Jacob
We should not be comparing the Xray and electron beam fluxes in terms
of particle density as the scattering cross sections are very
different. I have to admit I did not see the number you are quoting,
which is very low. One needs 20-30 electrons per A^2 to acheive 3A
resolution. Pres
One of the figures they cite is 2.5 electrons per um^2, which I think
means once the whole bunch has gone through. That struck me as being
pretty far from where one needs to be to get structures. Do you know
off hand a comparable figure for the FEL experiment? I assume it would
be many orders of ma
Petr
Well, not sure - are we doing imaging or diffraction/scattering? What energy
are the electrons in these sources? The idea of pulsed sources is to put more
electrons/A^2 and still beat radiation damage. Can one do this when there are
only around 10^6 electrons in perhaps a rather divergent b
Colin,
We know that with a dose of 20-30 electrons per A^2, a lot of image processing,
and insane amount of luck, one can reconstruct cryoEM images to 3 A resolution
or better. A typical protein molecule is say 100 A in diameter, which is ~8000
A^2 in projection. So, in an ideal case one needs
Petr
Yes, I saw the figure. Similar ones appear in the Hastings et. al. paper (the
SLAC one I referenced). They use a much higher energy beam to get the short
pulse length.
I still believe the issues are
1. For diffraction, can you get a low enough electron beam divergence to
resolve larger un
Dear Colin and all interested in the FEL development.
Please look at the figures in the first link I mentioned. Jom Luiten et al. are
able to record a 1.25 A resolution diffraction pattern of a gold foil using a
pulse compressed to 50 fs. Ahmed Zewail is a pioneer of the technique but as
far as
Petr has provided the Eindhoven links.
For more details on fast electron imaging (as opposed to diffraction) see
https://e-reports-ext.llnl.gov/pdf/343044.pdf
Apparently stochastic scattering of the electrons at the high current densities
necessary for short pulsed sources result in blurring i
Hello,
I often see these vdW contact distance cut-off numbers (see below) in papers,
but no
reference was given.
"Contact distances are the following maximum allowed values: C-C, 4.1 Å; C-N,
3.8 Å;
C-O, 3.7 Å; O-O, 3.3 Å; O-N, 3.4 Å; N-N, 3.4 Å; C-S, 4.1 Å; O-S, 3.7 Å; N-S,
3.8 Å."
I am c
Thanks a lot!
> If you are trying to make a mask in spacegroup P21, that;s not the way
> to do it.
>
> Make the mask in NCSMASK without a symmetry keyword. Then run mapmask to
> change the spacegroup to P 21 and use EXPAND OVERLAP to generate the
> symmetry copies of the mask.
>
> Hailiang Zhang wr
Dear Jacob,
Ahmed Zewail's papers are worth consulting on this, although not protein/bio.
See also the book by Zewail and Thomas, recently published, easily findable on
amazon etc, as a handy overview.
Best wishes,
John
Prof John R Helliwell DSc
On 14 Apr 2011, at 14:38, Jacob Keller wrote:
Only bear in mind that superpose relies on the presence of secondary structure,
so that your selections should always include at least 3 SSEs.
Eugene.
On 14 Apr 2011, at 15:45, goslar wrote:
> (Should have) found it!
> http://www.ccp4.ac.uk/html/pdbcur.html#atom_selection
> Did not fully RTM.
People are looking into how to fit the old retired MeV microscopes with pulsed
electron guns (problem is there are very few of those beasts left). If this
works, such a machine will produce equivalent results to FEL but at a fraction
of the cost.
The group at Eindhoven, which Colin had mention
(Should have) found it!
http://www.ccp4.ac.uk/html/pdbcur.html#atom_selection
Did not fully RTM. My aplogies.
W.
-- Forwarded message --
From: goslar
Date: Thu, Apr 14, 2011 at 10:19 AM
Subject: superpose atom selection
To: CCP4BB@jiscmail.ac.uk
Hello all,
from the ccp4 manual:
I have not seen MUSTANG in the list yet.
http://pxgrid.med.monash.edu.au:8080/mustangserver/
Jürgen
On Apr 14, 2011, at 9:06 AM, Katie Carr wrote:
I would like to compare several very similar structures (more than 10) to get
the rms deviation over all. Is this possible with any program?
Thanks
K
Jacob
Very good question.
People are considering this sort of thing. See for example
http://www-spires.slac.stanford.edu/cgi-wrap/getdoc/slac-pub-12162.pdf
Due to coulomb explosion one normally needs MeV beams to get the short bunch
length. MeV beams also give a more reasonable penetration depth
Hello all,
from the ccp4 manual:
http://www.ccp4.ac.uk/html/superpose.html
superpose foo_1st.pdb [-s CID1] foo_2nd.pdb [-s CID2] [ foo_out.pdb ]
where [-s CID1/2] are optional selection strings in MMDB convention,
and [foo_out.pdb] is optional output file.
Please, could someone point me to docum
I once had a similar problem. The crystals only reproduced when grown in
condition containing PEG 8000 from SIGMA but not from FLUKA. This difference
may not affect crystals from other proteins but some proteins are more
sensitive to slight changes than others. Since you found out that the stock
If you are trying to make a mask in spacegroup P21, that;s not the way
to do it.
Make the mask in NCSMASK without a symmetry keyword. Then run mapmask to
change the spacegroup to P 21 and use EXPAND OVERLAP to generate the
symmetry copies of the mask.
Hailiang Zhang wrote:
Hi,
I want to ge
Dear Crystallographers,
is there any reason why we are not considering using super-intense
femtosecond electron bursts, instead of photons? Since the scattering
of electrons is much more efficient, and because they can be focussed
to solve the phase problem, it seems that it might be worthwhile to
I would like to compare several very similar structures (more than 10) to get
the rms deviation over all. Is this possible with any program?
Thanks
Katie Carr
University of Nottingham
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor
Dodson
Hey Jun,
If it's an old batch check and see if you have microorganisms living in the
stock or proliferating in the drop - see the paper by Bai et al:
doi:10.1107/S1744309107002904
In this paper they demonstrated how they could not reproduce a crystal hit
from an old screen up until they realized a
See this thread:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A1=ind1009&L=CCP4BB#58
Cheers
-- Ian
On Wed, Apr 13, 2011 at 10:05 PM, Jiamu Du wrote:
> Dear All,
> I am wondering about the ranges of RMSD bond lengths and angles. What are
> the acceptable ranges for these two values? Is there som
On 04/13/2011 09:18 PM, REX PALMER wrote:
Dear All
What is the best program to use for comparing two protein structures which are
very similar both structurally and wrt aa sequence? ie to get the rms
deviations both generally and in selected regions.
Rex Palmer
Birkbeck College
Using CCP4 g
Jun Yong and Jobichen
(I've mentioned this before, but ) - both of your projects jump out as very
good targets for microseeding with random screens. This method often gives
extra hits and better crystals because it is more likely that crystals will
grow in the metastable zone. It often reduces t
This tool looks cool also (especially to all the maximum likelihood fans
of this list I guess):
http://www.theseus3d.org/
---
Theseus is a program that simultaneously superimposes multiple
macromolecular structures. Instead of using the conventional
least-squares criteria, Theseus finds the opt
Yes, I forgot about escet. The more up to date wab address is
http://webapps.embl-hamburg.de/escet/
even though that page still lists Thomas' address in Italy
Tim
On Thu, Apr 14, 2011 at 10:05:47AM +0200, Gergely Katona wrote:
> ESCET is also very useful to reveal small, but significant
> differe
ESCET is also very useful to reveal small, but significant
differences. It also identifies conformationally invariant regions for
superposition.
http://schneider.group.ifom-ieo-campus.it/escet/index.html
Gergely
On Thu, Apr 14, 2011 at 9:34 AM, Tim Gruene wrote:
> Hello Rex,
>
> most programs p
Hello Rex,
most programs probably use similar algorithms for superpositions, so you can
pick your choice:
- O
- lsqman
- lsqkab
- coot
- ...
are all similarily comfortable to use in my opinion.
Tim
On Wed, Apr 13, 2011 at 09:18:27PM +0100, REX PALMER wrote:
> Dear All
> What is the best program
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