Can we have a moratorium on plugs for books please?
James
--
Dr. James W. Murray
David Phillips Research Fellow
Division on Molecular Biosciences
Imperial College, LONDON
Tel: +44 (0)20 759 48895
________________________________________
From: CCP4 bulletin board [[log in to unmask]] On Behalf Of Bernhard Rupp [[log in to unmask]]
Sent: Tuesday, December 15, 2009 8:25 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] When can I say the refinement is done?
page 682 :-)
BR
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Pavel Afonine
Sent: Monday, December 14, 2009 9:24 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] When can I say the refinement is done?
This is pointed out (in absolutely unobvious way - I wish I can add voice to that PDF) at the slide #19 -:)
(except loosening weights).
P.
On 12/14/09 8:35 AM, Anastassis Perrakis wrote:
A less exact answer, albeit less precise and informative than the very nice PDF and the very useful Polygon ideas, is:
"very well done, but have another look at this couple of Ramachandran outliers and also consider loosening up the geometry a bit".
;-)
A.
On Dec 14, 2009, at 17:04, Pavel Afonine wrote:
Hi,
the exact answer to your question is here:
http://cci.lbl.gov/~afonine/for_ak/validation.pdf<http://cci.lbl.gov/%7Eafonine/for_ak/validation.pdf>
In particular, your question below is spelled out is discussed staring
from slide #2.
Pavel.
On 12/14/09 7:50 AM, rui wrote:
Hi, All,
I have a general question for refinement. I tried to refine a dataset
that is about 2.3A and got R/Rfree is about o.18/0.24. RMS(angles):
0.77, RMS(bonds): 0.003
however, when I check with molprobity, There are still some outliers
and some bad contact that is overlap > 0.4 A.
Ramachandran outliers: 0.2% (Goal: < 0.2%)
Ramachandran favored: 97.7% (Goal: > 98%)
Rotamer outliers: 1.4% (Goal: 1%)
C-beta outliers: 0 (Goal: 0)
Clashscore: 14.16
Generally speaking, should I remove all those bad contact or is there
any miminum requirement that ok, the structure is acceptable? I know
the refinement can be endless, but I just want to get an idea how far
away I'm . Thanks.
R
P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
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