of a 3SSP
file. WHAT IF will then extract all molecules that show significant
homology from this file and
puts them, superimposed on the mother molecule, in a mol-item.
GRL3SP only shows the homologous fragments. GRM3SP shows the whole
molecules.
The command GRW3SP will cause WHAT IF to prompt you for the name of a 3SSP
file. WHAT IF will then extract all molecules that show significant
homology from this file and
puts them, superimposed on the mother molecule, in the movie. The lower right
dial of the dial box can now be used to dial through the individual hits.
The LED connected to this dial will show the number of the hit.
GRA3SP only shows the homologous fragments. GRW3SP shows the whole
molecules.
The command GRD3SP will cause WHAT IF to prompt you for the name of a 3SSP
file. WHAT IF will then extract one molecule of your choice
from this file and
puts it, superimposed on the mother molecule, in a MOL-item.
The command GRI3SP will cause WHAT IF to prompt you for the name of a 3SSP
file. WHAT IF will then extract all molecules that show significant
homology from this file and
puts them, superimposed on the mother molecule, in the movie. In this
movie you get interleaved the fragments that superpose well and the
full superposed molecules.
The command GRF3SP is not yet ready.
The parameters used by 3SSP and the SUPPOS menu are identical. See
the parameter paragraph in the SUPPOS chapter.
Not all commands are immediately active in the 3SSP menu. By typing
MORE, more commands will be activated.