THESEUS can do it, and it comes bundled with ccp4 so definitely on-topic.
If you want RMSD of “equivalent” amino acids, you must tell THESEUS which
residues are equivalent with a sequence alignment. Then use the -I option to
get the RMSD (and other stats) of the pdb files in their current
THESEUS should be able to do it rather easily. You can email me offlist if you
need some guidance.
On Jun 1, 2015, at 3:53 PM, jens j birktoft birkt...@nyu.edu wrote:
I apologize if this question this question has been asked before but I still
need help finding an answer to the
On May 12, 2015, at 3:19 PM, Robbie Joosten robbie_joos...@hotmail.com wrote:
I strongly disagree with rejecting paper for any other reasons than
scientific ones.
I agree, but … one of the foundations of science is independent replicability
and verifiability. In practice, for me to be able
Hi Randy,
So I've been playing around with equations myself, and I have some alternative
results.
As I understand your Mathematica stuff, you are using the data model:
ip = ij + ib'
ib
where ip is the measured peak (before any background correction), and ij is a
random sample from the
On Jul 7, 2013, at 1:44 PM, Ian Tickle ianj...@gmail.com wrote:
On 29 June 2013 01:13, Douglas Theobald dtheob...@brandeis.edu
wrote:
I admittedly don't understand TDS well. But I thought it was
generally assumed that TDS contributes rather little to the
conventional background
On Jun 27, 2013, at 12:30 PM, Ian Tickle ianj...@gmail.com wrote:
On 22 June 2013 19:39, Douglas Theobald dtheob...@brandeis.edu wrote:
So I'm no detector expert by any means, but I have been assured by those who
are that there are non-Poissonian sources of noise --- I believe mostly
you are using a
(non-physical) Gaussian model. Feel free to prove me wrong --- can you
derive Ispot-Iback, as an estimate of Itrue, from anything besides a
Gaussian?
Cheers,
Douglas
On Sat, Jun 22, 2013 at 12:06 PM, Ian Tickle ianj...@gmail.com wrote:
On 21 June 2013 19:45, Douglas Theobald
On Sat, Jun 22, 2013 at 1:04 PM, Douglas Theobald dtheob...@brandeis.eduwrote:
Feel free to prove me wrong --- can you derive Ispot-Iback, as an estimate
of Itrue, from anything besides a Gaussian?
OK, I'll prove myself wrong. Ispot-Iback can be derived as an estimate of
Itrue, even when
On Sat, Jun 22, 2013 at 1:56 PM, Ian Tickle ianj...@gmail.com wrote:
On 22 June 2013 18:04, Douglas Theobald dtheob...@brandeis.edu wrote:
--- but in truth the Poisson model does not account for other physical
sources of error that arise from real crystals and real detectors, such as
dark
?
Cheers
phx
On 22/06/2013 18:04, Douglas Theobald wrote:
Ian, I really do think we are almost saying the same thing. Let me try to
clarify.
You say that the Gaussian model is not the correct data model, and that
the Poisson is correct. I more-or-less agree. If I were being pedantic
On Jun 21, 2013, at 8:36 AM, Ed Pozharski epozh...@umaryland.edu wrote:
On 06/20/2013 01:07 PM, Douglas Theobald wrote:
How can there be nothing wrong with something that is unphysical?
Intensities cannot be negative.
I think you are confusing two things - the true intensities
. The Ispot-Iback=Iobs does not follow from a Poisson assumption.
On Jun 21, 2013, at 1:13 PM, Ian Tickle ianj...@gmail.com wrote:
On 21 June 2013 17:10, Douglas Theobald dtheob...@brandeis.edu wrote:
Yes there is. The only way you can get a negative estimate is to make
unphysical assumptions
in the end compared
with the 'post-correction' we're doing now?
Cheers
-- Ian
On 20 June 2013 18:14, Douglas Theobald dtheob...@brandeis.edu wrote:
I still don't see how you get a negative intensity from that. It seems you
are saying that in many cases of a low intensity reflection
On Jun 21, 2013, at 2:48 PM, Ed Pozharski epozh...@umaryland.edu wrote:
Douglas,
Observed intensities are the best estimates that we can come up with in an
experiment.
I also agree with this, and this is the clincher. You are arguing that
Ispot-Iback=Iobs is the best estimate we can come
:34 AM, Douglas Theobald dtheob...@brandeis.edu
wrote:
I kinda think we're saying the same thing, sort of.
You don't like the Gaussian assumption, and neither do I. If you make the
reasonable Poisson assumptions, then you don't get the Ispot-Iback=Iobs for
the best estimate of Itrue
Just trying to understand the basic issues here. How could refining directly
against intensities solve the fundamental problem of negative intensity values?
On Jun 20, 2013, at 11:34 AM, Bernhard Rupp hofkristall...@gmail.com wrote:
As a maybe better alternative, we should (once again)
values
for all models maybe we could get a start toward moving to intensity
refinement.
Dale Tronrud
On 06/20/2013 09:06 AM, Douglas Theobald wrote:
Just trying to understand the basic issues here. How could refining directly
against intensities solve the fundamental problem of negative
generated from the sigma's on I, and are very much undetermined for
small intensities and small F's.
Small molecule crystallographers routinely refine on F^2 and use all of the
data, even if the F^2's are negative.
Bernie
On Jun 20, 2013, at 11:49 AM, Douglas Theobald wrote:
Seems to me
:49, Douglas Theobald dtheob...@brandeis.edu wrote:
Seems to me that the negative Is should be dealt with early on, in the
integration step. Why exactly do integration programs report negative Is to
begin with?
On Jun 20, 2013, at 12:45 PM, Dom Bellini dom.bell...@diamond.ac.uk wrote
,
Department of Molecular Microbiology and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail: mbfro...@post.tau.ac.il
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Jun 20, 2013, at 20:07 , Douglas Theobald dtheob...@brandeis.edu
-0400, Douglas Theobald dtheob...@brandeis.edu
wrote:
I still don't see how you get a negative intensity from that. It seems you
are saying that in many cases of a low intensity reflection, the integrated
spot will be lower than the background. That is not equivalent to having a
negative
21:27, schrieb Douglas Theobald:
Kay, I understand the French-Wilson way of currently doing things, as you
outline below. My point is that it is not optimal --- we could do things
better --- since even French-Wilson accepts the idea of negative intensity
measurements. I am trying to disabuse
To me, that's not a problem. The wavy representation is more accurate (as far
as cartoon accuracy can go), as the strand actually follows the alpha
carbons. This is why Pauling called it a pleated sheet --- it's got pleats.
Beta sheets/strands *should* be wavy.
On May 29, 2013, at 11:29
On Mon, Feb 11, 2013 at 12:12 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
-BEGIN PGP SIGNED MESSAGE--
Hash: SHA1
Dear Bill,
I disagree to your criticism. From http://www.ccp4.ac.uk/ccp4bb.php:
CCP4bb is an electronic mailing list intended to host discussions
about topics of general
case, and 25 to 2.0 which would
be more reassuring.
eab
Douglas Theobald wrote:
Hi Ed,
Thanks for the comments. So what do you recommend? Refine against weak
data, and report all stats in a single Table I?
Looking at your latest V-ATPase structure paper, it appears you favor
in the PDB is 0.99 but
in your table 1* says 1.3?
Douglas Theobald wrote:
Hello all,
I've followed with interest the discussions here about how we should be
refining against weak data, e.g. data with I/sigI 2 (perhaps using all
bins that have a significant CC1/2 per Karplus and Diederichs 2012
of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Douglas
Theobald [dtheob
=100 (or 99.9) mean? Does it
mean the data is as good as it gets?
Alan
On 07/12/2012 17:15, Douglas Theobald wrote:
Hi Boaz,
I read the KK paper as primarily a justification for including extremely
weak data in refinement (and of course introducing a new single statistic
that can
Hello all,
I've followed with interest the discussions here about how we should be
refining against weak data, e.g. data with I/sigI 2 (perhaps using all bins
that have a significant CC1/2 per Karplus and Diederichs 2012). This all
makes statistical sense to me, but now I am wondering how I
On Nov 16, 2012, at 10:27 AM, Enrico Stura est...@cea.fr wrote:
As a referee I also dislike the word freezing but only if improperly used:
The crystals were frozen in LN2 is not acceptable because it is the outside
liquor that is rapidly cooled to cryogenic temperatures.
right, while the
elegantly).
Cheers, Tim
On Fri, Oct 15, 2010 at 11:55:54PM +0100, Ian Tickle wrote:
On Fri, Oct 15, 2010 at 8:11 PM, Douglas Theobald
dtheob...@brandeis.edu wrote:
Vectors are not only three-dimensional, nor only Euclidean -- vectors can
be
defined for any number of arbitrary dimensions
As usual, the Omniscient Wikipedia does a pretty good job of giving the
standard mathematical definition of a vector:
http://en.wikipedia.org/wiki/Vector_space#Definition
If the thing fulfills the axioms, it's a vector. Complex numbers do, as well
as scalars.
On Oct 15, 2010, at 8:56 AM,
-0400, Douglas Theobald
dtheob...@brandeis.edu wrote:
As usual, the Omniscient Wikipedia does a pretty good job of giving
the standard mathematical definition of a vector:
http://en.wikipedia.org/wiki/Vector_space#Definition
If the thing fulfills the axioms, it's a vector. Complex numbers do
On Oct 15, 2010, at 12:14 PM, William G. Scott wrote:
As usual, the Omniscient Wikipedia does a pretty good job of giving the
standard mathematical definition of a vector:
http://en.wikipedia.org/wiki/Vector_space#Definition
If the thing fulfills the axioms, it's a vector. Complex
Both MUSTANG and MATT are good choices:
http://www.cs.mu.oz.au/~arun/mustang/
http://groups.csail.mit.edu/cb/matt/
On Jan 12, 2010, at 7:17 AM, Ronnie Berntsson wrote:
Dear all,
A bit off the topic question perhaps.
I am trying to find a program which can do multiple structural sequence
On Dec 16, 2009, at 7:40 AM, Anastassis Perrakis wrote:
How very correct. And if anyone is doubt, remember the fiasco of the 'memory
of water', published in Nature.
To borrow the title of DVD's talks, Just because its in Nature, it does not
mean its true.
Or, as one of my colleagues is
Argument from authority, from the omniscient Wikipedia:
http://en.wikipedia.org/wiki/Radian
Although the radian is a unit of measure, it is a dimensionless quantity.
The radian is a unit of plane angle, equal to 180/pi (or 360/(2 pi)) degrees,
or about 57.2958 degrees, It is the standard
anything else) is perfectly valid for
an angle.
Marc
Quoting Douglas Theobald dtheob...@brandeis.edu:
Argument from authority, from the omniscient Wikipedia:
http://en.wikipedia.org/wiki/Radian
Although the radian is a unit of measure, it is a dimensionless quantity
James,
Graeme is right. While I does indeed (approximately) follow a
Gaussian, |I-I| cannot. The absolute value operator keeps it
positive (reflects the negative across the origin), and hence it is a
half Gaussian. Its mean cannot be zero unless the variance is zero.
For standard
- Dima Klenchin [EMAIL PROTECTED] wrote:
But how do we establish phylogeny? - Based on simple similarity!
(Structural/morphological in early days and largely on sequence
identity today). It's clearly a circular logic:
Hardly. Two sequences can be similar and non-homologous at all
- Dima Klenchin [EMAIL PROTECTED] wrote:
But how do we establish phylogeny? - Based on simple similarity!
This is a common, but erroneous, misconception. Modern phylogenetic
methods (Bayesian, maximum likelihood, and some distance-based) rely on
explicit models of molecular evolution, and
- Anastassis Perrakis [EMAIL PROTECTED] wrote:
I think we are getting a bit too philosophical on a matter which is
mainly terminology .
1. To quantify how similar two proteins are, one should best refer to
'percent identity'. Thats clear, correct and unambiguous.
2. One can also
- Dima Klenchin [EMAIL PROTECTED] wrote:
Having a generic dictionary definition is nice and dandy. However, in
the present context, the term 'homology' has a much more specific
meaning: it pertains to the having (or not) of a common ancestor.
Thus, it is a binary concept. (*)
But how
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