In certain instances initial fits based on multiple sequence
alignment will be far from accurate, such that even an initial
conformation based fit will not be able to correct the poor
initial superposition, and even genuine structural homology will
be missed. In these instances it is possible to make use of the
SCAN option to provide a more accurate initial superimposition.
To do this one need only select one representative of the
domains to be superimposed and use this domain in a sensiitve
scan of the other domains. By applying the same techinques as
used for the scan with the Ig light variable domain (above) one
can arrive at a set of initial transformations consisting of the
transformations of all other domains onto the domain which was
used as a query for the scan.
Aspartic Proteinase Domains
An example of how such an initial superimposition might be
obtained is shown by the alignment of the aspartly proteinase N
and C terminal lobes (see directory examples/ac_prot):
The N-terminal domain of 1CMS (in the file 1cmsN.domain) can be
used to scan a list of all aspartyl proteinase
N- and C- terminal domains (ac_prot.domains):
stamp -l 1cmsN.domain -n 2 -s -slide 5 -d ac_prot.domains -prefix ac_prot
Should produce:
Domain1 Domain2 Fits Sc RMS Len1 Len2 Align Fit Eq. Secs %I %S P(m)
Scan 1cmsN 1cmsN 1 9.800 10.091 175 175 175 175 174 18 99.43 94.29 0.00e+00
Scan 1cmsN 1cmsC 2 3.211 7.858 175 148 204 64 57 13 7.43 25.14 2.37e-03
Scan 1cmsN 4apeN 1 8.195 9.708 175 178 182 155 151 15 26.97 72.47 1.36e-13
Scan 1cmsN 4apeC 1 3.434 7.939 175 152 210 69 68 14 5.14 30.29 1.00e+00
Scan 1cmsN 3appN 1 7.967 9.830 175 174 183 149 148 18 26.86 74.86 2.51e-13
Scan 1cmsN 3appC 1 3.260 8.137 175 149 206 63 54 13 5.71 24.57 2.32e-02
Scan 1cmsN 2aprN 1 8.386 10.130 175 178 178 158 154 15 30.34 76.40 3.81e-17
Scan 1cmsN 2aprC 1 3.335 7.787 175 147 202 68 62 14 6.86 27.43 1.11e-02
Scan 1cmsN 4pepN 1 8.880 10.162 175 174 174 170 169 15 56.00 87.43 3.00e-53
Scan 1cmsN 4pepC 1 3.227 8.315 175 152 206 63 51 11 6.86 24.00 2.61e-03
See the file ac_prot.scan
The file ac_prot.scan will contain all 10 domains superimposed onto 1cmsN. Note that we haven't run the program with the `-cut' option, since the file ac_prot.domains contains an assignment of domains (done by me using molecular graphics). Running SORTTRANS removes any redundancies:
sorttrans -f ac_prot.scan -s Sc 2.5 > ac_prot.sorted
and running stamp will generate the multiple alignment as described for the serine proteinase and globin examples above.
stamp -l ac_prot.sorted -prefix ac_prot
The output files from running all of these programs appear in the directory examples/ac_prot.