As part of a long-term collaboration between the laboratories of Luca Jovine
and Rune Toftgård at the Department of Biosciences and Nutrition & the Center
for Biosciences of Karolinska Institutet, a postdoctoral position is available
from January 2013 on structural studies of protein-protein int
No such luck! If one calculated the Root Mean Square Deviation from
the Mean then F(000) makes no difference, but everyone I know calculates
the Deviation from 0.0. I guess that makes it an "rms" and not an
"rmsd".
We can use maps calculated w/o the F(000) because we are generally
more int
F000 contributes to the whole map as a level (F000/V). If calculated with a
only difference of with or w/o F000, should the sigma levels of the two maps be
the same? That is why we could rely on maps for modeling that are calculated
w/o F000 item. Lijun
On Nov 28, 2012, at 2:30 PM, Pavel
I can say that my chair is 10 meters above ground level and I
can also say that it is 100 meters above sea level. The units
of "meters" is equally valid in both cases. The value of any
measurement is useless without both the units and the origin (or
coordinate system in multidimensions). The
If a map was computed from map coefficients not having F000 included I
would not say it has *electron* per Angstrom cube (e/A**3) units, but it's
just a unit cell volume scaled map in some units.
Whether such a map more useful compared to sigma scaled one is a separate
question. In fact, it is, as
Actually one can make a lot of sense about e/A^3 in the absence of
F(000). You actually think of the density as difference from the
average and not an absolute measurement.
For an Fo-Fc style map the F(000) term is simply the difference
between the number of missing electrons in the model a
Without F000 we cannot get absolute density level vs zero, but still
I think electron density in units of e-/a^3 above the mean is much more
meaningful than sigma above the mean. I think the last one of these
mystery density questions generated a lot of discussion until someone
pointed out that
For map in e-/A^3 units to make sense one needs to obtain F000, which may
be more tricky than one may think. Interesting, how Coot does this given
just a set of Fourier map coefficients?
Pavel
On Wed, Nov 28, 2012 at 12:21 PM, Greg Costakes wrote:
> You stated that the map is set to 3 sigma, bu
Dear Andrea
There are two ways as they were mentioned by Tim and Ian:
1) Using external restraints mechanism. You define something like (it is an
example):
external plane first atom CA chain A residue 25 next atom CB chain B residue 50
next atom OG chain B residue 100 next atom CC chain C resid
Hi,
These sorts of questions are always difficult, particularly in the
absence of any information about the protein or the contents of the
mother liquor. If the carbonyl you are talking about is the little
magenta dot visible through the hole in your blob, this could be a
metal atom with some
could it be a PEG molecule?
Quoting "Read, Jon":
Anyone see anything like this before? The data is 1.7Angstrom data with
good statistics. The picture shows the solid FoFc density contoured at 3
Sigma in light brown and -3 Sigma in purple. The density is odd as it
appears to be bound to a peptid
Ok - annoying thing….
1) using /Applications/coot.app/Contents/Resources/script to launch Coot from
the command line (terminal window) works IF you don't have X11 open already.
2) if you DO have X11 open, coot pretty much always crashes with the
aforementioned "invalid window errors".
>>> Nov 2
Dear ccp4,
I am interested in membrane protein, and more precisely in ion channels.
I would like to know what are the folds found in the intracellular side
of membranes for membrane proteins/ion channels.
Do you have a resource or link of this kind ?
Best Regards.
Hi Andrea
You need to have an appropriate LINK record in the PDB file but you also
need to specify the link restraints in the CIF file, for example:
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atom
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Andrea,
Have a look at the section "External restraints" -> "Torsion angle
restraints" at the refmac documentation
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
You need to find out whether the 'similar type of keywords' for planar
restraints
Hi Dirk,
cctbx has tools to obtain N-gaussian approximation of scattering tables,
for any element, where the number of gaussians N is determined dynamically
to obtain desired accuracy of fit. That's what is used by phenix.refine and
other related tools.
See page 27 here:
http://cci.lbl.gov/public
Dear colleagues,
for a very simple calculation, I want to use a single-Gaussian atomic
scattering factor approximation (for nitrogen). I only find 2- or
5-Gaussian approximations. Could you please give me a pointer to values
of single-Gaussian atomic scattering factor approximations?
Best re
17 matches
Mail list logo
