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 orien
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 wrote:
>
> I apologize if this question this question has been asked before but I still
> need help finding an answer to the following.
>
> I am
urce, but not everything is destined to
> be open source).
>
> cheers, tom
>
> Tom Peat
> Proteins Group
> Biomedical Program, CSIRO
> 343 Royal Parade
> Parkville, VIC, 3052
> +613 9662 7304
> +614 57 539 419
> tom.p...@csiro.au
>
> ______
On May 12, 2015, at 3:19 PM, Robbie Joosten 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 to replicate and verify
On Jul 13, 2013, at 5:36 PM, Ian Tickle wrote:
> On 8 July 2013 18:29, Douglas Theobald wrote:
>
> > > Photons only have a Poisson distribution when you can count them:
> > > QM says it meaningless to talk about something you can't observe.
> >
> > A
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 true
On Jul 7, 2013, at 1:44 PM, Ian Tickle wrote:
>
> On 29 June 2013 01:13, Douglas Theobald
> 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 wrote:
> On 22 June 2013 19:39, Douglas Theobald 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 in
>> th
significantly?
>
> 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 mode
On Sat, Jun 22, 2013 at 1:56 PM, Ian Tickle wrote:
> On 22 June 2013 18:04, Douglas Theobald 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 noise an
On Sat, Jun 22, 2013 at 1:04 PM, Douglas Theobald wrote:
> 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 Ispot
he only reasonable model that gives Ispot-Iback as an
estimate of Itrue. This is why I claim that using Ispot-Iback as an
estimate of Itrue, even when Ispot wrote:
> On 21 June 2013 19:45, Douglas Theobald wrote:
>
>>
>> The current way of doing things is summarized by Ed&#x
, 2013 at 11:34 AM, Douglas Theobald
> 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
On Jun 21, 2013, at 2:48 PM, Ed Pozharski 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 up with. I
question is would it make any difference in the end compared
> with the 'post-correction' we're doing now?
>
> Cheers
>
> -- Ian
>
>
> On 20 June 2013 18:14, Douglas Theobald wrote:
> I still don't see how you get a negative intensity from t
hence
negativity. The Ispot-Iback=Iobs does not follow from a Poisson assumption.
On Jun 21, 2013, at 1:13 PM, Ian Tickle wrote:
> On 21 June 2013 17:10, Douglas Theobald wrote:
>> Yes there is. The only way you can get a negative estimate is to make
>> unphysical assumptions.
On Jun 21, 2013, at 8:36 AM, Ed Pozharski 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 - th
wrong!
>
> Kay
>
> Am 20.06.13 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 i
mber is more complicated than the amplitude ML formula,
> or is not an analytical formula at all, but maybe somebody knows better).
>
> best,
>
> Kay
>
>
> On Thu, 20 Jun 2013 13:14:28 -0400, Douglas Theobald
> wrote:
>
>> I still don't see how you g
and Biotechnology,
> 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
>
&g
> Andrew
>
>
> On 20 Jun 2013, at 11:49, Douglas Theobald 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?
>>
>>
&g
d a derived esd since they can't be
> formally 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 a
se the F based R values are lower
> when you refine against F's, that means nothing.
>
> If we could get the PDB to report both the F and I based R values
> for all models maybe we could get a start toward moving to intensity
> refinement.
>
> Dale Tronrud
>
&g
tly assume a Gaussian, right?
>
> If we could get the PDB to report both the F and I based R 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
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 wrote:
>> As a maybe better alternative, we should (once again) consider to refine
>> again
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 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 interest to macr
;> Bart Hazes (I think) suggested a statistic called "effective
>> resolution" which is the resolution to which a complete dataset
>> would have the number of reflectionin your dataset, and we
>> reported this, which came out to something like 1.75.
>>
>>
x27;ll ask anyway - what does CC1/2=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 K&K paper
Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University 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
>
>
>
>
>
>
gt; and the resolution was really 1.9 A? And Rsymm 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. d
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
On Nov 16, 2012, at 10:27 AM, Enrico Stura 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 crystals wi
ed to
>> make nature follow the semantics of your programming language but can adjust
>> your code to the problem you are tackling.
>> The question you post would nicely fit into a first year's course on C++
>> (and of
>> course can all be answered very elegantly).
&g
numbers fulfil the axioms of a
> vector space is applicable only in the case of a 1D vector space, and
> therefore is not relevant. My original observation which started this
> thread was intended to be general one, not for a particular special
> case.
>
> -- Ian
>
> On Fri, O
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.
ector
>
>
> Ganesh
>
>
>
> On Fri, 15 Oct 2010 11:20:04 -0400, Douglas Theobald
> wrote:
>> As usual, the Omniscient Wikipedia does a pretty good job of giving
>> the standard mathematical definition of a "vector":
>>
>> http://en.wik
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,
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 seque
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 i
s is
> convenient.
>
> Therefore, stating alpha = 15 (without anything else) is perfectly valid for
> an angle.
>
> Marc
>
>
>
> Quoting Douglas Theobald :
>
>> Argument from authority, from the omniscient Wikipedia:
>>
>> http://en.wikipe
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
James,
Graeme is right. While does indeed (approximately) follow a
Gaussian, <|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 norm
- "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-h
- "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. (*)
>
- "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
- "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,
This also depends on how you have set up the statistical problem, and
what statistical philosophy you adhere to. If you have a hierarchical
model (which can fit in a likelihood paradigm) or you are a Bayesian,
then all of these values are random variables.
This argument is mostly just sema
IANAL, but I have been advised by lawyers in highly similar situations.
Publicly accusing someone of either criminal fraud and/or academic
fraud is serious business, and it is certainly something that could
get you prosecuted for criminal libel, as the accusation will likely
have the effect
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