[ccp4bb] Postdoctoral Position in Structural Biology

[김 경규]

Postdoctoral Position in Structural Biology 

Sungkyunkwan University School of Medicine

Samsung Biomedical Research Institute

Suwon, Korea

 

A post-doctoral position in structure biology of the cell surface receptors and 
ubiquitin proteases is immediately available at Sungkyunkwan University School 
of Medicine/Samsung Biomedical Research institute in Suwon, Korea. The 
production of large quantities of proteins was already established using 
bacterial or mammalian cell expression systems. This project will be 
complemented by functional studies using biochemistry, molecular biology and 
cell biology as well as alternative biophysical techniques including NMR and 
SAXS. Hence, the applicant will be exposed to a variety of disciplines.

 

The unit is equipped with an automatic crystallization robot, an X-ray facility 
comprising a Rigaku rotating anode X-ray generator, an R-Axis IV dual imaging 
plate detector with a confocal mirror optics, and an X-stream cryo-cooling 
system. Recent crystallographic studies in the lab also have utilized 
synchrotron sources in Pohang Synchrotron Light Source, Korea and in Spring-8 
and Photon Factory, Japan. In the same building, there are excellent facilities 
for other biological experiments. 

 

The applicant should have a PhD in crystallography or related research area 
such as chemistry, biophysics, biochemistry or molecular biology. However, 
experiences in protein biochemistry and crystallography are highly preferred. 
Interested applicants please send a CV with the names of two references to the 
address below. E-mail inquiries about the position are welcome. Review of 
applications begins in the middle of Dec, 2008 and will continue until the 
position is filled. 

 

Suwon is located in about half hour driving distance from Seoul, the capital 
city of Korea and the one of the most developed cities in the world. Lab 
information will be found in http://smsb1.skku.ac.kr.

 

Kyeong Kyu Kim, Ph. D.

Professor

Department of Molecular Cell Biology

Samsung Biomedical Research Institute

Sungkyunkwan University School of Medicine

Suwon 440-746, Korea

tel : 82-31-299-6136

fax : 82-31-299-6159

e-mail : [EMAIL PROTECTED]

web: http://smsb1.skku.ac.kr  

 

Re: [ccp4bb] MR with DNA

[Phoebe Rice]

There are certainly reasons why it shouldn't work: 
 - the protein may alter the structure - even if its not a
"big bender", it may tweak the groove widths or introduce a
shallow overall bend in a long binding site
 - the phosphates move the most between DNA structures, and
unfortunately they also scatter the most.

That said, it really can work!  My student got very nice
results using phaser and model-built 5-bp chunks of duplex
DNA.  Using short chunks avoided the problem of an unknown
overall bend.  It didn't find everything, but it certainly
helped us get a toehold on the phase problem.

So go for it.

   Phoebe



 Original message 
>Date: Fri, 5 Dec 2008 16:32:14 -0600
>From: UT MDACC <[EMAIL PROTECTED]>  
>Subject: [ccp4bb] MR with DNA  
>To: CCP4BB@JISCMAIL.AC.UK
>
>Is there any existing example about anybody trying to do
molecular
>replacement for a protein-DNA complex using any B-DNA from
the pdb database.
>I am wondering 1) whether it is doable 2)if it is not doable,
why not?
>Thanks in advance for the feedback
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123

RNA is really nifty
DNA is over fifty
We have put them 
  both in one book
Please do take a 
  really good look
http://www.rsc.org/shop/books/2008/9780854042722.asp

[ccp4bb] Postdoctoral Research Positions

[L. Wayne Schultz]

Hauptman-Woodward Medical Research Institute
Virus-Host Interactions and Structures
 
The laboratories of Drs. L. Wayne Schultz and Tim Umland are seeking highly
motivated individuals to participate in a joint interdisciplinary research
project investigating virus-host protein-protein interactions. Two positions
at the Post-Doctoral level are expected to be hired in early 2009.
Competitive applicants should have demonstrated scientific productivity and
innovation at the graduate level, and should have a Ph.D., M.D., or similar
degree. Experience working with mammalian cell culture based assays, virus
replicon systems, and/or detection of protein-protein interactions is highly
desirable. Applicants with previous post-doctoral experience will be
considered, but such experience is not necessary. During the course of the
project, the successful applicant will have an opportunity to learn
structural biology techniques (X-ray crystallography, small angle X-ray
scattering), but previous experience in these techniques is not required.
Salary and benefits are competitive, and the appointment may be for up to 3
years.
 
The Hauptman-Woodward Medical Research Institute (HWI) is a private,
not-for-profit organization studying the structures and functions of
macromolecules of biomedical interest. Additionally, HWI houses the
Department of Structural Biology of the State University of New York at
Buffalo's School of Medicine and Biomedical Sciences. HWI is part of the
Buffalo-Niagara Medical Campus, a consortium of research, clinical, and
educational institutions founded to cultivate a world-class medical campus
in state-of-the art facilities in downtown Buffalo, NY, USA.
 
To apply for a post-doctoral position, please send your CV and the names of
three references to Drs. Schultz ([EMAIL PROTECTED]) and Umland
([EMAIL PROTECTED]).
 
Please visit the web site for the Laboratory for the Study of Infectious
Diseases (LSID) for additional information: http://labs.hwi.buffalo.edu/lsid
 
The Hauptman-Woodward Medical Research Institute is an equal opportunity
employer.
 

[ccp4bb] high brilliance Rigaku system available (FR-D gen. /R-Axis IV ++ detector)

[Erin Curry]

Hi all,
We have available a complete Rigaku crystallography system, purchased in 
2002.  It includes a high-brilliance FR-D generator, an R-Axis IV++ detector, 
Mirror Confocal Purple optics, X-Stream 2000, Haskris chiller, and all 
accompanying accessories and software.  Please contact us for more 
information.
Thanks,
[EMAIL PROTECTED]
(650) 804-7008

Re: [ccp4bb] Modeling residues with very poor density

[Pavel Afonine]

This might help:

Acta Cryst. (1997). D53, 540-543   
Local Improvement of Electron-Density Maps


Pavel.

PS> It will be implemented in PHENIX sometime in future, but for the 
moment you will need to so some scripting.



On 12/8/2008 11:08 AM, Andy Millston wrote:
I am trying to build a model of a 6 Da protein from the 
diffraction data collected at 2.0 A resolution. There is a 10-residue 
stretch that has such bad electron density that even at 0.4 sigma 
level one can hardly see any well defined density for residues with 
long side chains.


My question is: are such poorly defined regions left unmodeled in 
protein structures? Or is it conventional to model the whole chain no 
matter how poor the density? The region in question is in the middle 
of the chain and has several long side chain residues - both charged 
and uncharged.


AM

[ccp4bb] Modeling residues with very poor density

[Andy Millston]

I am trying to build a model of a 6 Da protein from the diffraction data 
collected at 2.0 A resolution. There is a 10-residue stretch that has such bad 
electron density that even at 0.4 sigma level one can hardly see any well 
defined density for residues with long side chains. 

My question is: are such poorly defined regions left unmodeled in protein 
structures? Or is it conventional to model the whole chain no matter how poor 
the density? The region in question is in the middle of the chain and has 
several long side chain residues - both charged and uncharged.

AM


  

Re: [ccp4bb] AW: [ccp4bb] suggestions for UV spectrometer

[Edward Snell]

Getting even further off topic, we had a Nanodrop demo for trial shortly
after hearing that a significant number of crystallization groups were
using them. I won't go into the trial details, but I'd be interested in
hearing from people (via email rather then the ccp4 postings) who did
systematic trials in comparison to more conventional spectrometers;
especially concerning the accuracy and reproducibility. The ease of use
was very nice but we did not buy one.

Thanks,

Eddie.

Edward Snell Ph.D.
Assistant Prof. Department of Structural Biology, SUNY Buffalo,
Hauptman-Woodward Medical Research Institute
700 Ellicott Street, Buffalo, NY 14203-1102
Phone: (716) 898 8631 Fax: (716) 898 8660
Email: [EMAIL PROTECTED]  Telepathy: 42.2 GHz
 
Heisenberg was probably here!
 

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Jose Antonio Cuesta-Seijo
Sent: Monday, December 08, 2008 12:54 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] suggestions for UV spectrometer

I also have to come in defense of the nanodrop here.
I have measured up to A280 = 98 and the curve is always reasonably  
smooth, spikes normally mean that bubbles have formed. And "proper  
cleaning" seems to be rubbing with a kimwipe three or four times  
after each drop. If the last user does not clean after the last  
measurement, then things will dry up in the pedestals and that can of  
course be a problem. Also bubbles do not form if you are careful. I  
always use 2uL, 1uL can be too little, and even with 20% detergent I  
get a column and no bubbles nearly every time. You have to pipet  
carefully and lower the lever slowly (think of a vinyl record here).  
For tricky samples, use 2.2uL instead. A bubble might still form  
occasionally, but looking at the spectrum will quickly tell you that  
something went wrong.

Cheers,

Jose.

**
Jose Antonio Cuesta-Seijo
Cancer Genomics and Proteomics
Ontario Cancer Institute, UHN
MaRS TMDT Room 4-902M
101 College Street
M5G 1L7 Toronto, ON, Canada
Phone:  (416)581-7544
Fax: (416)581-7562
email: [EMAIL PROTECTED]
**


On Dec 5, 2008, at 7:00 PM, wangsa tirta ismaya wrote:

> Dear all,
>
> Thanks a lot for raising the issue with the not reproducibility of  
> protein measurement with Nanodrop. We use the instrument as a  
> workhorse in the lab. Indeed, recently I observed that the protein  
> concentration suggested by Nanodrop is sometimes differ to the  
> usual colorimetric measurement (Bradford method, measured with our  
> Pharmacia's Ultrospec 2000 spectrometer). Since the cell in  
> Nanodrop is very small, could it be due to the homogeneity of the  
> sample in the cell? Also what I have observed, we have to be sure  
> that the cell is cleaned properly before use. Another thing is, at  
> high protein concentration I obtained noisy absorption curve at the  
> peak (like a seismograf ) thus the protein concentration  
> measured is doubtful, I have to dilute the sample to have good  
> curve (thank God it requires only 2 mikroliter for a measurement).  
> Well, I think nanodrop is a good, fast, and powerful instrument,  
> however it would be better if we established a reference of our  
> daily practice to a normal spectrometer measurement.
>
> cheers,
>
>
> Wangsa
>
> 2008/12/5 Martin Hallberg <[EMAIL PROTECTED]>
> Which brings us back to the Hellma "TrayCell" solution where you  
> can, from the same spectrometer, have both the cuvette option and  
> the quickness of the NanoDrop/NanoVue system.
>
> Anyone that can comment on the performance of the TrayCell from  
> Hellma?
>
> Cheers,
>
> Martin
>
>
> On Dec 5, 2008, at 9:06 AM, Gregor Witte wrote:
>
> Agree!
> I think for crystallographic use the nanodrop is perfectly okay to  
> see if the protein is 5mg/ml or 30mg/ml. But in fact I also do not  
> trust our instrument if it comes to more important issues like  
> preparing solutions for titrations or assays. And due to the small  
> pathlength I do not trust absorptions of small concentrated samples  
> at all. I always prefer a "real" 2-beam spectrophotometer  
> (monochromators) with a quarz-cuvette and a nice pathlength. Of  
> course, you cannot reliably measure solutions exceeding Abs 1 or  
> maybe 1.5 OD in a spectrophotometer with 1cm pathlength.
>
> There's also one quite strange thing about the nanodrop - they sell  
> the "calibration check solution" (which is some kind of yellow  
> chromate-solution with known absorption), then you check your  
> nanodrop with it and maybe find out that it's off to some certain  
> extend: But then you're stuck(!), because you cannot calibrate it  
> on your own. I guess it would be quite easy to integrate a  
> calibration-option into the software, but at the moment the  
> instrument tells you "calibration failure" and you have to call the  
> service guys who then carry it home and calibrate it by t

[ccp4bb] Postdoctoral Associate Positions in Structural Biology

[Xiaorui Chen]

Postdoctoral Associate Positions in Structural Biology

Two Postdoctoral Associate positions are immediately available in the
Department of Biochemistry and Molecular Biology at Baylor College of
Medicine.  The first position is to focus on structural and functional
studies of influenza virus.  The second position is on structural and
functional studies of complexes involved in epigenetic silencing.  Both
positions employ techniques such as biochemistry, molecular biology, tissue
cell culture and X-ray crystallography, and will have the opportunity to
expose to state-of-the-art computational techniques and drug discovery.  The
minimum requirement is a doctoral degree in biochemistry, protein chemistry
or other related fields.  Prior experience in structural biology is not
required but is encouraged.  The successful applicant must be
self-motivated, enthusiastic and highly devoted.  Competitive salary and
fringe benefit will be provided. 

Baylor College of Medicine is located in the Texas Medical Center, Houston,
TX.  Houston is ranked the top #1 on Kiplinger's 2008 Best Cities.  It is
the fourth most populous city in the United States, and an international
city that is a leader in the arts, education, and health care.  

Interested individuals should submit a CV, a cover letter, and names of
three referees to: 

Qinghua Wang, Ph.D., Assistant Professor
Department of Biochemistry and Molecular Biology
Baylor College of Medicine
One Baylor Plaza, BCM-125
Houston, TX 77030
Email: [EMAIL PROTECTED]


Baylor College of Medicine is an Equal Opportunity/ 
Affirmative Action/and Equal Access Employer

Re: [ccp4bb] AW: [ccp4bb] suggestions for UV spectrometer

[Jose Antonio Cuesta-Seijo]

I also have to come in defense of the nanodrop here.
I have measured up to A280 = 98 and the curve is always reasonably  
smooth, spikes normally mean that bubbles have formed. And "proper  
cleaning" seems to be rubbing with a kimwipe three or four times  
after each drop. If the last user does not clean after the last  
measurement, then things will dry up in the pedestals and that can of  
course be a problem. Also bubbles do not form if you are careful. I  
always use 2uL, 1uL can be too little, and even with 20% detergent I  
get a column and no bubbles nearly every time. You have to pipet  
carefully and lower the lever slowly (think of a vinyl record here).  
For tricky samples, use 2.2uL instead. A bubble might still form  
occasionally, but looking at the spectrum will quickly tell you that  
something went wrong.


Cheers,

Jose.

**
Jose Antonio Cuesta-Seijo
Cancer Genomics and Proteomics
Ontario Cancer Institute, UHN
MaRS TMDT Room 4-902M
101 College Street
M5G 1L7 Toronto, ON, Canada
Phone:  (416)581-7544
Fax: (416)581-7562
email: [EMAIL PROTECTED]
**


On Dec 5, 2008, at 7:00 PM, wangsa tirta ismaya wrote:


Dear all,

Thanks a lot for raising the issue with the not reproducibility of  
protein measurement with Nanodrop. We use the instrument as a  
workhorse in the lab. Indeed, recently I observed that the protein  
concentration suggested by Nanodrop is sometimes differ to the  
usual colorimetric measurement (Bradford method, measured with our  
Pharmacia's Ultrospec 2000 spectrometer). Since the cell in  
Nanodrop is very small, could it be due to the homogeneity of the  
sample in the cell? Also what I have observed, we have to be sure  
that the cell is cleaned properly before use. Another thing is, at  
high protein concentration I obtained noisy absorption curve at the  
peak (like a seismograf ) thus the protein concentration  
measured is doubtful, I have to dilute the sample to have good  
curve (thank God it requires only 2 mikroliter for a measurement).  
Well, I think nanodrop is a good, fast, and powerful instrument,  
however it would be better if we established a reference of our  
daily practice to a normal spectrometer measurement.


cheers,


Wangsa

2008/12/5 Martin Hallberg <[EMAIL PROTECTED]>
Which brings us back to the Hellma "TrayCell" solution where you  
can, from the same spectrometer, have both the cuvette option and  
the quickness of the NanoDrop/NanoVue system.


Anyone that can comment on the performance of the TrayCell from  
Hellma?


Cheers,

Martin


On Dec 5, 2008, at 9:06 AM, Gregor Witte wrote:

Agree!
I think for crystallographic use the nanodrop is perfectly okay to  
see if the protein is 5mg/ml or 30mg/ml. But in fact I also do not  
trust our instrument if it comes to more important issues like  
preparing solutions for titrations or assays. And due to the small  
pathlength I do not trust absorptions of small concentrated samples  
at all. I always prefer a "real" 2-beam spectrophotometer  
(monochromators) with a quarz-cuvette and a nice pathlength. Of  
course, you cannot reliably measure solutions exceeding Abs 1 or  
maybe 1.5 OD in a spectrophotometer with 1cm pathlength.


There's also one quite strange thing about the nanodrop – they sell  
the "calibration check solution" (which is some kind of yellow  
chromate-solution with known absorption), then you check your  
nanodrop with it and maybe find out that it's off to some certain  
extend: But then you're stuck(!), because you cannot calibrate it  
on your own. I guess it would be quite easy to integrate a  
calibration-option into the software, but at the moment the  
instrument tells you "calibration failure" and you have to call the  
service guys who then carry it home and calibrate it by turning of  
the two small screws at the top of it and then glue them with  
locktite.
Anyway, at least for our mid to high concentrated samples the  
nanodrop is not showing large fluctuations so we are happy with it.  
But everyone using a nanodrop should check it from time to time –  
as I found out that ours was off more than 20% at one day - which  
raised some trouble of course…


Cheers,

Gregor


Von: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Im Auftrag  
von Filip Van Petegem

Gesendet: Donnerstag, 4. Dezember 2008 22:20
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] suggestions for UV spectrometer

I want to add I absotely hate the nanodrop.  We've had a demo for  
it, and found the readouts to be very unreliable.  Fluctuations of  
20% and more. Just leaving the same drop in and measuring the  
sample multiple times gives different values (going in both  
directions, so not only due to evaportations). Sure, it's easy and  
fast, and maybe good to have a rough idea about your protein  
concentration, but I would never want to use it for exact  
measurements such as needed for e.g. a CD or an ITC instrument.  

Re: [ccp4bb] suggestions for UV spectrometer

[Pius Padayatti]

nanodrop system is wonderful. it helps very much in solutions with
high interference from detergents etc etc.

i highly receommend nanodrop specs

PSP

On Thu, Dec 4, 2008 at 10:16 AM, Tim Gruene <[EMAIL PROTECTED]> wrote:
> Dear all,
>
> we would like to purchase a UV spectrometer for measuring protein
> concentrations (280nm), and I would like to here your comments and
> especially recommendations.
>
> We don't need anything fancy, a small, fast device would be sufficient.
>
> Tim
>
>
> --
> Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>



-- 
Pius S Padayatti
Scientist,
Polgenix, Inc.
11000 Cedar Ave, Suite 260
Cleveland, OH 44106
Phone: 216-658-4528
Fax: 216-658-4529

Re: [ccp4bb] meaning of R free of perfect twin

[George M. Sheldrick]

A good compromise in the case of suspected perfect merohedral twinning
is to select the free R reflections using thin shells. Since the twin
related reflections have the same sin(theta)/lambda values they will
not be split over the working and reference sets. XPREP offers this
option. A disadvantage is the the maps may not be quite as good as
when the free R reflections are selected randomaly.

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582


On Mon, 8 Dec 2008, Eleanor Dodson wrote:

> you need to select the Free R in the highest possible Laue group , then use
> cad to extend this to all reflections in the chosen point group. This is best
> done  immediately post-truncate..
> 
> eg if you twinning operator is k,h,-l, then if
> 1,2, 3 is assigned to the free set so should 2, 1, -3 be.
> 
> PHENIX.xtriage does it properly
> 
> REFMAC does not use it properly I dont think, but maybe that has been fixed..
> 
> Eleanor
> 
> Serge Cohen wrote:
> > -BEGIN PGP SIGNED MESSAGE-
> > Hash: SHA1
> >
> > I guess the independence is mostly depending on how you select the
> > reflection that lie in the free-set.
> >
> > If (from the beginning) you select reflections that are related by the twin
> > operator to be both in the free-set you keep the "independence" of the
> > free-set.
> >
> > Serge.
> >
> > Le 5 déc. 08 à 13:50, Agnieszka Kiliszek a écrit :
> >
> > > Hi,
> > >
> > > What is the meaning of R free of perfect twin? Shelxl counts it but it
> > > seems that the R f is no longer independent.
> > >
> > > Aga
> >
> > -BEGIN PGP SIGNATURE-
> > Version: GnuPG v1.4.8 (Darwin)
> >
> > iEYEARECAAYFAkk5KCgACgkQlz6UVQtc2uy09ACg69gIYn0Lc1e2tSRzoi1EJOe9
> > g/gAoOplij/XAxmGoZaNjFjAUx/etD/1
> > =QpB8
> > -END PGP SIGNATURE-
> >
> >
> >
> 
> 

Re: [ccp4bb] meaning of R free of perfect twin

[Eleanor Dodson]

you need to select the Free R in the highest possible Laue group , then 
use cad to extend this to all reflections in the chosen point group. 
This is best done  immediately post-truncate..


eg if you twinning operator is k,h,-l, then if
1,2, 3 is assigned to the free set so should 2, 1, -3 be.

PHENIX.xtriage does it properly

REFMAC does not use it properly I dont think, but maybe that has been 
fixed..


Eleanor

Serge Cohen wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

I guess the independence is mostly depending on how you select the 
reflection that lie in the free-set.


If (from the beginning) you select reflections that are related by the 
twin operator to be both in the free-set you keep the "independence" 
of the free-set.


Serge.

Le 5 déc. 08 à 13:50, Agnieszka Kiliszek a écrit :


Hi,

What is the meaning of R free of perfect twin? Shelxl counts it but it
seems that the R f is no longer independent.

Aga


-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.8 (Darwin)

iEYEARECAAYFAkk5KCgACgkQlz6UVQtc2uy09ACg69gIYn0Lc1e2tSRzoi1EJOe9
g/gAoOplij/XAxmGoZaNjFjAUx/etD/1
=QpB8
-END PGP SIGNATURE-

Re: [ccp4bb] R pim and Rmeans

[Winter, G (Graeme)]

Hi Frank,

This is an interesting point, and also relates to the knee-jerk
reactions to e.g. Rmerge > 100%. Certainly for the sqrt(1/(n-1)) term
the assumption is that the meaurements come from the same underlying
population so that increasing the number of observations should increase
the accuracy of the mean value. Your example of merging data in the
wrong symmetry would contradict this.

One thing though - although it may increase the accuracy, I guess it may
not necessarily increase the rightness (for want of a better word) of
the mean, as any tiny systematic error will begin to dominate the
results. The correct way to handle this may be to confirm that the
measurements still conform to the Wilson distribution... But there are
almosty certainly better qualified people to comment.

Anyway, as I said this also relates to Rmerge. Despite the well
documented limitations of this statistic it is certainly one which
people look at. I have processed data with comical levels of
multiplicity where the measurements at high resolution are probably good
- but they have an Rmerge > 100% because the individual measurements are
pretty poor, and Rmerge is proportional (ish) to 0.8/(i/sigma) where the
i/sigma is for the individual reflections. [straightforward to calculate
and stated in the paper mentioned below]. People are often unhappy with
this.

So one statistic in isolation is never helpful... And no amount of
weighting will get you out of the hole.

Cheers,

Graeme


-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Frank von Delft
Sent: 07 December 2008 22:16
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] R pim and Rmeans

Hi Manfred

I've been using and thinking Rmeas ever since I first saw it; but
(embarrassingly) I've only just woken up to Rpim -- so thanks for the
prompt. So I trawled the original references (Weiss and Hilgenfeld,
1997) to find out why it has the form it does, but I must have skimmed
too quickly, because I couldn't find the explanation.

Rpim, as I understand it, is trying to do two things (See Eq 3 in link
below):
1) penalise me for bad data
2) reward me for high redundancy

But why that *particular* balance of redundancy vs badness? And how do
we know that it was the best one?

And is this really waterproof? Since the redundancy factor (1/(N-1))
tends to zero for large N, does it not dominate for large redundancy? 
For instance, for terrible data (e.g. wrong symmetry) but very high
redundancy, then Rpim will still tend to zero, won't it?

So to counteract that, N might be downweighted it turn by the data
badness. Which could in its turn again be I don't think I like where
this is going :)

Cheers
phx.








Manfred S. Weiss wrote:
> Dear Deb,
>
> R_meas or R_rim is a merging R-factor which is independent of the 
> redundancy or multiplicity of the data (hence its name), R_pim stands 
> for precision indicating merging R-factor. R_pim gives you the 
> precision of the averaged measurement, which is the one you are 
> actually using for structure solution and refinement.
>
> SCALA will calculate both R_rim (R_meas) and R_pim, XDS/XSCALE will 
> calculate R_rim (R_meas) only, and SCALEPACK neither of the two. 
> However, you may produce a file from SCALEPACK with scaled but 
> unmerged intensities (option NO MERGE ORIGINAL INDEX) and then 
> download a program from my site called RMERGE or RMERGE_4LINUX, which 
> will do the job for you.
>
> If you have further questions, please see the page 
> http://www.embl-hamburg.de/~msweiss/projects/msw_qual.html
> or ask me.
>
> Cheers, Manfred
>
> 
> *  *
> *Dr. Manfred S. Weiss  *
> *  *
> * Team Leader  *
> *  *
> * EMBL Hamburg OutstationFon: +49-40-89902-170 *
> * c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
> * D-22603 Hamburg   Email: [EMAIL PROTECTED] *
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>
>
> On Sat, 6 Dec 2008, Debajyoti Dutta wrote:
>
>   
>>   
>> 
> Dear members,
>
> I have a little query hare about Rpim and Rmeans. How these are used
to mark data quality, and how can one calculate it.
>
> Thak you for your reply in advance.
>
> Sincerely
> Deb
>