Re: [ccp4bb] Statistics differences

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Subject: Re: Statistics differences
From: Ronald E Stenkamp stenkamp {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-09-07

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Subject: Re: Statistics differences
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2007-09-07

Subject: Re: Statistics differences
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-09-07

Dear Jacob

The main reason why different programs produce different resutls is
that methods used in these programs are different.
For example refinement programs use different methods for scaling.
Some include bulk solvent a Babinet, some use
mask bulk slvent and some use anisotropic scaling others do not use.
Even for each parameterisation there are variations.
Fortunately for most of the cases the results are mathematically
equivalent and maps do not change too much.

Regards
Garib

On 7 Sep 2007, at 16:27, Jacob Keller wrote:

> Dear list,
>
> I have for some time now wondered why different programs output
> different statistics. A low FOM
> from program A might be much better than a high FOM from program B,
> and so on. I wonder why, then,
> considering that statistical measures are precisely, mathematically
> defined, how is there any
> discrepancy? I have also wondered whether people might prefer
> certain programs because they are
> statistically flattering. I think in my experience I have seen even
> statistics like Rfree to be
> different from different programs, I think even without any
> refinement--so should one use that
> program last, right before composing "Table I" for publication?
> That seems suspicious...
>
> Jacob Keller
>
>
>
> ==============Original message text===============
> On Fri, 07 Sep 2007 3:39:27 am CDT Andreas Kohl wrote:
>
> Dear all,
>
> we have currently two open postdoctoral positions in our
> department. We
> would very much appreciate it if you could bring this announcement to
> the attention of suitable candidates.
> All inquiries and applications should be send to:
>
> Prof. Pär Nordlund (par.nordlund@ki.se) or Dr. Said Eshaghi
> (said.eshaghi@ki.se)
>
> Andreas
>
>
> ######################################################################
> ##############
>
> Postdoctoral positions available at Karolinska Institutet, Sweden
>
> Two postdoctoral positions are available at the division of Biophysics
> in the department of Medical Biochemistry and Biophysics, at
> Karolinska
> Intitutet in Stockholm. The division is headed by Professor Pär
> Nordlund
> and is focused on functional characterization of proteins, primarily
> using X-ray crystallography. In addition, new technologies are being
> developed and improved as tools to enable high-throughput approaches
> within protein production. The group has a strong record in structure
> determination of soluble and membrane proteins. The laboratory is
> well-equipped with state-of-the-art instruments for protein production
> and crystallization.
>
> Currently, two postdoctoral positions are available in the membrane
> protein group, working with medically important proteins from
> different
> families, such as solute transporters, ion channels and enzymes:
> 1. Membrane protein chemistry/structural biology. The applicant should
> have strong background in recombinant membrane protein production
> in E.
> coli system, preferably with some experience in protein
> crystallization.
> The main topic is to develop new and improved methods for purification
> and crystallization of integral membrane proteins. Knowledge about
> X-ray
> crystallography is ideal but not a requirement. The successful
> candidate
> will be part of a dynamic team that is working on production,
> crystallization and structure determination of membrane proteins. The
> applicant must therefore have the ability to work as a team-player as
> well as independently. The position is initially announced for two
> years.
> 2. Membrane protein X-ray crystallography. The applicant should have a
> strong background in X-ray crystallography with a good track
> record. The
> main tasks are crystallization screening, crystal optimization, data
> collection and structure determination of integral membrane proteins.
> Previous experience with membrane proteins is ideal but not a
> requirement. The successful candidate will be part of a team that is
> working on production and crystallization of membrane proteins. The
> applicant must therefore have the ability to work as a team-player as
> well as independently. The position is initially announced for two
> years.
>
> Applicants should send a full CV, including a publication list,
> together
> with the name and contact details of three references to:
>
> Prof. Pär Nordlund (par.nordlund@ki.se) or Dr. Said Eshaghi
> (said.eshaghi@ki.se)
>
> ----------------------------------------------------------------------
> ---------------------------------------------
> Prof. Pär Nordlund
>
> Par.Nordlund@ki.se
> Institutionen för Medicinsk Biokemi och Biofysik (MBB)
> Karolinska Institutet, 171 77 Stockholm
> Biofysik
> ===========End of original message text===========
>
>
>
> ***********************************
> Jacob Keller
> Northwestern University
> 6541 N. Francisco #3
> Chicago IL 60645
> (847)491-2438
> j-keller2@northwestern.edu
> ***********************************
>
>
>
>

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CCP4bb <-- 2007 <-- September 2007 <-- 07 September 2007

Previous message:
Subject: Re: Statistics differences
From: Ronald E Stenkamp stenkamp {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-09-07

Next message:
Subject: Re: Statistics differences
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2007-09-07