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 Scan 1cmsN 1cmsN 1 9.744 0.000 174 175 175 174 173 18 99.43 94.86 Scan 1cmsN 1cmsC 1 2.749 2.352 204 175 148 63 58 13 8.00 41.14 Scan 1cmsN 4apeN 1 7.854 1.314 181 175 178 155 153 15 27.53 80.90 Scan 1cmsN 4apeC 1 2.901 2.207 208 175 152 69 68 14 7.43 40.57 Scan 1cmsN 3appN 1 7.574 1.291 182 175 174 148 147 18 26.86 83.43 Scan 1cmsN 3appC 1 2.775 2.422 205 175 149 61 58 13 7.43 41.71 Scan 1cmsN 2aprN 1 8.246 1.115 177 175 178 160 157 15 32.02 83.15 Scan 1cmsN 2aprC 1 2.941 2.099 201 175 147 65 58 14 9.14 39.43 Scan 1cmsN 4pepN 1 8.901 1.020 173 175 174 169 168 15 56.57 89.71 Scan 1cmsN 4pepC 1 2.738 2.561 206 175 152 64 52 11 8.00 40.00 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.