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Hello All,
After announcing the "make-bdna" server, the number one feature request was
that it make RNA. Tied with that (at one request) was the request to produce
mmCIF files. Due to this overwhelming number of responses (two) I have
re-written the server from the ground-up. Not only did I ditch the nauseating
perl programming language in favor of the pleasing python language, I also
added these features:
1. DNA/RNA hetero-duplexes
2. A,B, & Z DNA and A & B RNA
3. Option to write out hydrogens
4. Option to use apostrophes instead of asterisks for hydrogens
5. Backbone regularization
6. Uneven over-/under-hangs
7. Mismatches
8. User specified chain IDs
9. User specified residue numbering
10. User specified code length
11. mmCIF support
12. Appropriate mime types for server response (useful with chime)
12. Ditched using CNS for regularization (now using NAB leap)
13. Massive (in my opinion) error checking
I need to build libraries for modified bases, so this feature is still on the
horizon somewhere. Also, mismatches are not yet regularized.
As a result of its more general usefulness, I have decided to change the name
from "make-bdna" to "make-na". I anticipate shortening the name even more as
its functionality becomes more general and the program becomes more powerful.
Eventually, I believe the program will become unlimited in its function and
its name will accordingly be assigned an empty string. At this point, I
suspect "" will attract intense theological interest.
The home-page is a redirection from
<http://www.doe-mbi.ucla.edu/~jstroud/make-na>. This redirection is a
consequence of the fact that the server will be moving from Colorado to
California in a few weeks, so please bookmark the above link and not the
landing point.
If I get enough requests, I will make the source available via the web page.
Please give it a try and let me know of any problems or suggestions. I will be
very responsive to bug reports.
James
--
James Stroud
UCLA-DOE Institute for Genomics and Proteomics
Box 951570
Los Angeles, CA 90095
http://www.jamesstroud.com/
