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Since Frank has cited me, I should say that I believe that NCS would
indeed improve the location of the heavy atoms in the dual space method,
but it is difficult to find a robust and efficient algorithm to do it.
If the NCS analysis is applied each dual space cycle it could cost more
time than it saves, and the secret of the dual space method is its
computational efficiency. If I find a good way of course I will put in
into shelxd.
I am not aware of a larger successful substructure solution than Frank's
160 Se problem (it has to be added that shelxd only finds 152 of them,
so there is room for improvement). This was a SAD dataset (I presume
that the crystal was dead before the other wavelengths could be
measured) and MAD data contains more information than SAD, so I am
optimistic that we will be able to solve larger substructures. It is
just a question of "careful data collection" as Frank so rightly says.
George
Frank von Delft wrote:
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Since I was being cited (*blush*), I should add that I very much doubt that
160 is very close to the upper limit, given the relative ease with which
(any!) dual space methods seem to deal with that dataset, if run properly
(RTFM!!!). "Careful data collection" mostly involved paying radiation
damage its due respect: sacrificing resolution to low exposure times, using
fresh crystal volumes, that sort of healthy paranoia. Not that there was no
damage (which only goes to show) but it could have been a lot worse.
I did also have a fairly favourable Se/protein ratio (8 Se / 260 aa) and
there was high NCS (two decamers) which obviously helped phase improvement.
I heard at least one Person Who Probably Knows (ZO) suggest that the NCS
itself would help dual-space methods (something about intensity
distributions, I did not catch the full argument); although at least one
other Person Unlikely Not To Know (George Sheldrick) dismissed that it would
make a difference (if memory serves me).
phx
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Eleanor Dodson
Sent: 21 October 2005 09:00
To: Ho-Leung Ng
Cc: [email protected]
Subject: Re: [ccp4bb]: finding heavy atom sites in large structures
Ho-Leung Ng wrote:
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Hello,
I am working on a large protein complex and would like to know
what are the protein size limits for finding heavy atom sites (not
clusters), either by Patterson-based or dual space recycling methods.
For example, what is the largest ASU that has been solved by
selenomethionine phasing?
Thanks,
ho
UC Berkeley
The most I know of is the 160 Se in a pentamer solved by
Frank von Delft . His email is: not sure if/where it is
published Frank von Delft <[EMAIL PROTECTED]>
He could find them using dual space methods, but he had
collected the data exquisitely carefully.. You prob. need to
do that too.
You are looking for very small diffs
Eleanor
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
