On Jul 31, 2007, at 15:24, Tommi Kajander wrote:
Hi,
i would be interested in hearing about people's preferences on
programs
for doign auto-tracing of protein chains (with not so great maps),
I do like ARP/wARP (objective opinion).
so far
my feeling has been nothing is at least much better than resolve in
doing
this. but i was wondering if people would care to share examples on
cases
where there was some difference to what you started with...
..of course one can always complete and correct by hand but when
you are
doing this with phasing iteratively it would be interesting to hear
opinions..
A bit more seriously now, my feeling is as follows:
1. If the automated program does not deliver more than 80-90% of the
structure,
all of it reliably in sequence and without out of register errors,
I would personally go back and do it in O. Being a big fun of Coot, I
still like O better
for building form scratch - I guess it is most likely just habit though.
2. Even if I would do things by hand, having a resolve, arp/warp,
bucaneer, textal
model in parallel can be helpful as guidance. I would run all these,
it takes
less time to run them than think if they can be useful or not.
3. arp/warp (.. yes,yes) can deal with extremely bad maps if high
resolution data is available.
I have seen it doing things I could not do by hand. I have also seen
it (more often ...)
to fail to trace 2.5 A maps that it would only take me a day or two
to trace completely.
so, what is a 'not so great map' is not clear to me. an awful looking
1.1 A map with 70 deg. phase error,
is not the same as an awful looking 3.2 A map with similar errors,
and a MAD 3.2 A map can be
easy to trace either by hand or automatically. And sorry for the
shameless plug as usual, but arp/warp
does work at low resolution. not as well as in high resolution, but
we do get successes (>75%) with some
real 3.0 a datasets .. although not often ... but its worth a try.
And of course the Quick Fold (albe) module
of ARP/wARP can also be useful and it takes for 500 residues less
time to run than me writing this email ;-)
Tassos
thanks,
tommi
--
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
PO box 65 (Street address: Viikinkaari 1, 4th floor)
University of Helsinki
FIN-00014 Helsinki, Finland
Tel. +358-9-191 58903
Fax +358-9-191 59940
