Hi Chen,
I see your point now. Yes, I agree that the 80:20 method (or 75:25 as stated
in the paper, http://www.mail-archive.com/ccp4bb@dl.ac.uk/msg01063.html) is
a very useful technique. The fact that it does not take much effort or lead
to uncertainties makes it very worth trying.
Here I add my two cents: when performing such optimizations, try both
seeding and no-seeding if quantity of protein permits. If protein quantity
is limited and the crystals are reluctant to appear under the original
condition, then seeding is always a good idea.
Zhijie
--------------------------------------------------
From: "chen c" <chenc...@gmail.com>
Sent: Sunday, April 29, 2012 6:09 PM
To: "Zhijie Li" <zhijie...@utoronto.ca>
Subject: Re: [ccp4bb] Anisotropic diffraction
I accept your advice. In fact, this is the first time I am involved in
anisotropic issue. And I learned a lot from all the above discussion.
However, the 80:20 optimization method(an example of "long-tail
theory") rather than surface mutation is what I want to emphasis in my
last email. As illustrated in the attached pdf, it defenitely deserve
a try. One more thing to mention is that this very 80:20 method can be
very versatile and useful in optimising macromolecular crystals in
case of issues more than anistropic problem.
best regards
chen
2012/4/30 Zhijie Li <zhijie...@utoronto.ca>:
Hi Chen,
It is a reality that a usable protein dataset could take years of hard
work
to obtain. Compared to problems such as twining, bad diffraction
patterns,
excessive mosaicity, low resolution, weak, noisy anomalous signal, etc.,
anisotropic diffraction should probably be regarded most benign. There is
nothing wrong with publishing a properly treated anisotropic dataset.
Then
why risking another year trying to find a better mutant? There is no
guarantee that the mutants would work better, or even work.
Unless the crystal is naturally isotropic, such as that it is in a cubic
space group, the diffraction of protein crystals will probably always be
more or less anisotropic. This only reflects the fact that the crystal
packing is indeed anisotropic, consequently the movements of the Unit
cell
is anisotropic. It does not mean that there would be defects in the
resulting structure. For instance, a 3A isotropic dataset, and a 2.5-2A
anisotropic dataset, which one is going to give a better description of
the
protein?
Zhijie
--------------------------------------------------
From: "chen c" <chenc...@gmail.com>
Sent: Sunday, April 29, 2012 5:03 AM
To: "Zhijie Li" <zhijie...@utoronto.ca>
Subject: Re: [ccp4bb] Anisotropic diffraction
If we might be able to eliminate the anisotropic diffraction issue,
which might mean and reflect defect in structure. Why not just
restrain our thought to solve this question by data processing, etc?
chen
2012/4/28 Zhijie Li <zhijie...@utoronto.ca>:
Hi Cheng,
This paper looks quite irrelevant to Theresa's question.
Zhijie
--------------------------------------------------
From: "chen c" <chenc...@gmail.com>
Sent: Friday, April 27, 2012 10:28 PM
To: <CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Anisotropic diffraction
Birtley and Curry used a novel optimization method, in their paper
"Crystallization of foot-and-mouth disease virus 3C protease: surface
mutagenesis and a novel crystal-optimization strategy", which might be
inspiring for you.
在 2012年4月28日 上午3:21，David Schuller <dj...@cornell.edu> 写道：
Anisotropic truncation should have no effect on the space group
symmetry.
On 04/27/12 15:18, Theresa Hsu wrote:
Dear crystallographers
A very basic question, for anisotropic diffraction, does data
truncation
with ellipsoidal method change the symmetry? For example, if
untruncated
data is space group P6, will truncated data index as P622 or P2?
Thank you.
Theresa
--
=======================================================================
All Things Serve the Beam
=======================================================================
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
--
Cheng Chen, Ph.D. Candidate
Laboratory of Structural Biology
Life Science Building,Tsinghua University
Beijing 100084
China
Tel:+86-10-62772291
Fax:+86-10-62773145
E-mail:che...@xtal.tsinghua.edu.cn
北京市海淀区清华大学生命科学馆201-212室
邮编：100084
--
Cheng Chen, Ph.D. Candidate
Laboratory of Structural Biology
Life Science Building,Tsinghua University
Beijing 100084
China
Tel:+86-10-62772291
Fax:+86-10-62773145
E-mail:che...@xtal.tsinghua.edu.cn
北京市海淀区清华大学生命科学馆201-212室
邮编：100084
--
Cheng Chen, Ph.D. Candidate
Laboratory of Structural Biology
Life Science Building,Tsinghua University
Beijing 100084
China
Tel:+86-10-62772291
Fax:+86-10-62773145
E-mail:che...@xtal.tsinghua.edu.cn
北京市海淀区清华大学生命科学馆201-212室
邮编：100084
