there are a couple TiBS articles in press on the publication of molecular
models in .pdf documents :
Kumar, et. al.
"Grasping molecular structures through publication-integrated 3D models"
http://tinyurl.com/686hvz
the 3D models are in the _supplemental_ .pdf file, so when it "doesn't
work", m
On Wed, 18 Jun 2008, Paul Kraft wrote:
Are there any reports of the comparison of the number of bound waters
in crystal structures vs NMR structures? Paul Kraft
this is discussed inter alia in :
Mattos, C. & Ringe, D., Solvent Structure, in International Tables for
Crystallography (Rossman,
On Thu, 15 May 2008, William Scott wrote:
On May 15, 2008, at 10:01 AM, Ed Pozharski wrote:
1.2A (not surprisingly since this is about the length of covalent
bond).
A carbon-carbon single bond is about 1.55 Å.
the van der Waals radius of hydrogen is 1.2A (Eisenberg/Crothers, Pauling,
1960 )
> mosflm
Bill just beat me to writing the same. I would mention XDS as well.
labelit will index your images
http://adder.lbl.gov/labelit/
... then you give the scripts to mosflm. there's plenty of Acta Cryst.
there to read too.
-bryan
an interesting way to compare structures from the same protein sequence is
reported here :
acta cryst D56 714-721, 2000 "objective comparison of protein structures :
error-scaled difference distance matrice"
acta cryst D60 2269-2275, 2004 "domain identification by iterative
analysis of error
At 10:13 AM 3/28/2008, Lucas Bleicher wrote :
Some time ago I've heard about the idea of proposing an ensemble of
models (as in NMR), instead of a single model for x-ray crystallography
structures. If I remember correctly, this idea has been published
somewhere. Can anyone tell me what article
On Fri, 18 Jan 2008, Edwin Pozharski wrote:
So Rmerge does tell you something, but only in context with all the
other information.
this is what Whewell termed the consilience of inductions in the 19th
century (which others have expanded since).
-bryan
just want to check my understanding on scala. the manual says :
"SdB may be omitted in the input and its use is not recommended. Default
values are 1.0, 0.0, 0.02"
the example shown is :
sdcorrection full 1.4 0.11 part 1.4 0.05
.. i.e. if SdB were set, it would have been between the 1.4 and
do any of fffear/pirate/buccaneer use SIGFP in a significant/meaningful
way?
-bryan
On Wed, 16 Jan 2008, Jacob Keller wrote:
I would like to plot as a "heat" or "color map" on the 2d rectangle
[...] cannot figure out how to do this in gnuplot or anywhere,
consider gnuplot pm3d (not readily obvious for googling, is it)
http://t16web.lanl.gov/Kawano/gnuplot/plotpm3d-e.html
-br
running pirate 0.4.9 w/ gui 1.4.4.2 ; the documentation suggests that
R-free can be left unassigned - yet, pirate fails, claiming :
colin-wrk-free /*/*/[Unassigned]
CCP4MTZfile: import_hkl_data - Missing column, crystal or dataset:
/*/*/Unassigned
... so i really need R-free?
-bryan
could anyone drop the name of a source for those tweezer-like clamps whose
ends fit perfectly around a Nunc/CryoCap cryovial? one very famous source
seems not to have them.
these are not the locking clamps or thick metal tongs, but are more like
tweezers with the ends curved into half-circles
i can't seem to find any reviews that specifically consider how NCS
influences space group / symmetry determination - though there are plenty
individual accounts.
can anyone cite a review or even a book chapter on such a topic? or maybe
even some cases of non-obvious indexing errors? of cour
when pointless (1.2.0) finds enantiomorphic SG's, what is the criterion
for 'Selecting' one over the other?
e.g. i ran pointless on some tetragonal data, and the enantiomorphs
SG92/SG96 are selected as strong candidates
Spacegroup TotProb SysAbsProb Reindex Conditions
neglecting e-density, packing, etc. - what matters most to people when
running phaser - LLG or Z-score? in what function (RF, TF)?
further, if you 'refine' the RMSD to find the best RMSD, what is the more
robust indicator - LLG or Z-score?
lastly - is it better to have a high LLG/Z-score wit
On Mon, 29 Oct 2007, Iain Kerr wrote:
The cumulative intensity distribution plot from crystal A did suggest partial
twinning (attached, doesn't look too bad though..)
notwithstanding other plots/statistics, does the cum. intens. dist. plot (e.g.
from truncate) really show a continuum from untw
On Mon, 29 Oct 2007, Iain Kerr wrote:
The cumulative intensity distribution plot from crystal A did suggest
partial twinning (attached, doesn't look too bad though..)
notwithstanding other plots/statistics, does the cum. intens. dist. plot
(e.g. from truncate) really show a continuum from untw
On Fri, 19 Oct 2007, Kay Diederichs wrote:
Acta Cryst. (2004). D60, 2196-2201
Direct incorporation of experimental phase information in model refinement
P. Skub?k, G. N. Murshudov and N. S. Pannu
the refmac documentation(s) mention Rice, MLHL, etc., but i didn't see
explicit mention of SAD - i
On Wed, 10 Oct 2007, Jim Pflugrath wrote:
It has come to my attention that the wavelength of a Copper Kalpha may
have changed over the years. At least this appears to be true if you
look at the International Tables.
the 'natural' isotopic distribution must have changed, as it has with the
bi
does the mosflm orientation matrix specify the crystal system and only the
crystal system?
i.e, given an orientation matrix from autoindexing, it would be correct to
simply use keyword 'SYMMETRY SPACEGROUP' in mosflm to refine then
integrate in any of the spacegroups within a given crystal sys
a quick summary on 'the worst MR probes'
Pierre Rizkallah:
X-ray Structure Solution of Amaryllis Lectin by Molecular Replacement
with Only 4% of the Total Diffracting Matter.
L. Chantalat, S.D. Wood, P.J. Rizkallah, C.D. Reynolds (1996).
Acta Crystallographica, D52, pp. 1146-1152
Poul Nissen:
Ni
would anyone be willing to share stories of the worst molecular
replacement search probes they used to get the correct solution purely
with MR?
perhaps in terms of %-scattering, RMSD, Z-score, LLG, or other possibly
specific scoring values.
-bryan
should i take it that when given > 1 .pdb in an ensemble, phaser will
output only the first member of the ensemble, and its up to the user to
tranform the others?
if so, i gather there are no keywords to make phaser do that
automatically?
-bryan
i wrote
"(ensemble) / (sequence)" to get a percent composition
i forgot to emphasize that i do not mean the Vm or the "Z" composition,
but the composition as one would enter e.g.
COMPosition ENSEmble mol1 FRACtional 0.22
or
COMPosition SCAttering
-bryan
the phaser docs/tutorial indicate that phaser calculates what could be
called "(ensemble) / (sequence)" to get a percent composition, however i
cannot seem to find the direct result from this in any output (.sol, .sum,
.pdb, .log... other?)
any tips appreciated as to if this can be found / whe
On Thu, 6 Sep 2007, William Scott wrote:
I think the reason it works is because the lack of closure error is
nearly random and the signal is not
interesting notion
Low initial FOM in many senses are good [..] because density
modification has more latitude
my understanding was that density m
general question - perhaps the fundamental question -
for anyone who had "weak/poor/bad" phases from some source, that were
later actually used to solve a structure when combined w/ another source -
HOW bad were the worst phases on their own, in terms of resolution, FOM,
CC, e-density, (any ot
if it doesn't now, will phaser be able to run a phased translation
function in the future?
-bryan
[1] is there a way to make pointless read only up to a certain batch
number?
[2] should pointless compare axial reflections along all axes regardless
of input spacegroup? i.e, is it a waste of time to permute axes when
indexing?
e.g, if pointless reports this :
Zone Nu
On Fri, 31 Aug 2007, William Scott wrote:
That interface
in the grand modern bazaar of free software, we shall see (not from me) an
elegant bleeding edge gui this afternoon... late this afternoon.. ok, an
overnight build... in a CVS repository... SOMEthing..
-bryan
could anyone comment on the use of these adjustable cryoloops that are out
there? could you bend the loop without unmounting from the goniometer?
how many times could you adjust it?
and has anyone seen cryomounting equipment that is something akin to a
capillary mount? i.e., capillary action
this post is is tangential to the model building/hardware thread -
anything useful presented here is purely coincidental:
tangible model building action shot:
http://puffer.tamu.edu/cs_computer.htm
[slide all the way to the right]
http://www.bassictech.com/blogs/bassictech_news_blog/archive/200
On Fri, 8 Jun 2007, Anthony Addlagatta wrote:
Seeding!
since these crystals are undesirable, how about heterogeneous nucleation
w/ xtals that have nice properties, or even something like this:
pnas 2006 17jan06 103 3 596-691
-bryan
are there any free programs which, given a diffraction image, will
calculate the rotations necessary to align any of the reciprocal space
axes w/ the beam?
i looked through mosflm and dataman, so unless i missed it...
-bryan
does anyone know of any reports where heavy atom positions were identified
by any method (or mol. rep.) in a Laue data set (or sets)?
also - i thought there was some Laue work out there on watching virus
nucleic acids move around in a crystal, so again, if anyone knows any
references (or names
could anyone share their experience in seeding from a low-twin fraction
crystal found in a drop with high twin-fraction crystals?
-bryan
i heard that some journals will give the referees the coordinates if they
ask.
so next time you review a paper, ask.
-bryan
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