[ccp4bb] column profile

[sajid akthar]

Hi all

If anyone have, please post the calibration profile for GE Sephacryl S100 26/60 
Hiprep column. Sorry I could not locate in the GE Healthcare site.

Thankx in advance

Sajid

Re: [ccp4bb] SCALA bugs in CCP4 6.3.0?

[David Waterman]

Hi Peter,

We're still working on the resolution of this bug. In the meantime you may
wish to replace 6.3.0's scala.exe with the one from 6.2.0, which is linked
to from the Windows Problems
pages.
Scala has not changed much between the two releases, only an increase in
the maximum number of allowed batches from 5000 to 1. If this limit is
a problem for you, then Phil's advice is to use Aimless instead.

Best regards

-- David


On 3 August 2012 19:02, Peter Goettig  wrote:

> In the Windows version of the new CCP4 release SCALA produces a summary
> table (same in the full text) that contains only some rudimentary data,
> such as
>
>   Overall  InnerShell
>  OuterShell
>   Low resolution limit   19.97 0.00  0.00
>   High resolution limit 3.00 0.00  0.00
>
>   Rmerge  0.000 0.000 0.000
>   Rmerge in top intensity bin0.115- -
>   Rmeas (within I+/I-)   0.000 0.000 0.000
>
>   aso
>
> while the final statement of SCALA is ** Normal termination **
>
> Has anyone else experienced similar problems and found a way to solve
> them? Otherwise, I would ask the developpers to take care of the bugs.
> However, the corresponding tables generated by AIMLESS contain the full
> information.
>
> Regards,
>
> Peter
>
>
> Peter Goettig
> Structural Biology
> University of Salzburg
> Billrothstrasse 11
> Salzburg, Austria
>

[ccp4bb] CC1/2, XDS and resolution cut off

[Marcus Fislage]

Dear all,

We have in our lab a data set collected and are discussing where to cut
the resolution for refinement. According to the work of Kai Diederichs
and Andy Karplus one should use CC 1/2 of 12.5% (in case it is
significant) to determine the highest resolution independent of the
I/sigI and R factor rules used earlier. But I would like to know if this
also counts for low completeness data?
The problem is that we have in the highest resolution shell an I/sigI of
4, a good cc1/2 but only a completeness of 30%. Which I guess means we
measured the high resolution data very accurate but not complete. Would
you still use the low complete data in the highest resolution shell or
should that be still a valid argument to cut your data towards lower
resolution?
My guess would be to use the data still even if the completeness drops,
since the data we measured is good and according to CC1/2 significant.
Are we right to do so or would you disagree?

Thanks for any input
Marcus

-- 
Marcus Fislage
Structural Biology Brussels
Vrije Universiteit Brussel
Department of Structural Biology, VIB
Oefenplein, Gebouw E
Pleinlaan 2,
1050 Brussel
Belgium
Tel: +32-2-629 18 51
Email : marcus.fisl...@vib-vub.be
Url: http://www.verseeslab.structuralbiology.be

Re: [ccp4bb] CC1/2, XDS and resolution cut off

[Ian Tickle]

Hi Marcus

I don't use CC(1/2) as a criterion for cut-off though I do keep an eye
on it.  It's not clear to me how you apply the CC(1/2) criterion when
the data are incomplete (as they invariably are).  Also there seems to
be some debate whether the cut-off should be at CC = 0.5 or much
lower, e.g. 0.125 representing the level of statistical significance,
as you suggest.  In the end I suspect it makes little difference.

Instead I use the average (I / sigma(I)) for all reflections, i.e.
including unmeasured for which I take (I / sigma(I)) = 0, as the
cut-off criterion with a cut-off value of 1.  This value allows for
the possibility that there will still be a significant fraction of
meaningful measurements in the shell, even if the majority may be
below the noise threshold.  This does make the tacit assumption that
the unmeasured reflections are distributed randomly in reciprocal
space, which is clearly not entirely true, but it's hard to see how
one could account for the non-random distribution.  Again, in any case
I find the exact resolution cut-off makes very little difference to
the maps, so it's really not worth arguing over!

It's easy to show that:

_all = shell_completeness * _measured

So low completeness shells automatically get cut by the 
criterion.

Cheers

-- Ian

On 6 August 2012 12:21, Marcus Fislage  wrote:
> Dear all,
>
> We have in our lab a data set collected and are discussing where to cut
> the resolution for refinement. According to the work of Kai Diederichs
> and Andy Karplus one should use CC 1/2 of 12.5% (in case it is
> significant) to determine the highest resolution independent of the
> I/sigI and R factor rules used earlier. But I would like to know if this
> also counts for low completeness data?
> The problem is that we have in the highest resolution shell an I/sigI of
> 4, a good cc1/2 but only a completeness of 30%. Which I guess means we
> measured the high resolution data very accurate but not complete. Would
> you still use the low complete data in the highest resolution shell or
> should that be still a valid argument to cut your data towards lower
> resolution?
> My guess would be to use the data still even if the completeness drops,
> since the data we measured is good and according to CC1/2 significant.
> Are we right to do so or would you disagree?
>
> Thanks for any input
> Marcus
>
> --
> Marcus Fislage
> Structural Biology Brussels
> Vrije Universiteit Brussel
> Department of Structural Biology, VIB
> Oefenplein, Gebouw E
> Pleinlaan 2,
> 1050 Brussel
> Belgium
> Tel: +32-2-629 18 51
> Email : marcus.fisl...@vib-vub.be
> Url: http://www.verseeslab.structuralbiology.be

Re: [ccp4bb] CC1/2, XDS and resolution cut off

[Edward A. Berry]

Ian Tickle wrote:


below the noise threshold.  This does make the tacit assumption that
the unmeasured reflections are distributed randomly in reciprocal
space, which is clearly not entirely true, but it's hard to see how
one could account for the non-random distribution.  Again, in any case


What about collecting in the corners of a square detector?
Due to the crystal diffracting better than expected  or
the need to sacrifice resolution for spot separation?

eab

Re: [ccp4bb] CC1/2, XDS and resolution cut off

[Edward A. Berry]

Oh - you meant how one could take  nonrandom distrubution
into account in the analysis-
funny how I always understand what someone meant after
i push send on an inappropriate reply

Edward A. Berry wrote:

Ian Tickle wrote:


below the noise threshold. This does make the tacit assumption that
the unmeasured reflections are distributed randomly in reciprocal
space, which is clearly not entirely true, but it's hard to see how
one could account for the non-random distribution. Again, in any case


What about collecting in the corners of a square detector?
Due to the crystal diffracting better than expected or
the need to sacrifice resolution for spot separation?

eab

Re: [ccp4bb] CC1/2, XDS and resolution cut off

[Ian Tickle]

Sorry yes you're quite right, I hadn't noticed the ambiguity of
'account for': 'take into account' would have been better.

-- Ian

On 6 August 2012 14:39, Edward A. Berry  wrote:
> Oh - you meant how one could take  nonrandom distrubution
> into account in the analysis-
> funny how I always understand what someone meant after
> i push send on an inappropriate reply
>
>
> Edward A. Berry wrote:
>>
>> Ian Tickle wrote:
>>
>>> below the noise threshold. This does make the tacit assumption that
>>> the unmeasured reflections are distributed randomly in reciprocal
>>> space, which is clearly not entirely true, but it's hard to see how
>>> one could account for the non-random distribution. Again, in any case
>>>
>> What about collecting in the corners of a square detector?
>> Due to the crystal diffracting better than expected or
>> the need to sacrifice resolution for spot separation?
>>
>> eab
>>
>

Re: [ccp4bb] CC1/2, XDS and resolution cut off

[Marcus Fislage]

Hello

> Edward A. Berry wrote:
> What about collecting in the corners of a square detector?
> Due to the crystal diffracting better than expected  or
> the need to sacrifice resolution for spot separation?

This is actually our reason that we have problem. The strategy initially
suggested lower resolution, but after we shot the crystal and analyzed
the data we could see diffraction way into the corners of the detector.


> Ian Tickle wrote:
> Instead I use the average (I / sigma(I)) for all reflections, i.e.
> including unmeasured for which I take (I / sigma(I)) = 0, as the
> cut-off criterion with a cut-off value of 1.

Do you think that this averaged I/sig I could also be transferred to a
averaged CC1/2 giving unobserved spots a CC1/2 of 0.
--> _all = shell_completeness * _measured?

Marcus

On Mo, 2012-08-06 at 09:33 -0400, Edward A. Berry wrote:
> Ian Tickle wrote:
> 
> > below the noise threshold.  This does make the tacit assumption that
> > the unmeasured reflections are distributed randomly in reciprocal
> > space, which is clearly not entirely true, but it's hard to see how
> > one could account for the non-random distribution.  Again, in any case
> >
> What about collecting in the corners of a square detector?
> Due to the crystal diffracting better than expected  or
> the need to sacrifice resolution for spot separation?
> 
> eab

Re: [ccp4bb] CC1/2, XDS and resolution cut off

[Ian Tickle]

> Do you think that this averaged I/sig I could also be transferred to a
> averaged CC1/2 giving unobserved spots a CC1/2 of 0.
> --> _all = shell_completeness * _measured?

Actually yes it did occur to me (just after I hit 'send') that that
would be just as valid (or invalid depending on ones POV!) a tactic as
the  one I suggested.  However since the ink is barely
dry on the K & D paper, it seemed somewhat premature to suggest
modifying their statistic! - and in any case it's still not clear to
me what is the consensus cut-off value for CC(1/2).

Cheers

-- Ian

[ccp4bb] not strictly crystallography-related

[Kay Diederichs]

Dear all,

a colleague needs a protein for a biophysical experiment. The 
requirement is that the protein "looks like a disk", and that it can be 
bought for a reasonable price.


Is anyone aware of a commercially available protein of disk-like shape? 
I am out of ideas of how to find this out myself, at least not with 
reasonable effort ...


thanks a lot,

Kay
--
Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
email: kay.diederi...@uni-konstanz.deTel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

This e-mail is digitally signed. If your e-mail client does not have the
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[ccp4bb] PPI-Net Young Researchers Meeting

[Thomas Edwards]

Dear CCP4bb,

A symposium on protein-protein interactions organised by young researchers from 
around the UK.
Will probably appeal to some from the UK, but obviously all welcome.
Please respond to the organising committee (yr2...@ppi-net.org) rather than to 
me.

Thanks
Ed




 This symposium aims to provide a platform for early career Protein-Protein 
Interaction researchers from a broad range of backgrounds to come together, 
share their work and discuss the latest research. In addition to our excellent 
guest speakers there will also be opportunities for young researchers to 
present their work through short talks and posters chosen from abstracts. 
Please submit your abstract when you register for the symposium.

Plenary Lecture: Paramjit Arora (NYU)

Invited speakers: Dan Davis (Imperial college); Chun-wa Chung (GSK).


Please register at ppi-net.org/events.

If you have any questions please contact us at yr2...@ppi-net.org


T.A.Edwards Ph.D.
Deputy Director Astbury Centre for Structural Molecular Biology
Lecturer in Biochemistry
Garstang 8.53d
University of Leeds, Leeds, LS2 9JT
Telephone: 0113 343 3031
http://www.fbs.leeds.ac.uk/staff/tae/
-- The universe is full of magical things patiently waiting for our wits to 
grow sharper.  ~Eden Phillpotts

[ccp4bb] Phenix.pdbtools Algorithm

[Scott Foy]

Hello everyone,

I am having a difficult time determining what type of geometry regularization 
algorithm is used in Phenix.pdbtools (e.g., least squares, maximum likelihood, 
energy minimization, etc.).  I would appreciate if anyone can clarify, as well 
as point me to the appropriate documentation. 

Thank you for your help.

Re: [ccp4bb] Phenix.pdbtools Algorithm

[Pavel Afonine]

Hi,

there is Phenix mailing list for questions like this (
http://phenix-online.org/).

This should answer your question:
http://cci.lbl.gov/publications/download/iucrcompcomm_aug2004.pdf

Pavel


On Mon, Aug 6, 2012 at 9:07 AM, Scott Foy  wrote:

> Hello everyone,
>
> I am having a difficult time determining what type of geometry
> regularization algorithm is used in Phenix.pdbtools (e.g., least squares,
> maximum likelihood, energy minimization, etc.).  I would appreciate if
> anyone can clarify, as well as point me to the appropriate documentation.
>
> Thank you for your help.
>

Re: [ccp4bb] CC1/2, XDS and resolution cut off

[Kay Diederichs]

Dear Marcus,

I have a few comments:
- we do not suggest any fixed value (like 0.125) for a CC1/2 cutoff. One reason 
why a fixed value should not be carved in stone is that future data processing 
and  refinement programs might extract more information from the weak data than 
current ones do. Another reason is that the significance of a given CC1/2 value 
depends on the number of pairs it is calculated from. Generally, we suggest to 
do paired refinements as a technique to validate that some cutoff is better 
than another. We really suggest you convince yourself (and 
colleagues/reviewers) of the value of your high-resolution data, by performing 
the comparison like we document in the paper (and its supporting online 
material which has all technical details!). 
- in the same way, you can can assess the value of your incomplete 
high-resolution shell. It is easy enough to do. I expect that you will see 
model improvement when you include the data. The general rule is: throwing away 
significant data is bad.
- CC1/2 is a better guide than  because the latter depends on the sigma 
estimate of the data processing program, and its adjustment by the scaling 
program. Different programs give (sometimes very) different sigma values.

Hope that helps,

Kay

On Mon, 6 Aug 2012 13:21:19 +0200, Marcus Fislage  
wrote:

>Dear all,
>
>We have in our lab a data set collected and are discussing where to cut
>the resolution for refinement. According to the work of Kai Diederichs
>and Andy Karplus one should use CC 1/2 of 12.5% (in case it is
>significant) to determine the highest resolution independent of the
>I/sigI and R factor rules used earlier. But I would like to know if this
>also counts for low completeness data?
>The problem is that we have in the highest resolution shell an I/sigI of
>4, a good cc1/2 but only a completeness of 30%. Which I guess means we
>measured the high resolution data very accurate but not complete. Would
>you still use the low complete data in the highest resolution shell or
>should that be still a valid argument to cut your data towards lower
>resolution?
>My guess would be to use the data still even if the completeness drops,
>since the data we measured is good and according to CC1/2 significant.
>Are we right to do so or would you disagree?
>
>Thanks for any input
>Marcus
>
>--
>Marcus Fislage
>Structural Biology Brussels
>Vrije Universiteit Brussel
>Department of Structural Biology, VIB
>Oefenplein, Gebouw E
>Pleinlaan 2,
>1050 Brussel
>Belgium
>Tel: +32-2-629 18 51
>Email : marcus.fisl...@vib-vub.be
>Url: http://www.verseeslab.structuralbiology.be