People keep asking me if buccaneer can build loops. In response to which
I usually point them to 'loopy' and 'rapper', both of which do an
excellent job.
However, I seem to have written a loop building program by accident, and
since people have been asking I guess I may as well release it.
The origins of this are a library I'm writing for Coot to implement
'O'-style lego-build tools using the Richardson's Top500 protein library
as a basis. The same library can also be used for C-alpha->mainchain and
possibly chain growing; I also hope to use it for several new jobs in
buccaneer.
Using the same code for loop fitting (basically incomplete fragment
matching) is trivial, and since that is a bit different from the normal
approaches it seemed worth a try. It is also blisteringly fast.
Is it useful? I don't know, but if you want to give it a try it is
pretty simple. Please tell me how you get on.
Get it here:
http://www.ysbl.york.ac.uk/~cowtan/sloop/sloop.html
On a related note, has anyone found sequins (the sequence validation
program) to be useful? I know it works on my synthetic problems, but I
don't if those cases are actually relevant to the real world. I've had
no feedback about it and am looking for ways to reduce my maintenance
workload.
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