1. Printout of usage instructions:
gesamt --help
2. Alignment and superposition of two structures:
gesamt foo_1st.pdb [{-s|-d} SEL1] foo_2nd.pdb [{-s|-d} SEL2] [-high|-normal] [foo_out.pdb]
3. Screening a pdb archive:
gesamt foo.pdb [{-s|-d} SEL] -pdb pdb-dir
[-high|-normal] [hits.txt]
where SEL1/2 are optional selection strings and foo_out.pdb is an optional output file.
Keys "-s" and "-d" are used for the selection of a substructure. By default, all
structure given in the corresponding file, is used. If there are more than one
chain in the file, all chains are considered as a single structure. Selection
format depends on the key used. Key "-s" correspondds to MMDB selection format,
identical to what is used by
Superpose. The
format is described in pdbcur
documentation. CCP4i interface works only with this type of selections.
Selection key "-d" provides a more flexible selection scheme used by SCOP:
"*", "(all)" | - | take all file |
"-" | - | take chain without chain ID |
"a:Ni-Mj,b:Kp-Lq,..." | - | take chain a residue number N insertion code i to residue number M insertion code j plus chain b residue number K insertion code p to residue number L insertion code q and so on |
"a:,b:..." | - | take whole chains a and b and so on |
"a:,b:Kp-Lq,..." | - | any combination of the above. |
In difference of
Superpose, Gesamt allows for arbitrary selection of residues, and
disregards the secondary structure pattern of structures. Gesampt may be
applied to non-contiguous sets of residues, partially complete and
short chains.
Keys "-high" and "-normal" specify "High" and "Normal" mode, respectively. In "Normal" mode (default), Gesamt balances the quality of alignment and computation speed. This is a recommended mode for most applications. In "High" mode, Gesamt attempts to reach maximal quality with no reference to speed considerations. In "High" mode, Gesamt is about 10 times slower and achieves quality improvement in few percents of all instances on comparison with "Normal" mode.
The program then gives a residue-by-residue listing of the alignment. Strands and helices in the two structures are identified and given in the output. The output also lists distances between all matched residues at best structure superposition.