Is that also how you would restrain refinement at low resolution when
using a high-resolution model? (e.g. a 1.8A model into 4A data)
phx.
Garib Murshudov wrote:
In newer version of refmac you can use harmonic restraints.
Take the new stable version of refmac from
www.ysbl.york.ac.uk/YSBLP
In newer version of refmac you can use harmonic restraints.
Take the new stable version of refmac from
www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
and use harmonic restraints as described in:
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html
Keyword is:
external harmonic residues f
i get the same error on OS X 10.5.2 and 10.4.11:
>sfcheck -f refmac2.mtz -m refmac2.pdb -out y -nomit 2 -map
the error:
Open failed: Unit: 11, File: sfcheck_scr.dat (logical: sfcheck_scr.dat)
Last system error message: Bad file descriptor
C
How one can fix position of few residues when refining in SHELX or Refmac5.
Thanks. Sam.
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Hi All,
Many thanks for those who shared their inputs. And sorry for not giving
more information about how the crystal was tested in the first instance.
The posted diffraction was obtained using the local resource (new
installed x-ray generator and new CCD Saturn 944+).
The Crystal to dete
With regard to low levels of expression: Is there a particular reason
to use 293 cells? Transient expression in Cos-1/Cos-7 cells gives
~ 10 fold higher levels of expression because of the plasmid amplification
in these cells. (The only requirement is that the plasmid should
have SV40 ori; most ma
Dear Dima,
thank you for your reply
Since this is ectodomain, I presume it contains native sorting sequence.
The ectodomain contains a secretion signal: either its native or
another secretion signal. I have tested a few other, strong secretion
signals to boost the expression levels with m
If the space group is correct, it sounds to me this is strange
statistics
away from both an ideal untwined and a perfect twinned structure.
I do suggested the data should be checked if the I-->F was completed.
If used I as F, these two values sound reasonable.
<|I|^2>/(<|I|>)^2 = 3.2236 (2
Good point, if you mis-assign a P2(1) space group as C222(1) because of
the twinning-generated apparent extra 2-fold symmetry then you could get
into such a situation.
If the P2(1) space group only has space for a monomer in the asymmetric
unit then Vm will point out the problem, but if the mo
Kenneth,
> sorry for this off topic question. I am producing the ectodomain of a
>
> human receptor in HEK293T cells by transient expression. The
> expression
> levels are quite low. The protein contains a high number of disulfide
> bridges. It has been reported that overexpression of protei
Dear all,
sorry for this off topic question. I am producing the ectodomain of a
human receptor in HEK293T cells by transient expression. The expression
levels are quite low. The protein contains a high number of disulfide
bridges. It has been reported that overexpression of protein disulfide
Dear developers,
is there any chance that during the refinement with refmac the warning
"Problems in MAKE_U_POSITIVE" disappears again during the
ongoing refinement procedure?
If that is not the case, could refmac give a hint in which atom/TLS-group the
problem occours? So, a TLSANAL-step would be
Check this paper below - a C222(1) space group (a=212, b= 300, c=575) frequently appearing as a merohedral twin P2(1) with apparent C222(1) symmetry was exactly a major problem in the H. marismortui 50S structure determination. PoulBan N, Nissen P, Hansen J, Capel M, Moore PB, Steitz TA.Placement o
Hi Bart,
important are the dimensions of the reduced cell.
in this case his uc params are 99 167 125 90 90 90. parameters of the
niggli cell are
97, 97, 125, 90.0, 90.0, 118 which is pseudo hexagonal.
[running xtriage would give this info, including an L-test and other
various tests]
HTH
P
Hi,
Below is what I've thought would make a good, but inexpensive, 3D
system (not had the opportunity to try all the parts out though):
Edimensional glasses (not compatible with the old Stereographics
goggles and emitters - dunno the exact wavelengths, but from visual
appearance of the LEDs
I just realized that this is an orthorhombic C222(1) space group. I
didn't check it up but unless two of the cell-dimensions are nearly
identical I think merohedral twinning is not possible for this space
group, because the symmetry of the unit cell shape is not higher than
the symmetry of the
Hey there,
I know this was recently rehashed, but of course I wasn't thinking too
much about it at the time (and now somebody has made me interested). In
any event, a colleague (go figure) of mine saw an article on projecting
stereo for a classroom. The way it works uses a dlp projector conn
It is not really possible to detect twinning by the simple moment and
cumulative distribution tests for data from a crystal with pseudo
translation. As Bart says, twinning decreases the value of the moments,
whilst pseudo-translation increases them, so the two effects tend to
cancel out.
The
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