Dear *Gloria*
In CNS, you can do it use buried_suface.inp.
On 4/28/07, Gloria Borgstahl <[EMAIL PROTECTED]> wrote:
Hello all,
What is the easiest way, these days, to calculate the buried surface area
between two subunits of a protein?
Thanks, and Happy Friday, Gloria
*
Hello all,
What is the easiest way, these days, to calculate the buried surface area
between two subunits of a protein?
Thanks, and Happy Friday, Gloria**Gloria BorgstahlEppley In
I'm working on a 4.5-A structure with 4-fold NCS. I've generated a SA
composite omit map and all the protomers look pretty good, but with
weaker density in mostly different parts for each. Am I correct that CNS
doesn't do any NCS averaging automatically, and is there any reason why
I shouldn't
Such high R values usually mean there are many many very weak relections..
You havent kept in the h+k+l = 2n+1 reflections have you?
Do a native Patterson check too to make sure there are not other
translations which might distort the data
Eleanor
Yi Xue wrote:
Dear all:
I have a datas
Dear all:
I have a dataset diffracted to about 3A, and it is supposed to be
protein/DNA complex. The spacegroup could be I4, I422, I222, or F222.
I used the protein structure to start molecular replacement. There are
three copies of complexes if assuming I422 symmetry. For the search o
Dear all, please get your applications in for beamtime at BM14 before the
end of next week -i.e. Friday 4th May if you would like beamtime in june or
july and want to solve some structures before the August break - if you want
good phases then get your applications in to us sooner rather than later
An additional fix of Clemens' made in 3.2.29
ftp://ftp.mrc-lmb.cam.ac.uk/scala_3.2.29.tar.gz
Phil
On 27 Apr 2007, at 10:10, Clemens Vonrhein wrote:
Hi Phil,
these diffs I made to 3.2.27 - seem to fix some other things too.
Cheers
Clemens
On Fri, Apr 27, 2007 at 09:50:16AM +0100, Phil Evan
Andrew,
Did you try the NCS maps in Coot and it didn't work and therefore
you are going down this rather convoluted route?
On Fri, Apr 27, 2007 at 10:20:12AM +0100, Eleanor Dodson wrote:
> Well - I would do it the same way as you are - find a matrix with
> lsqkab, then apply that to the map wit
Hi Yuan,
Basically all tRNA structures in pdb will contain pseudo-U, and
starting from old tRNAPhe literature you will find a lot on the
structural consequences of having pseudo-U in RNA.
Poul
On 27/04/2007, at 3.45, Yuan Lin wrote:
Dear All,
I solved a structure of a pseudouridylated
Well - I would do it the same way as you are - find a matrix with
lsqkab, then apply that to the map with maprot.
It should be OK.
However there are some tricks which might help. Small differences in
cell dimensions sometimes muddle coot I think and also I think it gets
confused by different s
Yuan
All other tRNA structures, free or engaged in complex with their cognate
synthetase (as for Arnez & Steitz' structure), contain at least a
pseudoUridine. Cytoplasmic tRNAs almost invariably contain the conserved
sequence T(54)-PseudoU(55)-C(56) in the so-called TPsi-loop.
There are many such
I believe this is a combination of errors in COMBAT (not setting cell
constraint flags correctly) and SCALA (not detecting properly that
they are unset)
I believe that I have fixed the Scala error in my latest version
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/scala_3.2.28.tar.gz
(I hope!)
There
Hi Paola
This looks like a bug in Scala to me. The error message should only be printed
out if the Relative Length Error exceeds 0.03 or the Angle error exceeds 0.5,
whereas in your case both errors are zero. The relevant lines of code are a new
addition in 6.0.2, which explains why you didn't
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