Hi,
I completely agree with Tassos: I do like ARP/wARP.
... not being involved with ARP/wARP makes this a objective 'objective
opinion'?
Since you mention that you would like to do this iteratively with
phasing it might also be important in what context you want to do the
automatic building. Since your initial phases will not have seen a
model (I guess) you might want to get some initial model built that is
as good as possible (i.e. has the correct residues at the correct
position) and doesn't necessarily need to be complete. Then you can
compbine this model with your phasing or your density modification and
get some better maps - which will get you a more complete good model
etc etc.
We had some cases with ARP/wARP (previous version - not the
latest/greatest 7.0) where this approach worked very well for those
low-resolution maps Tassos mentioned - see
Morris RJ, Zwart PH, Cohen S, Fernandez FJ, Kakaris M, Kirillova O,
Vonrhein C, Perrakis A, Lamzin VS. (2004). Breaking good resolutions
with ARP/wARP. J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):56-9. Epub
2003 Nov 28.
<non-objective-mode>
In SHARP/autoSHARP we use ARP/wARP to do the automatic building. The
model can then be combined either at the HA-atom refinement/phasing
step in SHARP or during the density-modification step (where we use
SOLOMON) in various ways.
</non-objective-mode>
Anything iteratively not only needs to have the best program/module at
each step, also the interaction between them is very important.
Cheers
Clemens
On Tue, Jul 31, 2007 at 04:02:57PM +0200, Anastassis Perrakis wrote:
> 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
>
--
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* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--------------------------------------------------------------
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