Zheng Zhou wrote:
Hi, Ed
I am dealing the similar problem. I checked CNS qindividual.inp. But how
do I refine one compound with two or more possible conformations (mainly
due to one bond rotation), each of wihich has a different occupancy?
Thanks in advance.
Hi Zheng,
Others can answer bet
Hi, Ed
I am dealing the similar problem. I checked CNS qindividual.inp. But how do
I refine one compound with two or more possible conformations (mainly due to
one bond rotation), each of wihich has a different occupancy? Thanks in
advance.
Joe
On Dec 17, 2007 2:24 PM, Edward Berry <[EMAIL PROTE
I thought that I would never have to disagree with both Eleanor and
Tassos in the same email, let alone risk being burnt at a stake as a
heretic for doubting the Gospel according to Kleywegt, but in my
but ... but ... i haven't even said anything! i'm innocent! my name is being
used in vain!
I think the correlation between occupancy and B-factor depends
also on the size of the ligand (relative to resolution).
Bob Stroud, I think, has estimated occupancy by comparing
the integrated electron density of the ligand with that of
a well-defined, isolated water (assumed to be at unit occuanc
In the danger of getting corrected by George twice in the same time
(burning stakes excluded...)
I am not doubting at all if its doable, but if the final result will
be more accurate / useful.
Thinking about it, with 1.5 A data it is very likely to be more
accurate than manual handling,
but
I would also ask what is the actual goal in refining the occupancy of the
ligand?
While I agree wholeheartedly with George, the B-factors will adequately
model a lower ligand occupancy. Usually the question you want to resolve
is "Is the ligand really bound in the active site, or is this an artif
I thought that I would never have to disagree with both Eleanor and
Tassos in the same email, let alone risk being burnt at a stake as a
heretic for doubting the Gospel according to Kleywegt, but in my
experience, given the very fortunate position that you have data to
1.5A, the refinement of o
I have already changed occupancies as Eleanor mentioned, and got
approximate values. But my hope is to try to get much precise ones if
possible.
I never expected to preach the 'Kleywegt Gospel' in the ccp4bb,
but in this case what you need is more accurate answers, not more
precise ones
(or be
ou mentioned.
Isaac
--
Dr Isaac Westwood
Department of Pharmacology
University of Oxford
Mansfield Road
Oxford
OX1 3QT
tel: 01865 271595
email: [EMAIL PROTECTED]
From: Eleanor Dodson <[EMAIL PROTECTED]>
Date: 2007年 12月 17日 19:02:28:JST
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4b
I dont think REFMAC can refine occupancy, but the way I would tackle it
is to first refine B factors, then if those for the ligand are much
higher than for the protein maybe test changing those occupancies to 0.7
, 0,5 and so on..
But in fact B factors and occupancies are highly correlated, an
Dear all,
This is my first mail to CCP4BB.
I'm now refining crystal structures of an enzyme at a resolution of
1.5A using refmac5 through CCP4i. Before X-ray data collections,
the substrate and co-factor ions were soaked into the crystals. Their
occupancies seem to be less than the unity because
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