[ccp4bb] residuewise rmsd for multiple chain superposition

[sreetama das]

Dear all,
   Is there any software which will print the RMSDs (residue wise, and 
not chain wise) for more-than-2 chains (having similar/same sequences) 
superposed together?
Thanks in advance,
sreetama

Re: [ccp4bb] residuewise rmsd for multiple chain superposition

[Thomas Holder]

Dear Sreetama,

theseus can superpose multiple structures and reports RMSD per residue.

http://www.theseus3d.org/

If your sequences are not identical and you want least squares 
superposition, run it like this:


theseus_align -l -f *.pdb

This will produce several output files. The file "theseus_variances.txt" 
contains the RMSD per residue.


Cheers,
  Thomas


On 02/21/2012 10:33 AM, sreetama das wrote:

Dear all,
Is there any software which will print the RMSDs (residue wise, and not
chain wise) for more-than-2 chains (having similar/same sequences)
superposed together?
Thanks in advance,
sreetama



--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

[ccp4bb] proper or improper ncs?

[Francis E Reyes]

Hi all

This structure has the following ncs (output via phenix.simple_ncs_from_pdb)
OPERATOR 1
CENTER:   18.3443  -55.4605   23.0986

ROTA 1:1.0.0.
ROTA 2:0.1.0.
ROTA 3:0.0.1.
TRANS: 0.0.0.

OPERATOR 2
CENTER:   37.0405  -23.8676  -14.9388

ROTA 1:   -0.5444   -0.22020.8094
ROTA 2:0.8330   -0.02780.5526
ROTA 3:   -0.09910.97510.1985
TRANS:45.3456  -78.7231   53.0085


It looks two-foldish but I'm not sure if it's proper or improper. (I'm trying 
to rationalize the lack of peaks on the self rotation maps). 


Any help would be appreciated. 

F



-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

[ccp4bb] EMBO Course on Macromolecular Complexes, Grenoble 4-9 June 2012

[Carlo Petosa]

Dear All,

We are organizing an EMBO Practical Course on the Structural
Characterization of Macromolecular Complexes.

The course is primarily intended for Ph.D. students and postdocs 
working on

challenging structural projects involving macromolecular complexes.

WHEN:  4-9 June 2012

WHERE: Grenoble, France

TOPICS INCLUDE:
   Expression & purification of multi-subunit complexes
   Biophysical & biochemical characterization of complexes
   Combining different structural methods (MX, NMR, SAXS, EM, MS)

LECTURERS INCLUDE:
   Radu Aricescu (Oxford U.)
   Imre Berger (EMBL Grenoble)
   Elisabetta Boeri Erba (IBS Grenoble)
   Anne-Claude Gavin (EMBL Heidelberg)
   Kay Grünewald (Oxford U.)
   Edward Lemke (EMBL Heidelberg)
   Malene Ringkjobing (IBS Grenoble)
   Christophe Romier (IGBMC Illkirch)
   Vladimir Rybin (EMBL Heidelberg)
   Michael Sattler (Technische U. Munich)
   Helen Saibil (Birkbeck, U. London)
   Christiane Schaffitzel (EMBL Grenoble)
   Carsten Schultz (EMBL Heidelberg)
   Bertrand Séraphin (IGBMC Illkirch)
   Montserrat Soler López (IRB Barcelona)
   Dmitri Svergun (EMBL Hamburg)
   Song Tan (Pennsylvania State U.)

SPONSORED BY: EMBO, P-CUBE, ESRF, Instruct

APPLICATION DEADLINE: 4 April 2012

COURSE DETAILS & REGISTRATION:  
http://events.embo.org/12-characterization/


Please forward this announcement to anyone who might be interested
in attending this course.

Best regards,
Carlo Petosa, Darren Hart, Elspeth Gordon,
Guy Schoehn, Winfried Weissenhorn


Carlo Petosa
Institut de Biologie Structurale (IBS)
41 rue Jules Horowitz, 38042 Grenoble, France
Tel:+33 438 78 40 24
E-mail: carlo.pet...@ibs.fr

Re: [ccp4bb] proper or improper ncs?

[Randy Read]

Hi,

I'm sure there's a way to do this in CCP4, but using some little jiffy programs 
I've collected over the years...

That's a 133 degree rotation around an axis defined by the unit vector 
0.290647, 0.624977, 0.724519, and there's a small screw component of about 2.4A 
along the axis, so it's an improper rotation.

On the other hand, if you combine a crystallographic symmetry operator with 
that transformation, you might still find that it's equivalent to a proper 
rotation.

Regards,

Randy Read

On 21 Feb 2012, at 13:47, Francis E Reyes wrote:

> Hi all
> 
> This structure has the following ncs (output via phenix.simple_ncs_from_pdb)
> OPERATOR 1
> CENTER:   18.3443  -55.4605   23.0986
> 
> ROTA 1:1.0.0.
> ROTA 2:0.1.0.
> ROTA 3:0.0.1.
> TRANS: 0.0.0.
> 
> OPERATOR 2
> CENTER:   37.0405  -23.8676  -14.9388
> 
> ROTA 1:   -0.5444   -0.22020.8094
> ROTA 2:0.8330   -0.02780.5526
> ROTA 3:   -0.09910.97510.1985
> TRANS:45.3456  -78.7231   53.0085
> 
> 
> It looks two-foldish but I'm not sure if it's proper or improper. (I'm trying 
> to rationalize the lack of peaks on the self rotation maps). 
> 
> 
> Any help would be appreciated. 
> 
> F
> 
> 
> 
> -
> Francis E. Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk

Re: [ccp4bb] proper or improper ncs?

[Dirk Kostrewa]

Hi Francis,

a quick insertion of your rotation matrix into CONVROT (by Alexandre 
Urzhumtsev) gives the following equivalent polar rotation angles 
(definition as in X-PLOR/CNS or Rossmann, 1962):


phi,psi,kappa   :  111.86  128.68  133.38 291.86   51.32  226.62

For a proper two-fold, a kappa of 180 degrees would be expected. This 
looks (very) improper to me.


Best regards,

Dirk.

Am 21.02.12 14:47, schrieb Francis E Reyes:

Hi all

This structure has the following ncs (output via phenix.simple_ncs_from_pdb)
OPERATOR 1
CENTER:   18.3443  -55.4605   23.0986

ROTA 1:1.0.0.
ROTA 2:0.1.0.
ROTA 3:0.0.1.
TRANS: 0.0.0.

OPERATOR 2
CENTER:   37.0405  -23.8676  -14.9388

ROTA 1:   -0.5444   -0.22020.8094
ROTA 2:0.8330   -0.02780.5526
ROTA 3:   -0.09910.97510.1985
TRANS:45.3456  -78.7231   53.0085


It looks two-foldish but I'm not sure if it's proper or improper. (I'm trying 
to rationalize the lack of peaks on the self rotation maps).


Any help would be appreciated.

F



-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder


--

***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***

Re: [ccp4bb] proper or improper ncs?

[Ian Tickle]

Francis,

It's very easy to spot a 2-fold rotation or screw because the matrix
must be symmetric (or nearly so)**.  Your matrix very obviously is not
(i,e, A12 ne A21, A13 ne A31 etc).

** Proof:

 A rotation matrix is orthogonal, which implies inverse = transpose: A^-1 = A~.

A 2-fold rotation is proper which implies AA = I or A^-1 = A.

Take these together and you get A = A~ i.e. A is symmetric.

Surprising how many people aren't aware of this!

Cheers

-- Iann

On 21 February 2012 13:47, Francis E Reyes  wrote:
> Hi all
>
> This structure has the following ncs (output via phenix.simple_ncs_from_pdb)
> OPERATOR 1
> CENTER:   18.3443  -55.4605   23.0986
>
> ROTA 1:    1.    0.    0.
> ROTA 2:    0.    1.    0.
> ROTA 3:    0.    0.    1.
> TRANS:     0.    0.    0.
>
> OPERATOR 2
> CENTER:   37.0405  -23.8676  -14.9388
>
> ROTA 1:   -0.5444   -0.2202    0.8094
> ROTA 2:    0.8330   -0.0278    0.5526
> ROTA 3:   -0.0991    0.9751    0.1985
> TRANS:    45.3456  -78.7231   53.0085
>
>
> It looks two-foldish but I'm not sure if it's proper or improper. (I'm trying 
> to rationalize the lack of peaks on the self rotation maps).
>
>
> Any help would be appreciated.
>
> F
>
>
>
> -
> Francis E. Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder

Re: [ccp4bb] proper or improper ncs?

[Randy Read]

I've had a couple of requests for the jiffy program that interpreted the 
transformation, so here's the FORTRAN source code for decomp.f, for anyone who 
is interested.  It's very simple, so all you should need to do is something 
like:

gfortran decomp.f -o decomp

to get an executable (or replace gfortran by g77 or f77, as appropriate).  Put 
the matrix and vector into a file (say matvec.dat), then:

decomp < matvec.dat

It takes a matrix and vector as four lines on standard input, then decomposes 
the transformation into a rotation around an axis, a point on the axis, and a 
translation parallel to the axis.

Regards,

Randy



decomp.f
Description: Binary data

On 21 Feb 2012, at 14:01, Randy Read wrote:

> Hi,
> 
> I'm sure there's a way to do this in CCP4, but using some little jiffy 
> programs I've collected over the years...
> 
> That's a 133 degree rotation around an axis defined by the unit vector 
> 0.290647, 0.624977, 0.724519, and there's a small screw component of about 
> 2.4A along the axis, so it's an improper rotation.
> 
> On the other hand, if you combine a crystallographic symmetry operator with 
> that transformation, you might still find that it's equivalent to a proper 
> rotation.
> 
> Regards,
> 
> Randy Read
> 
> On 21 Feb 2012, at 13:47, Francis E Reyes wrote:
> 
>> Hi all
>> 
>> This structure has the following ncs (output via phenix.simple_ncs_from_pdb)
>> OPERATOR 1
>> CENTER:   18.3443  -55.4605   23.0986
>> 
>> ROTA 1:1.0.0.
>> ROTA 2:0.1.0.
>> ROTA 3:0.0.1.
>> TRANS: 0.0.0.
>> 
>> OPERATOR 2
>> CENTER:   37.0405  -23.8676  -14.9388
>> 
>> ROTA 1:   -0.5444   -0.22020.8094
>> ROTA 2:0.8330   -0.02780.5526
>> ROTA 3:   -0.09910.97510.1985
>> TRANS:45.3456  -78.7231   53.0085
>> 
>> 
>> It looks two-foldish but I'm not sure if it's proper or improper. (I'm 
>> trying to rationalize the lack of peaks on the self rotation maps). 
>> 
>> 
>> Any help would be appreciated. 
>> 
>> F
>> 
>> 
>> 
>> -
>> Francis E. Reyes M.Sc.
>> 215 UCB
>> University of Colorado at Boulder
> 
> --
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research  Tel: + 44 1223 336500
> Wellcome Trust/MRC Building   Fax: + 44 1223 336827
> Hills RoadE-mail: rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk

Re: [ccp4bb] HKL2000 indexing problem

[Kelly Daughtry]

Sounds exactly like something is off in your site.def file. I would look to
the beam center.

Also, have you tried indexing with another program? Mosflm perhaps. I find
that if one program cannot index the data, another usually can (as long as
the data isn't too horrible!). Thus I always try to process my data in
several programs in parallel.

Best,
Kelly Daughtry

***
Kelly Daughtry, Ph.D.
Post-Doctoral Fellow, Raetz Lab
Biochemistry Department
Duke University
Alex H. Sands, Jr. Building
303 Research Drive
RM 250
Durham, NC 27710
P: 919-684-5178
***


On Mon, Feb 20, 2012 at 7:28 PM, Peter Hsu  wrote:

> Hi all,
>
> I recently collected a data set off a single crystal and have had problems
> with indexing it. Every time I go pick peaks for indexing it constantly
> picks peaks that are just slightly off the actual peak. After indexing, it
> would always be that 2 of the 3 cell dimensions would be fairly normal,
> while the 3rd would have some impossible value such as 1.
>
> On some other occasions if it manages to pick peaks properly, and every
> time I go to index it, it gives back an error that I don't have enough
> peaks picked to index (picked nearly 500).
>
> I've tried using a number of different images to index from and have run
> into the same problem.
>
> Has anyone else run into these problems? Does anyone have any idea what
> might be wrong w/my dataset and/or crystal?
>
> Thanks in advance for any insight,
>
> Peter
>

Re: [ccp4bb] proper or improper ncs?

[Alexandre OURJOUMTSEV]

Hi, everybody,

In addition to all comments, just as a pleasure to remind an old-fashion "no 
computer" way to calculate the rotation angle. The trace of a rotation matrix 
(the sum of its diagonal elements) is always equal to 2*cos(kappa)+1. Calculate 
it yourself for kappa = 180° and compare with the trace of the Francis's matrix.

ROTA 1:   -0.5444   -0.22020.8094
ROTA 2:0.8330   -0.02780.5526
ROTA 3:   -0.09910.97510.1985

One can easily reject (still without a computer) other "crystallographic" 
angles.

Best regards,

Sasha Urzhumtsev


-Message d'origine-
De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de Ian Tickle
Envoyé : mardi 21 février 2012 15:13
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] proper or improper ncs?

Francis,

It's very easy to spot a 2-fold rotation or screw because the matrix must be 
symmetric (or nearly so)**.  Your matrix very obviously is not (i,e, A12 ne 
A21, A13 ne A31 etc).

** Proof:

 A rotation matrix is orthogonal, which implies inverse = transpose: A^-1 = A~.

A 2-fold rotation is proper which implies AA = I or A^-1 = A.

Take these together and you get A = A~ i.e. A is symmetric.

Surprising how many people aren't aware of this!

Cheers

-- Iann

On 21 February 2012 13:47, Francis E Reyes  wrote:
> Hi all
>
> This structure has the following ncs (output via 
> phenix.simple_ncs_from_pdb) OPERATOR 1
> CENTER:   18.3443  -55.4605   23.0986
>
> ROTA 1:    1.    0.    0.
> ROTA 2:    0.    1.    0.
> ROTA 3:    0.    0.    1.
> TRANS:     0.    0.    0.
>
> OPERATOR 2
> CENTER:   37.0405  -23.8676  -14.9388
>
> ROTA 1:   -0.5444   -0.2202    0.8094
> ROTA 2:    0.8330   -0.0278    0.5526
> ROTA 3:   -0.0991    0.9751    0.1985
> TRANS:    45.3456  -78.7231   53.0085
>
>
> It looks two-foldish but I'm not sure if it's proper or improper. (I'm trying 
> to rationalize the lack of peaks on the self rotation maps).
>
>
> Any help would be appreciated.
>
> F
>
>
>
> -
> Francis E. Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder

Re: [ccp4bb] HKL2000 indexing problem

[Green, Todd]

Hello Peter-

Is it possible that you are shooting close to an axis? If you are shooting near 
parallel to one of the crystal axis, you will get values that are reasonable 
for 2 cell lengths but extremely low values for the third. Try indexing a frame 
that is say 30 degrees into the collection and see if you have the same 
problem. If the crystal is aligned with one axis along the direction of the 
x-ray beam, and the goniometer rotating around that direction then you may 
likely have to reorient the crystal and recollect the data. This may be why you 
it hasn't worked for several images. Outside of beam center, i think this is 
something for you to have a look at.

-Todd


-Original Message-

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Peter Hsu 
[hsuu...@u.washington.edu]
Sent: Monday, February 20, 2012 6:28 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] HKL2000 indexing problem

Hi all,

I recently collected a data set off a single crystal and have had problems with 
indexing it. Every time I go pick peaks for indexing it constantly picks peaks 
that are just slightly off the actual peak. After indexing, it would always be 
that 2 of the 3 cell dimensions would be fairly normal, while the 3rd would 
have some impossible value such as 1.

On some other occasions if it manages to pick peaks properly, and every time I 
go to index it, it gives back an error that I don't have enough peaks picked to 
index (picked nearly 500).

I've tried using a number of different images to index from and have run into 
the same problem.

Has anyone else run into these problems? Does anyone have any idea what might 
be wrong w/my dataset and/or crystal?

Thanks in advance for any insight,

Peter


This email was scanned with Mcafee's Anti-Virus appliance, but this 
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Re: [ccp4bb] HKL2000 indexing problem

[Jacob Keller]

Is the direction of rotation correct? I got some data that were going
the wrong way once.

JPK

Re: [ccp4bb] Putting Text into Movies

[Jason Vertrees]

Hi Jacob,

> is there a good way to put text labels into movies from pymol or
> otherwise? It would be helpful for conveying some ideas...

Check out the pseudoatom command
(http://www.pymolwiki.org/index.php/Pseudoatom) which is commonly used
as an on-screen placeholder for text. The label command
(http://www.pymolwiki.org/index.php/Label) will also help.

How much text are you looking to add?

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

Re: [ccp4bb] HKL2000 indexing problem

[Green, Todd]

This is a possibility, but probably you should be able to get the initial index 
in this situation. The integration is a different story. To fix that problem, 
usually you can change the def.site fix with: {alig,1} {180}   as opposed to 0.

-Todd


-Original Message-
From: CCP4 bulletin board on behalf of Jacob Keller
Sent: Tue 2/21/2012 9:54 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] HKL2000 indexing problem
 
Is the direction of rotation correct? I got some data that were going
the wrong way once.

JPK


This email was scanned with Mcafee's Anti-Virus appliance, but this 
is no guarantee that no virus exists. You are asked to make sure you
have virus protection and that it is up to date.

[ccp4bb] Vacancy for a Data Analysis Scientist: Diffraction and crystallography

[Alun Ashton]

Dear All, 

Please see below details of a data analysis scientist post available within the 
scientific software team at Diamond. For full details please go to the web 
pages at:

http://www.diamond.ac.uk/Home/Jobs/Current/DIA0686-TH.html

Job Title: Data Analysis Scientist  
Job Reference: DIA0686/CG  
Post Type: Full time, permanent 
Division: Science 
Salary information: Circa £34k - a higher salary may be available for an 
exceptionally experienced and qualified candidate. 
Application deadline: 25/03/2012 

Regards,
Alun Ashton
___
Alun Ashton, alun.ash...@diamond.ac.uk Tel: +44 1235 778404
Scientific Software Team Leader,  http://www.diamond.ac.uk/
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.

Re: [ccp4bb] HKL2000 indexing problem

[Appu kumar]

Hi peter,
 I agreed with Kelly, You should try indexing your data in
different program. I recently collected a diffraction data which showed
problem in indexing in HKL2000, but data indexed very fine in imosflm
giving right cell parameter. So it is worthfull to index your data in
different program.



On 21 February 2012 21:31, Green, Todd  wrote:

> **
>
> This is a possibility, but probably you should be able to get the initial
> index in this situation. The integration is a different story. To fix that
> problem, usually you can change the def.site fix with: {alig,1} {180}   as
> opposed to 0.
>
> -Todd
>
>
>
> -Original Message-
> From: CCP4 bulletin board on behalf of Jacob Keller
> Sent: Tue 2/21/2012 9:54 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] HKL2000 indexing problem
>
> Is the direction of rotation correct? I got some data that were going
> the wrong way once.
>
> JPK
>
>
> This email was scanned with Mcafee's Anti-Virus appliance, but this
> is no guarantee that no virus exists. You are asked to make sure you
> have virus protection and that it is up to date.
>
>
>

[ccp4bb] Modified Cys by TCEP?

[Björn Kauppi]

Hi all,

I recently encountered a modified surface cysteine residue in one of my 
structures. The protein  is expressed in E.coli and my data is to 1.7Å so I am 
positive of the number of extra atoms. It really look like one of the tails 
(the Propanoic acid) of a TCEP molecule. TCEP was added during purification at 
2 mM. I tried to look in pdb (or google) but I could not find any reference of 
that TCEP could do this. The modified Cystein is involved in a nice crystal 
contact (salt bridge) to a Lysine, and thereby stabilizing it further. Looking 
back at older structures of the same protein, I see the same modification of 
this Cys, but not as pronounced since they were done at lower resolution.

Does anyone recognize this behavior of TCEP? Or, any other ideas?


Björn Kauppi
Structure and Design
Karo Bio AB


__
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Re: [ccp4bb] Modified Cys by TCEP?

[Bart Hazes]

On 12-02-21 10:11 AM, Björn Kauppi wrote:

Hi all,

I recently encountered a modified surface cysteine residue in one of my 
structures. The protein  is expressed in E.coli and my data is to 1.7Å so I am 
positive of the number of extra atoms. It really look like one of the tails 
(the Propanoic acid) of a TCEP molecule. TCEP was added during purification at 
2 mM. I tried to look in pdb (or google) but I could not find any reference of 
that TCEP could do this. The modified Cystein is involved in a nice crystal 
contact (salt bridge) to a Lysine, and thereby stabilizing it further. Looking 
back at older structures of the same protein, I see the same modification of 
this Cys, but not as pronounced since they were done at lower resolution.

Does anyone recognize this behavior of TCEP? Or, any other ideas?


Björn Kauppi
Structure and Design
Karo Bio AB


__
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Karo Bio AB and is meant for the intended addressee(s) only. Any
unauthorized review, use, disclosure or distribution is prohibited.
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Did you use cacodylate as buffer. TCEP may have reduced some of the 
dimethylarsenate, which is really what cacodylate is, to 
dimethylarsenite which can react with cysteine residues. It works best 
if the cysteine has a depressed pKa, as it is reactive in the thiolate 
form, and the proximity to the lysine you mention might do just that.


There are several structures with arsenylated cysteine, the one we came 
across was a poxviral glutaredoxin (2HZE, Bacik & Hazes)


Bart

Re: [ccp4bb] Modified Cys by TCEP?

[Björn Kauppi]

Hi again,

Thanks for all the suggestions. But no I really have not used either 
cacodylate-buffers, DTT or BME. Which I am aware can give Cys-aducts. Further I 
have not treated my protein with protease inhibitors, of which I have heard 
some can modify cysteins.

I have checked the DNA sequence, since an Arginine side chain fits perfectly in 
the density but on refinement I get strong positive density on the Arg-beta 
carbon suggesting a sulfur. Also an Arginine  would do a lousy interaction with 
the lysine in the crystal contact...

Maybe it is no big deal, but I want to have control on what happens to my 
protein and get rid of any sources of heterogeneity.


--Björn


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bart Hazes
Sent: den 21 februari 2012 18:26
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Modified Cys by TCEP?

On 12-02-21 10:11 AM, Björn Kauppi wrote:
> Hi all,
>
> I recently encountered a modified surface cysteine residue in one of my 
> structures. The protein  is expressed in E.coli and my data is to 1.7Å so I 
> am positive of the number of extra atoms. It really look like one of the 
> tails (the Propanoic acid) of a TCEP molecule. TCEP was added during 
> purification at 2 mM. I tried to look in pdb (or google) but I could not find 
> any reference of that TCEP could do this. The modified Cystein is involved in 
> a nice crystal contact (salt bridge) to a Lysine, and thereby stabilizing it 
> further. Looking back at older structures of the same protein, I see the same 
> modification of this Cys, but not as pronounced since they were done at lower 
> resolution.
>
> Does anyone recognize this behavior of TCEP? Or, any other ideas?
>
>
> Björn Kauppi
> Structure and Design
> Karo Bio AB
>
>
> __
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>

Did you use cacodylate as buffer. TCEP may have reduced some of the 
dimethylarsenate, which is really what cacodylate is, to dimethylarsenite which 
can react with cysteine residues. It works best if the cysteine has a depressed 
pKa, as it is reactive in the thiolate form, and the proximity to the lysine 
you mention might do just that.

There are several structures with arsenylated cysteine, the one we came across 
was a poxviral glutaredoxin (2HZE, Bacik & Hazes)

Bart

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[ccp4bb] Aggregated protein for crystallization

[Raji Edayathumangalam]

Hi Folks,

As crazy as it sounds, if you have crystallized and managed to solve the
structure of a protein from aggregated protein, please could you share your
experience.

After many constructs, many many expression schemes and after the usual
rigmarole of optimization that is also often discussed on ccp4bb (buffers,
glycerol, salt concentrations, pH, detergent, additives etc.), I now have a
decently expressing truncated construct for my protein (80 kDa) that is
pure but aggregated (elutes in the void volume from a Superdex200 column).
I am tempted to make a boatload of aggregated protein and set up some
crystal trays (after perhaps testing by CD). So I'd like to hear from folks
who have been successful in solving structures from aggregates when many
many known and tested optimization methods still leave one with aggregated
protein.

Thanks.
Raji

-- 
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University

Re: [ccp4bb] Aggregated protein for crystallization

[Jacob Keller]

Hey, it could be that you just have a big oligomer--any support for
that in the relevant literature? A 10-mer would probably beat out an
s200, no? Do you have any other way to ascertain the oligomeric state?

Jacob

On Tue, Feb 21, 2012 at 5:21 PM, Raji Edayathumangalam
 wrote:
> Hi Folks,
>
> As crazy as it sounds, if you have crystallized and managed to solve the
> structure of a protein from aggregated protein, please could you share your
> experience.
>
> After many constructs, many many expression schemes and after the usual
> rigmarole of optimization that is also often discussed on ccp4bb (buffers,
> glycerol, salt concentrations, pH, detergent, additives etc.), I now have a
> decently expressing truncated construct for my protein (80 kDa) that is pure
> but aggregated (elutes in the void volume from a Superdex200 column). I am
> tempted to make a boatload of aggregated protein and set up some crystal
> trays (after perhaps testing by CD). So I'd like to hear from folks who have
> been successful in solving structures from aggregates when many many known
> and tested optimization methods still leave one with aggregated protein.
>
> Thanks.
> Raji
>
> --
> Raji Edayathumangalam
> Instructor in Neurology, Harvard Medical School
> Research Associate, Brigham and Women's Hospital
> Visiting Research Scholar, Brandeis University
>
>



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] Aggregated protein for crystallization

[Phoebe Rice]

I probably it depends on whether you've got gunk or a functionally relevant 
oligomer in that void volume.  Is it active?

RecA and Rad51 both form open-ended head-to-tail oligomers and yet they still 
crystallize.

=
Phoebe A. Rice
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
http://www.rsc.org/shop/books/2008/9780854042722.asp


 Original message 
>Date: Tue, 21 Feb 2012 18:21:03 -0500
>From: CCP4 bulletin board  (on behalf of Raji 
>Edayathumangalam )
>Subject: [ccp4bb] Aggregated protein for crystallization  
>To: CCP4BB@JISCMAIL.AC.UK
>
>   Hi Folks,
>   As crazy as it sounds, if you have crystallized and
>   managed to solve the structure of a protein from
>   aggregated protein, please could you share your
>   experience.
>   After many constructs, many many expression schemes
>   and after the usual rigmarole of optimization that
>   is also often discussed on ccp4bb (buffers,
>   glycerol, salt concentrations, pH, detergent,
>   additives etc.), I now have a decently expressing
>   truncated construct for my protein (80 kDa) that is
>   pure but aggregated (elutes in the void volume from
>   a Superdex200 column). I am tempted to make a
>   boatload of aggregated protein and set up some
>   crystal trays (after perhaps testing by CD). So I'd
>   like to hear from folks who have been successful in
>   solving structures from aggregates when many many
>   known and tested optimization methods still leave
>   one with aggregated protein.
>   Thanks.
>   Raji
>   --
>   Raji Edayathumangalam
>   Instructor in Neurology, Harvard Medical School
>   Research Associate, Brigham and Women's Hospital
>   Visiting Research Scholar, Brandeis University

Re: [ccp4bb] Aggregated protein for crystallization

[Puey Ounjai]

Hi,

Your idea does sound really crazy but actually Jacob had made a very good
valid point.
Question is do you think your aggregate still functioning or not, if not,
can you revive them in vitro and how effective is your refolding process if
you are going to refold them?

You may want to take a look at structures of some bacterial pore-forming
proteins. Many of them can be expressed as large inclusion bodies in
heterologous host of which we call "aggregate". I know it sound fishy but
after refolding and proper proteolytic activation, those proteins retain
the ability to induce mortality to their host cell as good as the real one.

Anyway, good luck with your endeavors!
Puey


On Tue, Feb 21, 2012 at 3:26 PM, Jacob Keller <
j-kell...@fsm.northwestern.edu> wrote:

> Hey, it could be that you just have a big oligomer--any support for
> that in the relevant literature? A 10-mer would probably beat out an
> s200, no? Do you have any other way to ascertain the oligomeric state?
>
> Jacob
>
> On Tue, Feb 21, 2012 at 5:21 PM, Raji Edayathumangalam
>  wrote:
> > Hi Folks,
> >
> > As crazy as it sounds, if you have crystallized and managed to solve the
> > structure of a protein from aggregated protein, please could you share
> your
> > experience.
> >
> > After many constructs, many many expression schemes and after the usual
> > rigmarole of optimization that is also often discussed on ccp4bb
> (buffers,
> > glycerol, salt concentrations, pH, detergent, additives etc.), I now
> have a
> > decently expressing truncated construct for my protein (80 kDa) that is
> pure
> > but aggregated (elutes in the void volume from a Superdex200 column). I
> am
> > tempted to make a boatload of aggregated protein and set up some crystal
> > trays (after perhaps testing by CD). So I'd like to hear from folks who
> have
> > been successful in solving structures from aggregates when many many
> known
> > and tested optimization methods still leave one with aggregated protein.
> >
> > Thanks.
> > Raji
> >
> > --
> > Raji Edayathumangalam
> > Instructor in Neurology, Harvard Medical School
> > Research Associate, Brigham and Women's Hospital
> > Visiting Research Scholar, Brandeis University
> >
> >
>
>
>
> --
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> email: j-kell...@northwestern.edu
> ***
>

Re: [ccp4bb] Aggregated protein for crystallization

[Bernhard Rupp (Hofkristallrat a.D.)]

Well, depends on what 'aggregated' really means. If it implies reasonably
weak oligomerization interaction - and it 
might not be too strong given that the oligomers remain soluble - a
chaotropic crystallization agent (on the 
extreme end certain high salts, consult Hofmeister for chaotropicity) may
rip such soluble 
aggregates apart or at least get them into a conformationally reasonably
well defined state. 
Crystals do appear/transform even from precipitates on occasion.  CD will
tell you about
the (secondary structure) folding state, not the aggregation state, DLS/MALS
would give an estimate for
and distribution of the aggregation state. With light scattering, you can
also do some systematic experiments 
exploring what might reduce the aggregate size.  

I think soluble, defined secondary structure,  and a lot of it, is already a
good sign.
  
BR


On Tue, Feb 21, 2012 at 5:21 PM, Raji Edayathumangalam 
wrote:
> Hi Folks,
>
> As crazy as it sounds, if you have crystallized and managed to solve 
> the structure of a protein from aggregated protein, please could you 
> share your experience.
>
> After many constructs, many many expression schemes and after the 
> usual rigmarole of optimization that is also often discussed on ccp4bb 
> (buffers, glycerol, salt concentrations, pH, detergent, additives 
> etc.), I now have a decently expressing truncated construct for my 
> protein (80 kDa) that is pure but aggregated (elutes in the void 
> volume from a Superdex200 column). I am tempted to make a boatload of 
> aggregated protein and set up some crystal trays (after perhaps 
> testing by CD). So I'd like to hear from folks who have been 
> successful in solving structures from aggregates when many many known and
tested optimization methods still leave one with aggregated protein.
>
> Thanks.
> Raji
>
> --
> Raji Edayathumangalam
> Instructor in Neurology, Harvard Medical School Research Associate, 
> Brigham and Women's Hospital Visiting Research Scholar, Brandeis 
> University
>
>



--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] residuewise rmsd for multiple chain superposition

[Eric Pettersen]

On Feb 21, 2012, at 4:00 PM, sreetama das wrote:

   Is there any software which will print the RMSDs (residue  
wise, and not chain wise) for more-than-2 chains (having similar/ 
same sequences) superposed together?


In UCSF Chimera you can use the Match->Align tool to create a  
structure-based sequence alignment (or you can open an alignment file  
if you already have one).  The the alignment will show per-residue  
RMSD as a bar chart across the top of the alignment (if you opened  
your own alignment file you'd have to use the Headers->RMSD menu entry  
to show the bar chart).  You can save the numeric RMSD values to a  
file with Headers->Save.


Also, Match->Align will report a couple of additional normalized RMSD  
scores, namely Structural Distance Measure and Q-score.


Chimera home page:  www.cgl.ucsf.edu/chimera
Match->Align page: 
http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/matchalign/matchalign.html
sequence aignment viewer: 
http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multalignviewer/framemav.html

--Eric


Eric Pettersen
http://www.cgl.ucsf.edu/home/pett

"And isn't sanity really just a one trick pony anyway? I mean
all you get is one trick, rational thinking, but when
you're good and crazy, oooh oooh oooh, the sky is the
limit!"-The Tick

Re: [ccp4bb] Putting Text into Movies

[Eric Pettersen]

On Feb 21, 2012, at 4:00 PM, Jacob Keller wrote:


is there a good way to put text labels into movies from pymol or
otherwise? It would be helpful for conveying some ideas...


As Jason pointed out, PyMOL has some useful facilities for this.   
Chimera has a tool for placing standalone text and arrows called 2D  
Labels.  The arrows and text can be any color and the text can also be  
various sizes, styles (italics, etc.) and typefaces (serif etc.), all  
on a per-character basis.  You can place text and arrows interactively  
with the mouse or via commands.  Text can also be faded in or out as a  
movie plays/records.


A pretty nice example use of 2D Labels in the "DNA basics" movie on  
this page: http://crc.nd.edu/index.php/cyberinfrastructure/visualization/80


Chimera home page:  www.cgl.ucsf.edu/chimera
2D Labels page: 
http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/2dlabels/2dlabels.html

--Eric

Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu

[ccp4bb] Available positions for biophysicists with strong experience in SPR

[Bussiere, Dirksen]

Colleagues:

   This is a bit off-topic, but there are two positions available in our group 
for scientists with experience in biophysics and SPR.   The description of each 
position follows as does application instructions.   The first position listed 
is for an experienced Ph.D.-level scientist; the second position for an 
experienced B.S./M.S.-level scientist.

Novartis Institutes for BioMedical Research

SPR / Solution Biophysics Scientist - Inv III / Sr Inv I, Structural Chemistry

Requisition No. 93406BR
NIBR - Novartis Institutes for BioMedical Research
Emeryville, CA

About Novartis Institute of Biomedical Research

At Novartis Institutes for BioMedical Research ("NIBR"), the global research 
organization of Novartis, we are committed to discovering innovative medicines 
to cure disease and improve human health. By hiring the best academic, biotech, 
and pharmaceutical trained scientists, we have fostered an atmosphere for drug 
discovery where innovation is rewarded. It is ultimately the talent of the 
individual that determines our success, while our state-of-the-art technologies 
and resources enable these ideas to be realized.

NIBR has sites in Cambridge, Massachusetts; Emeryville, CA; Basel, Switzerland; 
Horsham, UK; and Shanghai, China. Our Emeryville location focuses on early drug 
discovery efforts for the Oncology Disease Area and offers a variety of 
positions in Biology, Chemistry, and functions such as Technology, Patents, 
Research Sciences and other areas that support our scientific resources.

About Structural Chemistry

The NIBR Emeryville Structural Chemistry group is responsible for actively 
pursuing protein-ligand interaction studies using NMR spectroscopy, X-ray 
crystallography, and complementary biophysical methods to support drug 
discovery projects. The group also determines the structures of macromolecular 
drug targets either as apo-proteins or in complex with lead compounds to help 
guide structure-based drug design, and actively participates in the drug 
discovery process.

We are seeking a multifaceted individual with a strong scientific background 
and relevant expertise in the use of surface plasmon resonance (SPR) and other 
biophysical methods, such as isothermal calorimetry, to discover small molecule 
inhibitors and activators of drug targets, particularly in the context of 
fragment-based lead discovery.


Responsibilities:


* Design, develop, and implement SPR and other biophysical assays 
suitable for hit identification and validation as part of ongoing 
fragment-based screening efforts.

* Drive the implementation of new technological approaches and 
capabilities in regards to solution biophysics.

* Create and implement project plans, and coordinate workflow and 
logistics to meet project goals and milestones.

* Participate on multidisciplinary teams to evaluate new leads and to 
validate new targets.

Qualifications:


* Ph.D. in Biochemistry, Biophysics, or other relevant field, with 3-10 
years of relevant postgraduate experience, including biotechnology and/or 
pharmaceutical industry experience.

* In-depth knowledge of biophysics is required, and experience with SPR 
technology and its application in fragment-based screen are essential.  
Experience with biophysics assay technologies such as fluorescence-based 
techniques (FP, FRET), calorimetry (ITC, DSC), light scattering (StarGazer) are 
highly desirable.

* Experience in structure-based drug design and the optimization of 
ligand-efficient fragments would be a plus.

* Experience with laboratory instrumentation and automation, data 
analysis and management, and a sound knowledge of the drug discovery process is 
also highly desirable.

* Some knowledge of current infectious disease and oncology research is 
a plus.

* Ability to devise experimental strategies and execute them in a 
timely manner to produce goal-oriented results is essential.

* Ability to work with Novartis scientists from multiple disciplines is 
required and exceptional written, verbal, and team skills are essential.

* Demonstrated solid track record of scientific achievements is 
required.



To apply for this position, please visit 
www.novartis.com, click on the Careers link, pull the 
menu down to Job Search, and search for job ID 93406BR.


Solution Biophysics Research Associate - Scientist II

Requisition No. 93761BR
NIBR - Novartis Institutes for BioMedical Research
Emeryville, CA

Responsibilities:


* Working with PhD-level scientists to develop and implement SPR and 
other biophysical assays suitable for hit identification and validation as part 
of ongoing fragment-based screening efforts.

* Implement project plans, and coordinate workflow and logistics to 
meet project goals and milestones.

* Participate on multidisciplinary teams to evaluate new leads and to 
validate

Re: [ccp4bb] Aggregated protein for crystallization

[Shya Biswas]

Hi,
Did you try using a different column like Superose 6? This column works
well to separate large molecular weight proteins including oligomers.
Ideally if your solution is not cloudy (coming out of void volume) those
are not aggregates those might be oligomers.
HTH,
Shya

On Tue, Feb 21, 2012 at 6:21 PM, Raji Edayathumangalam wrote:

> Hi Folks,
>
> As crazy as it sounds, if you have crystallized and managed to solve the
> structure of a protein from aggregated protein, please could you share your
> experience.
>
> After many constructs, many many expression schemes and after the usual
> rigmarole of optimization that is also often discussed on ccp4bb (buffers,
> glycerol, salt concentrations, pH, detergent, additives etc.), I now have a
> decently expressing truncated construct for my protein (80 kDa) that is
> pure but aggregated (elutes in the void volume from a Superdex200 column).
> I am tempted to make a boatload of aggregated protein and set up some
> crystal trays (after perhaps testing by CD). So I'd like to hear from folks
> who have been successful in solving structures from aggregates when many
> many known and tested optimization methods still leave one with aggregated
> protein.
>
> Thanks.
> Raji
>
> --
> Raji Edayathumangalam
> Instructor in Neurology, Harvard Medical School
> Research Associate, Brigham and Women's Hospital
> Visiting Research Scholar, Brandeis University
>
>
>

[ccp4bb] Research fellow position

[Hai Wei SONG (IMCB)]

The Institute of Molecular and Cell Biology (IMCB) is a leading research 
institute in biological sciences funded by the Agency for Science, Technology 
and Research (A*STAR). Its mission is to develop and foster a vibrant research 
culture for cutting-edge basic biomedical sciences. The research activities at 
IMCB focus on six major fields: Cell Biology, Developmental Biology, Structural 
Biology, Infectious Diseases, Cancer Biology and Translational Research with 
core strengths in Cell Cycling, Cell Signaling, Cell Death, Cell Motility and 
Protein Trafficking. IMCB is continuously looking out for talented people to 
contribute to its success. We are seeking an enthusiastic and self-motivated 
researcher to join our group as a research fellow at IMCB.  Our laboratory uses 
biochemical/biophysical, cellular and crystallographic techniques to understand 
the molecular mechanisms of translational control, eukaryotic mRNA decay, and 
the Hippo signaling pathway.  Candidate must have a strong publication record, 
good training either in structural biology or in Biochemistry and Molecular 
Biology.  All enquires should be made directly to Dr. Haiwei Song via email 
hai...@imcb.a-star.edu.sg.  Further 
information is available at http://www.imcb.a-star.edu.sg/php/shw.php



Note: This message may contain confidential information. If this Email/Fax has 
been sent to you by mistake, please notify the sender and delete it 
immediately. Thank you.

[ccp4bb] Server or software for B factor analysis

[Dialing Pretty]

Dear All,

Will you please tell me a server of software which can draw a curve for the B 
factor of the atoms in a protein PDB file from the first residue to the 
residue?Or a server or software by which we can easily order the B factors of 
the atoms in the PDB file according to the B factor in decrease or in increase? 
Or to get the residues with the highest B factor and the lowest B factor?

Cheers,

Dialing

Re: [ccp4bb] Server or software for B factor analysis

[Pavel Afonine]

Hi Dialing,

Will you please tell me a server of software which can draw a curve for the
> B factor of the atoms in a protein PDB file from the first residue to the
> residue?Or a server or software by which we can easily order the B factors
> of the atoms in the PDB file according to the B factor in decrease or in
> increase? Or to get the residues with the highest B factor and the lowest B
> factor?
>

I know one, you can do it in Excel (it is not Phenix !).

Hope this helps,
Pavel

[ccp4bb] R-mergd-F

[arka chakraborty]

Hi all ,

I will like to know which program we can use to calculate R-mergd-F( not
Rmerge) between two data sets, or more generally R factor between two data
sets.

Thanks in advance,

Regards,

ARKO

-- 

*ARKA CHAKRABORTY*
*CAS in Crystallography and Biophysics*
*University of Madras*
*Chennai,India*

Re: [ccp4bb] Best method for weighted averaging of Friedel pairs?

[arka chakraborty]

Hi all,
Can someone put in links of a few articles relevant to the above
discussion? ie where this kind of strategy was helpful in a specific
practical situation?

Thanks in advance,

Regards,

ARKO

On Tue, Feb 21, 2012 at 4:46 AM, ccp4  wrote:

> This is a case where it is really helpful to keep some record of the
> unmerged integrated data.
> And again rejecting the odd outlier does no harm to most analyses..
>
> I like to use scala to check for outliers looking at all i+ I-
> measurements; if there is a wild discrepancy for weak anomalous signals you
> have probably found an outlier which is best rejected.
>
> If you have a huge anomalous signal with good redundancy you probably
> shouldnt use Imean and the anomalous difference will be I= -I- with SD =
> sqrt (VarI+ VarI-).
>
> Most software which uses that signal will check for outliers in the Anom
> difference lists too, and it is usually safest to exclude them from anom
> site searches, and phase calculations.
> Eleanor
>
>  On 14.02.2012 06:30, Tim Gruene wrote:
>
>> -BEGIN PGP SIGNED MESSAGE-
>> Hash: SHA1
>>
>> Dear Markus,
>>
>> why don't you reintegrate the data with hkl2000 telling the program to
>> treat them as non-anomalous data-set? This should give you scalepack
>> output with the Bijvoet pairs merged and overcome the problem you
>> describe.
>>
>> Cheers,
>> Tim
>>
>> On 02/13/2012 06:19 PM, Markus Meier wrote:
>>
>>> On 11/02/12 02:52 PM, Bryan Lepore wrote:
>>>
 did you ever get a response on this? it is interesting but nobody
 posted publicly.

 -Bryan


>>> Dear Bryan,
>>>
>>> so far no one replied ... so please find my answer below. If someone
>>> disagrees, please post.
>>>
>>> None of the methods I have described are appropriate.
>>>
>>> If the negative Bijvoet mates and the positive Bijvoet mates have been
>>> merged separately to one intensity value for each (i.e. I+ or I-) plus
>>> the associated standard deviation (sigI+ or sigI-), any weighted method
>>> to calculate the mean will bias the intensity to either the I+ or the I-.
>>>
>>> Therefore the only appropriate method is to use the unweighted mean:
>>>
>>> Imean = 0.5*( I+ + I- )
>>> sigImean = 0.5 * sqrt( sigI+^2 + sigI-^2 )
>>>
>>> The only CCP4 program I found that actually does this is mtzMADmod. This
>>> method also has the advantage that the original intensity values of I+
>>> and I- can be reconstructed from the mean and the anomalous difference
>>> (albeit with the loss of the original standard deviations).
>>>
>>> Method 1 (scalepack2mtz)
>>> should not be used. The resulting value is not the best estimate
>>> (maximum likelihood)
>>>
>>> Method 2 (in book by B. Rupp)
>>> gives the maximum likelihood average in case that the reflections are
>>> equivalent and is thus appropriate for the merging of the negative (or
>>> positive) set of Bijvoet mates, centric reflections (where the anomalous
>>> differences are zero) or in the case of an non-anomalous dataset the
>>> merging of symmetry equivalent reflections.
>>>
>>> Method 3
>>> gives a more realistic sigma value in the case that the individual
>>> intensity values are far apart and their individual standard deviations
>>> are small. Consider the example I have posted:
>>>
>>> I+: 23841.50 sigI+: 634.01 I-: 9628.57, sigI-: 264.75
>>> Method 2: Imean=11738.95, sigIMean=244.31
>>> Method 3: Imean=11738.95, sigIMean=7106.47
>>>
>>> If the I+ and I- values above actually were symmetry equivalent
>>> reflections in an non-anomalous dataset, the sigImean from method 2 is
>>> ridiculously small and method 3 gives a far more realistic value. If
>>> method 3 is the best mathematical solution to this problem I am not able
>>> to judge and I have to trust the statistician (or programmer) who
>>> implemented this solution.
>>>
>>> Cheers,
>>> Markus
>>>
>>> On 10/02/12 01:47 PM, Markus Meier wrote:
>>>
 Dear all,
 I have a anomalous dataset, processed in HKL2000. Scalepack outputs a
 file containing the separately merged sets of the Friedel pairs I- and
 I+ and their standard deviations sigI+ and sigI-. Scalepack does not
 output the averaged intensities (Imean) and the standard deviations
 (sigIMean).

 The CCP4 program truncate that I use to convert the intensities to
 amplitudes requires Imean, I- and I+ and the respective standard
 deviations in its input file.

 I have now found at least three different methods to generate the
 averaged intensities from the Friedel pairs:

 1) scalepack2mtz

   uses standard deviations for the weights:
   weights w = 1/sigI

   Imean = (w+*I+ + w-*I- ) / (w+ + w-)
   sigImean = 1 / (w+ + w-)

 2) Method described in Biomolecular crystallography by Bernhard Rupp, p.
 332/333
   to average symmetry equivalent reflections

   uses variances for the weights:
   weight w = 1/sigI^2

   Imean = (w+*I+ + w-*I- ) / (w+ + w-)
   sigImean = 1 

[ccp4bb] Evidence for hydrogen bonds between adjacent residues

[arka chakraborty]

Hi all,

This is a general question regarding the formation of hydrogen bonds in
proteins. I have found hydrogen bond between the back-bone atoms of the
adjacent residues  using computational methods, ie, between NH4-CO5  of
enkephalins. Is this  kind of feature acceptable and is there any such
experimental evidence? I could'nt find any reference.

Thanks in advance,

Regards,

ARKO

-- 

*ARKA CHAKRABORTY*
*CAS in Crystallography and Biophysics*
*University of Madras*
*Chennai,India*

[ccp4bb] effects of salt on twinned crystals

[Peter Hsu]

Hi all,

Thanks to all those who responded to my query about indexing my dataset. I'm 
beginning to suspect that the crystals are twinned. the crystals initially 
started as fused plates which were then optimized to single crystals that 
diffracted poorly (3.5-4). I then set up an additive screen, found an additive 
that changed crystal form (looked more like the plates from earlier), went 
through much optimization and got what appeared to be single rods, that 
diffracted much more strongly (2.5-3), although some crystals in the same drop 
looked like fused crystals, despite having single rods. 

The initial condition used LiCl as the salt, which during the optimization I 
changed to NaCl. I'm now looking for ideas to see how much more I can optimize 
this condition since I haven't found crystals in any other conditions (even did 
a seed screen). Does anyone have any experience with varying the different 
salts to get untwinned crystals? KCl better than NaCl? Ammonium chloride better 
than the others? Been looking at the Hofmeister series to get ideas.

Long post I realize, but many thanks for any previous experiences with salts.

Peter