*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
I have tried this approach with several datasets of one protein.
It seems arp/warp actually traces more residues and assigns more
sequence when I follow the advice and limit resolution to something
like 2.3 - 7 A, even when I feel I have accurately measured data to
35 or 50 A, and more questionable data to 2.1 A in the other direction.
The protein may not be typical as it has a number of iron-sulfur
clusters. Secondary structure is a pretty reasonable mixture of
helix and sheet.
Now I have a 1.7 A dataset, I'll see how that does. Hope it gets
everything except the cis-serine, regardless of cutoff!
Ed
Martin A. Walsh wrote:
Why not do what i suspect most people do anyhow -i.e. run a job with and
without adhering to the criteria or are you paying for your cpu??...and it
doesn't take long to run a job!
I also rarely have found it telling me the Wilson was nice -but how many
nice Wilsons do you know?
So would opt to run ignoring arp expertise first (as even Perrakis does -it
this in the manual ;-), if it doesn't work try it again adhering -if that
doesn't try another program, if that doesn't work then try sitting in front
of your computer and do some manual building (its probably more fun anyhow)!
I'd suggest
the next release of arp/warp should do this automatically ;-)
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of
Anastassis Perrakis (NKI)
Sent: jeudi 17 novembre 2005 14:31
To: Phil Evans
Cc: [email protected]
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
On Nov 17, 2005, at 12:18, Phil Evans wrote:
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Anastassis Perrakis (NKI) writes:
Have you looked at the whole Wilson plot in general, if it has the
right peaks and valleys etc etc ?
You can do that with ccp4/Wilson and its also done by default when you
run ARP/wARP, the latter
having the advantage of seeing the expected shape as established in
the
'BEST' work of Popov et al.
I would comment that I have yet to find any dataset, including some
truly excellent ones, which pass the arp/warp Wilson plot test.
Has anyone else found a dataset that is OK according to this test?
I have seen one that passed the criteria ! ;-)
That is to say that the quality criteria are indeed too strict and will
be relaxed in the new release.
(a good thing is that it forces you to look at the Wilson plot, but its
indeed annoying...).
I admit in most cases I decide to 'Continue' ... ' with bad data'
unless the low resolution
or high resolution are really really very bad - visually. I don't like
personally the 'Limit Resolution' button.
Victor and Sasha might not agree with me though.
But, 'overly cautious' is a fare characterization, although Phil might
argue its a bit mild !
Tassos
Phil
