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Assign domains for your protein
If your protein is not in the list, or you can not find it by searching the
table, this option is useful for you to assign domain directly on this
server. Chose Assign on PDB code if your protein is in the
PBD bank (July 1995). Otherwise, you should chose other options.
There are three options to assign domain on coordinates. Assign by a form is
an easy way. You may paste the coordinates from a text editor to the Netscape
Form window. It is better to retrieve the C-alpha records, for the
assignment program needs only C-alpha coordinates. The easiest way to
retrieve C-alpha records is the UNIX shell command:
grep "^ATOM.*CA" PDB_file >C_alpha_file
Please note that it takes time to paste a big file to the Netscape Form
window. Also, problems were reported by users that it did not work smoothly
on their machines.
If the above option does not work on your site, please try the
Assign by a Perl program. In my own experience, this is
the best way to assign domain and
to get the results directly, if the network transmission is not too slow
between your local site and our server. However, in this case, you should
have Perl installed on your machine.
The third option to assign domain for your own protein is sending
us the coordiantes by E-mail. The result of domain assignment will be replied
to your E-mail address. You may send the coordinates by a stand-alone mail
program.
However, it is better to use the built-in mail function within Netscape by
clicking Assign by E-mail. Use the Attach
option to attach your coordiantes file. Please fill in the Subject
field with
assign before sending the mail. If you can not get the
reply of the results within a day, please send us a message.
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Copyright © March 1996
domain@irisg17.lif.icnet.uk
