Optional. If an email address is provided the alignment results will be sent as an email attachment and a link to the results page will be included in the message for future reference.

A list of entries that specify the range of selected C_α atoms for each structure that participates in the alignment and is downloaded directly from the Protein Data Bank.

An entry must be specified as the 4-character PDB ID of a protein, followed optionally by a range selection. The following are the possible ways to specify an entry:

For example, the HOMSTRAD family CUB consists of

• 1sfp, with residues 4 through 114 on chain A
• 1spp, with residues 4 through 113 on chain A
• 1spp, with residues 1 through 112 on chain B

To align the family CUB by retrieving the PDB files from the Protein Data Bank type:

1sfp:A:4:A:114  1spp:A:4:A:113  1spp:B:1:B:112

1sfp  1spp:A  1spp:B

A list of entries that specify the range of selected C_α atoms for each structure that participates in the alignment and is uploaded by the user in Local Files below.

The entry format is the same as the one defined for the Protein Data Bank Entries field.

Each uploaded file can have multiple entries associated with it. For example, to align the HOMSTRAD family CUB upload the files 1sfp.pdb and 1spp.pdb and type in the Local Files Entries field:

1sfp  1spp:A  1spp:B

Files in PDB format uploaded by the user. For each uploaded file a 4-character PDB ID must be provided. The PDB ID will be correlated with the entries in the Local Files Entries field.

For each uploaded file there may be multiple entries in the Local Files Entries as long as the entries select different chains or residues.

A ZIP archive containing multiple files in PDB format. The names of the files in the archive must be in the format XXXX.pdb where XXXX is the corresponding PDB ID.

For each file in the archive specify at least one entry in the Local Files Entries field.

For example, to align the HOMSTRAD family CUB create a ZIP archive containing the files 1sfp.pdb and 1spp.pdb and type in the Local Files Entries field:

1sfp  1spp:A  1spp:B

The server can be accessed remotely from within other software by constructing a URL with a combination of the parameters given below.

The URL for the service is:

The relevant parameters are:

• wsget -- (mandatory) indicates a web service request; possible values are:

  pdb -- get transformed coordinates (i.e. alignment.zip)

  all -- get all data computed by server (i.e. mapsci-output.zip)

  mat -- get only transformation matrices (i.e. alignment.mat, but no header)

• rcsb -- specifies structures to be downloaded from the PDB (e.g. rcsb="1sfp 1spp:A 1spp:B")

• local -- specifies structures to be uploaded from local disk (e.g. local="1sfp 1spp:A 1spp:B"); must be accompanied by the parameter archive

• archive -- archive with PDB files for the structures specified in the parameter local; see section Local Archive above for format

Here is an example in Python to obtain the transformed coordinates for the alignment of the CUB family, where the original structures are downloaded from the PDB:

import urllib

url = "http://www.geom-comp.umn.edu/mapsci/align.cgi"

params = {"wsget" : "pdb",
          "rcsb" : "1sfp  1spp:A  1spp:B" }
params = urllib.urlencode(params)
server = urllib.urlopen(url, params)

output = file("alignment.zip", "wb")
output.write(server.read())
output.close()
server.close()

import urllib

url = "http://www.geom-comp.umn.edu/mapsci/align.cgi"

archive = file("cub.zip", "rb")
data = archive.read()
archive.close()

params = {"wsget" : "pdb",
          "local" : "1sfp  1spp:A  1spp:B",
          "archive" : data }
params = urllib.urlencode(params)
server = urllib.urlopen(url, params)

output = file("alignment.zip", "wb")
output.write(server.read())
output.close()
server.close()