Hi Francisco,
I'll play devil's advocate, but a measurement without an estimate of its
error is closer to theology than to science. The fact that the standard
deviations are not used for calculating an electron density map via FFT is
only due to the hidden assumption that you have 100%
I may be wrong here (and please by all means correct me), but I think
it's not entirely true that experimental errors are not used in modern
map calculation algorithm. At the very least, the 2mFo-DFc maps are
calibrated to the model error (which can be ideologically seen as the
error of
Ed,
I may be wrong here (and please by all means correct me), but I think
it's not entirely true that experimental errors are not used in modern
map calculation algorithm. At the very least, the 2mFo-DFc maps are
calibrated to the model error (which can be ideologically seen as the
error of
Hi Ed,
I may be wrong here (and please by all means correct me), but I think
it's not entirely true that experimental errors are not used in modern
map calculation algorithm. At the very least, the 2mFo-DFc maps are
calibrated to the model error (which can be ideologically seen as the
Nicholas,
My experience from comparing conventional (FFT-based) and maximum-entropy-
related maps is that the main source of differences between the two maps
has more to do with missing data (especially low resolution overloaded
reflections) and putative outliers (for difference Patterson
On Wed, 2012-05-23 at 10:02 -0500, Pete Meyer wrote:
bviously
model and experimental errors do factor into calculation of a
2mFo-DFc
map - but is weight and structure factor calculation part of map
calculation, or a distinct stage of data processing?
Oh, I see. Sure, when the map
On Wed, 2012-05-23 at 18:06 +0300, Nicholas M Glykos wrote:
This is an amplitude modification. It does not change the fact that
the
sigmas are not being used in the inversion procedure
Nicholas,
I am not sure I understand this - perhaps we are talking about different
things. Even if by
On Wed, 2012-05-23 at 18:06 +0300, Nicholas M Glykos wrote:
It seems that although you are not doubting the importance of maximum
likelihood for refinement, you do seem to doubt the importance of
closely
related probabilistic methods (such as maximum entropy methods) for
map
calculation.
Does anyone know of a (non-commercial) software that can analyze results
of a crystallization screen? What I am looking for is some way to tell
what components/factors favor protein solubility/precipitation based on
binary input (clear drop/precipitate).
I did some googling, but please feel free
I just wanted to take a moment to thank all of the respondents to the post.
Indeed, my question was more practical in nature since I wanted to see the
density around the ligand in question. From the first suggestions, I quickly
did manage to generate the maps and accomplish my goal (special
Hi Jens,
You can try the free DS Visualizer:
http://accelrys.com/products/discovery-studio/visualization-download.php
It comes with a free molecular builder for proteins, dna/rna and ligands.
Please note that if you do need to make anything more interesting (energy
calculations,
On 05/23/12 08:06, Nicholas M Glykos wrote:
Hi Ed,
I may be wrong here (and please by all means correct me), but I think
it's not entirely true that experimental errors are not used in modern
map calculation algorithm. At the very least, the 2mFo-DFc maps are
calibrated to the model
Hi Jens,
You can try NAMOT (Nucleic Acid MOdelling Tool), from the links below.
http://namot.sourceforge.net/
http://sourceforge.net/projects/namot/
Best,
Tuhin.
Tuhin Bhowmick
Prof. S. Ramakumar’s Lab
Biocrystallography and Computation
Department of Physics
Indian Institute of Science
Dear community,
I am trying to cleave a hexaHis tag from my protein prior to crystallization.
As I was setting up my digestion, my protein started to precipitate as soon as
I added the recommended thrombin buffer.
My question is, if anyone has encountered this, how well does it cleave without
For the RNA I recommend Eric Westhof's Assemble.
F
On May 23, 2012, at 9:32 AM, jens j birktoft wrote:
Hi everybody,
Does anyone know of a (non-commercial) software that are suitable for
modeling DNA/RNA structures. Coot is great, however I am looking something
that allows more
Ed,
I looked into this a number of years ago, and remember the following papers. I
did not actually use any of the databases described due to IT issues at the
time. I hope this helps.
Kind regards,
Bryan
LISA: an intranet-based flexible database for protein crystallography project
management
Hi Ed,
I am not sure I understand this - perhaps we are talking about
different
things. Even if by inversion procedure you mean simple calculation
of
(2fo-fc)*exp(i*phi), the fc is still technically a product of the
refinement, which unless based on trivial least square target (i.e.
no
In SHELXL. a refinement program sometimes used by small molecule
crystallographers, all Fourier map for at least the last 20 years were
weighted by Ic^2/(Ic^2+sigma^2(I)), where Ic is the calculated squared
structure factor and sigma(I) is the square root of 1/w. w is the weight
assigned to a
Hi Pete,
I'm curious - which programs have you used for maximum-entropy for
map calculation?
Thanks, I thought no-one would ask :-)
http://utopia.duth.gr/~glykos/graphent.html
Don't download the program today. Or tomorrow. This coming weekend
there
will be a new release which
Thrombin works pretty good without any added calcium. We routinely added
thrombin to whatever buffer the protein is in provided it doesn't have a lot of
DTT. Some beta-mercaptoethanol is alright. What is the source of your
thrombin?
-Original Message-
From: CCP4 bulletin board
Dear all
A off-topic question - is there a practical limit for overexpression of
membrane protein complexes (about 200 kDa in total)? This includes chaperones
and my target proteins. Can I amplify the gene cluster and simply clone into a
plasmid?
Thank you.
On Wed, May 23, 2012 at 12:54 PM, Mark J van Raaij
mjvanra...@cnb.csic.es mailto:mjvanra...@cnb.csic.es wrote:
even more flexible than COOT?
- the only thing I can think of that I haven't worked out how to do in
COOT is grabbing and moving one atom at a time.
On 23/05/12 19:50, jens j
Hi,
Could someone refer me to some papers on using ANS to estimate amount of
hydrophobic surface in a protein? I tried the classic way by STEP 1:
titrating my protein into 1uM ANS till saturation to get the molar fluorescence
activity of ANS, then STEP 2: titrate ANS into protein to get
and if everything else fails including kicking the trash can one could
indeed read the manual/FAQ - thanks Paul
On Wed, May 23, 2012 at 4:27 PM, Paul Emsley paul.ems...@bioch.ox.ac.ukwrote:
On Wed, May 23, 2012 at 12:54 PM, Mark J van Raaij mjvanra...@cnb.csic.es
wrote:
even more flexible
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