Re: [ccp4bb] auto-tracing programs

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CCP4bb <-- 2007 <-- July 2007 <-- 31 July 2007

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Subject: Re: sodium ion on a 3A map?
From: Dr shekhar shekhar {- at -} CDFD {- dot -} ORG {- dot -} IN
Date: 2007-07-31

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Subject: Re: auto-tracing programs
From: Tommi Kajander tommi {- dot -} kajander {- at -} HELSINKI {- dot -} FI
Date: 2007-07-31

Subject: Re: auto-tracing programs
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2007-07-31

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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CCP4bb <-- 2007 <-- July 2007 <-- 31 July 2007

Previous message:
Subject: Re: sodium ion on a 3A map?
From: Dr shekhar shekhar {- at -} CDFD {- dot -} ORG {- dot -} IN
Date: 2007-07-31

Next message:
Subject: Re: auto-tracing programs
From: Tommi Kajander tommi {- dot -} kajander {- at -} HELSINKI {- dot -} FI
Date: 2007-07-31