Hi Ed,
I didn't see any way to refine with no free set in phenix, even with
> least-squares target function,
xray_data.r_free_flags.ignore_r_free_flags=true
will make phenix.refine use all reflections. Obviously, reported
Rwork=Rfree in this case. This works for any available refinement target.
Also it may have worked more as expected if I let it get a little farther away
from
the starting point before trying to return. If there is a circle of confusions
of points
in parameter space that give the same target function value (due to nearly
perfect compensation
of parameters in a small r
I didn't think about that. Yes, weights were being re-optimized each time.
On 01/04/2015 04:39 PM, Ian Tickle wrote:
Hi Ed
The R, Rfree and RMSDs will all depend to some extent on the Wa factor and this
may depend on the starting point, assuming of course that the program is
automatically adj
Hi Ed
The R, Rfree and RMSDs will all depend to some extent on the Wa factor and
this may depend on the starting point, assuming of course that the program
is automatically adjusting the Wa factor according to some criterion (you
didn't say). The obvious way to check this would be to keep the Wa
On 11/25/2014 01:41 PM, Tim Gruene wrote:
Hi Ed,
it is an easy excercise to show that theory (according to "by
definition") and reality greatly diverge - refinement is too complex to
get back to exactly the same structure. Maybe because one often does not
reach convergence, no matter how many c
Dear Ian,
it seems we have drifted a bit from the original thread. Maybe this is a
good point to allow the discussion to settle.
Best regards,
Tim
On 11/29/2014 01:41 PM, Ian Tickle wrote:
> Hi Tim
>
> On 29 November 2014 at 10:16, Tim Gruene wrote:
>
> I want to improve
>> crystallographic m
Hi Tim
On 29 November 2014 at 10:16, Tim Gruene wrote:
I want to improve
> crystallographic methods because people who solve crystal structures
> want an answer to a biological or chemical or physical question rather
> than because they enjoy watching the realisation of a mathematical
> definiti
Hi Pavel,
I think your email highlights one of the differences between us and one
of the reasons for this discussion:
I am a scientist, not a mathematician - I want to improve
crystallographic methods because people who solve crystal structures
want an answer to a biological or chemical or physic
Hi Tim,
your examples are valid and valuable, and clearly exemplify existing
problems, limitations as well as common misconceptions.
However, if you follow mathematics and strict definitions thereof, then
crystallographic structure refinement is nothing but an optimization
problem that, fundament
On 28 November 2014 at 19:40, Tim Gruene wrote:
> Where freedom is given, liberties are
> taken' by Kleywegt and Jones
>
Tim
First to summarise the correct procedure:
One performs optimisations with one of more starting models. By 'model' I
mean here the mathematical model which includes no
Dear Pavel,
there is a beautiful paper called 'Where freedom is given, liberties are
taken' by Kleywegt and Jones, but also a wide variety of articles that
(fortunately) fought hard for the introduction of Rfree to the
(macro-)crystallographic community.
In there is mentioned the threading of an
Hi Tim,
you don't necessarily want to find the global minimum (...)
this contradicts the definition of crystallographic structure refinement.
If finding the global minimum is not what you ultimately want then either
the refinement target or model parameterization are poor.
Clearly, given comple
Dear Ian,
On Fri, Nov 28, 2014 at 11:26:03AM +, Ian Tickle wrote:
> [...] Overfitting has nothing to do with whether or not the refinement is at
> the
> global (or local) minimum. [...]
I don't think I said that.
> Let's assume for a moment that you are right and optimisations should be
>
Tim,
Overfitting has nothing to do with whether or not the refinement is at the
global (or local) minimum. You can predict how much a model will be
overfitted before you even start the refinement, because it has everything
to do with choices you made or were forced upon you right at the beginning
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Dear Jacob,
you don't necessarily want to find the global minimum - the global
minimum of the target function might be an overfitted set of parameters.
At low resolution the (local) minimum you do want to reach may not be
very sharp. This is best illu
Greetings to ccp4bb readers!
This is a long-delayed reply to requests that I received after I
posted an observation on the ccp4bb almost three years ago. (I think it was
early 2012). The paper had not yet been published (pending finalization of
experiments unrelated to structural biology) a
>We just had a chance to read this most interesting discussion. We would agree
with Ian that jiggling or SA refinement may not be needed if refinement can in
fact be run to convergence. However, this will be difficult to achieve for large
structures, especially when only moderate to low resolution
We just had a chance to read this most interesting discussion. We would agree
with Ian that jiggling or SA refinement may not be needed if refinement can in
fact be run to convergence. However, this will be difficult to achieve for
large
structures, especially when only moderate to low resoluti
Hello guys,
There is too much text in this discussion to respond to every part of it. Apart
from “jiggle” in certain software like PHENIX and I believe in X-PLOR
derivatives the word “shake” means the same. In the “MAIN” environment I use
the word “kick” to randomly distort coordinates. It's fi
arlsberg Laboratory
>> Gamle Carlsberg Vej 10
>> DK-1799 Copenhagen V
>> Denmark
>>
>> Tlf +45 3327 5332
>> Email josea.cuesta.se...@carlsberglab.dk
>>
>>
>>
>> -Original Message-
>> From:
> Tlf +45 3327 5332
> Email josea.cuesta.se...@carlsberglab.dk
>
>
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim
> Gruene
> Sent: Tuesday, November 25, 2014 7:41 PM
> To: CCP4
carlsberglab.dk
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene
Sent: Tuesday, November 25, 2014 7:41 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Free Reflections as Percent and not a Number
Hi Ed,
it is an easy excerci
Hi Ed,
it is an easy excercise to show that theory (according to "by
definition") and reality greatly diverge - refinement is too complex to
get back to exactly the same structure. Maybe because one often does not
reach convergence, no matter how many cycles of refinement you run.
Best,
Tim
On
provided the jiggling keeps the structure inside the convergence radius of
refinement, then by definition the refinement will produce the same result
irrespective of the starting point (i.e. jiggled or not). If the jiggling
takes the structure outside the radius of convergence then the origina
Dear CCP4ers,
I can only second Ian's observation: also in my experience, it is
sufficient to run enough cycles of conventional refinement to get rid of
any previous bias after changing the free set of reflections, or
omitting parts of the structure.
I don't have the results anymore, but if my
Dear All
I'd like to raise the question again of whether any of this 'jiggling'
(i.e. addition of random noise to the co-ordinates) is really necessary
anyway, notwithstanding Dale's valid point that even if it were necessary,
jiggling in its present incarnation is unlikely to work because it's
un
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On 11/21/2014 12:35 AM, "F.Xavier Gomis-Rüth" wrote:
>
>
> As to the convenience of carrying over a test set to another
> dataset, Eleanor made a suggestion to circumvent this necessity
> some time ago: pass your coordinates through pdbset and add
To:* Keller, Jacob
> *Cc:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Free Reflections as Percent and not a Number
>
>
>
> Oh I see, I though the answer follows from that. Fraction is better (or
> may be fraction with a cap). Hardwiring a number may not always work. Fo
: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Free Reflections as Percent and not a Number
>
> Hello,
>
> choice of the size of free (or test, whatever you like to call them)
> reflections is important for three different purposes:
>
> - estimation of parameters for ML ta
lto:pafon...@gmail.com>]
Sent: Friday, November 21, 2014 11:02 AM
To: Keller, Jacob
Cc: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Free Reflections as Percent and not a Number
Hello,
choice of the size of free (or test, whatever you like to call them)
reflection
14 11:02 AM
> *To:* Keller, Jacob
> *Cc:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Free Reflections as Percent and not a Number
>
>
>
> Hello,
>
>
>
> choice of the size of free (or test, whatever you like to call them)
> reflections is important for three dif
Reflections as Percent and not a Number
Hello,
choice of the size of free (or test, whatever you like to call them)
reflections is important for three different purposes:
- estimation of parameters for ML target for refinement;
- map calculation (coefficients m&D in 2mFo-DFc or mFo-DFc map
Hello,
choice of the size of free (or test, whatever you like to call them)
reflections is important for three different purposes:
- estimation of parameters for ML target for refinement;
- map calculation (coefficients m&D in 2mFo-DFc or mFo-DFc map are
calculated using test reflections);
- vali
As pointed out by a reviewer recently, this has been object of study in
the past when Gerard K. and Axel B. found that actually 500-700
reflections should suffice to monitor Rfree with sufficient precision.
I guess everybody will agree on that we want to have the best refined
structure and this
Using a percentage might be justified as a trade-off between having ample free
reflections for statistics and cutting too deeply into your completeness of
working reflections for refinement.
It seems to be generally agreed that 2000 free reflections is sufficient to
guide your choice of refine
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I think is is just a matter of convenience when changing resolution
limits and trying to use the same test set. If you always want 1000
but your next crystal doesn't diffract as well you have to select a
few more reflections and they will have bee
Dear Crystallographers,
I thought that for reliable values for Rfree, one needs only to satisfy
counting statistics, and therefore using at most a couple thousand reflections
should always be sufficient. Almost always, however, some seemingly-arbitrary
percentage of reflections is used, say 5%.
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