[ccp4bb] Senior Protein Crystallographer at CRELUX

[Michael Schäffer]

To add additional capacity to our protein crystallography unit we are
looking for a Senior Research Scientist, PhD in Protein Biochemistry or
similar.

 

Senior Protein Crystallographer

The protein crystallographer will have the project responsibility for all
steps upstream of the purified protein. The position requires hands on work
as well as an up to date knowledge of modern crystallization techniques and
standard crystallographic software. Working knowledge in robotics supported
protein crystallization as well as data processing, structure solution,
model building, using (MR, MIR, MAD, SAD etc) methods is mandatory.

Working within multidisciplinary project teams your task will be the
determination of high-resolution, three-dimensional structures of
pharmaceutically important proteins, including crystallization and structure
solution of de novo protein structures and protein-ligand complexes. You
will be expected to have an interest in fragment-based screening, exploring
new ideas and implementing novel technologies 
 
Ideally you have a minimum of one year post-doctoral experience in protein
X-ray crystallography. Industrial experience would be a strong advantage.
The successful candidate has the ability for lab organization and will be a
strong team player actively supporting an in depth interaction with the
other R&D departments. Being responsible for customer projects the candidate
will also be involved in project management and strategic planning.
 

CRELUX offers crystallography services to its international customer
portfolio of Pharma-, Chemical- and Biotech companies. All steps from
concept to complex are performed by dedicated experts in house. CRELUX
provides fast and affordable access to relevant co-crystal structures as
well as de novo structure solution. 

 

Please send your application preferably via e-mail to: 

 

CRELUX GmbH

Am Klopferspitz 19a

82152 Martinsried

 

Dr. Michael Schäffer

[EMAIL PROTECTED]

Tel.: 089 700 760 170

www.crelux.com  

 

 



 

CRELUX GmbH

 

Dr. Michael Schaeffer

Chief Executive Officer

 

Am Klopferspitz 19a

82152 Martinsried

 

phone: +49 89 700760 170

e-mail:    [EMAIL PROTECTED]

web:  www.crelux.com

 

Amtsgericht München HRB 165552 - Managing Directors: Dr. Michael Schäffer,
Dr. Ismail Moarefi

 

This e-mail may contais confidential and/or privileged information. If you
are not the intended recipient (or have received this e-mail in error)
please notify the sender immediately and destroy this e-mail. Any
unauthorized copying, disclosure or distribution of the material in this
e-mail is strictly forbidden.

Diese E-Mail enthält vertrauliche und/oder rechtlich geschützte
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Re: [ccp4bb] space group R3(R32) or H3(H32)?

[Eleanor Dodson]

There is a lot of confusion about this!
You can call it R3:H  ( indexed with a=b and gamma = 120)
This is also called H 3 in the PDB deposition and the CCP4 symmetry 
libraries.
(But for the CCP4 library - it checks the axes and angles to decide 
whether this is using the H ( or hexagonal) convention..)


The name R3:R  or R3 is usually used for indexing where a=b=c, and 
alpha=beta=gamma.


However both conventions describe the same diffraction. pointless or 
othercell ( from the CCP4 prereleae) will give you the reindexing 
transformations to change from one convention to the other.


It is usually easier to visualise a protein molecule in the H3 
convention but not always..

Eleanor




linwoo kang wrote:

Dear all
 
Recently I collected a dataset, which is rhombohedral on indexing 
screen of HKL2000.

I processed the dataset as R3 and R32 at synchrotron.
But I realized it can be H3 or H32. Is it correct?
Cell dimensions are a=b >< c and alpha=90, beta=90, and gamma=120.
For me, synchrotron is only place to index and scale data.
 
Can I just change space group at CCP4i from sca file processed by R3 
into H3 space group or so?
Because cell dimensions are same, maybe indexing can be same. 
Accordingly just scaling can be enough for changing space groups but I 
am still concerned about completeness and rejected spots, which can be 
different at different space groups.  
 
Please advise me! Thanks.

Re: [ccp4bb] how to convert matrix to angle

[Eleanor Dodson]

Coot (and SSM) should give matrix - euler and polar angles! Paul?  Eugene?

But if you do the superposition with lsqkab (superpose molecules - match 
residues) then that gives all 3 ways.


Or use ROTMAT which converts everything to everything else.. ( rather 
clumsy though..)

Eleanor




Jiamu Du wrote:

Dear all:
I want to calculate the rotation angle between two similar domains. By 
using Coot, I can superposr the two domain and get the rotation 
matrix. But how to convert this matrix to an angle. Is there any 
program can calculate this ?

Thanks.


--
Jiamu Du
State Key Laboratory of Molecular Biology
Institute of Biochemistry and Cell Biology Shanghai Institutes for 
Biological Sciences

Chinese Academy of Sciences (CAS)

Re: [ccp4bb] how to convert matrix to angle

[Eleanor Dodson]

This sort of information is summarised on the MSDpisa site

http://www.ebi.ac.uk/msd/

Eleanor

U Sam wrote:


In this connection I like to know how symmetry (in degrees and 
translation) is calculated between two or more molecules in the 
asymmetric unit (A.U.).
Suppose if I download a PDB then I like to know the symmetry axis and 
center coordinate of symmetry axis between two or more molecules in A.U.


Thanks



Date: Sun, 8 Jul 2007 09:45:30 +0800
From: [EMAIL PROTECTED]
Subject: Re: [ccp4bb] how to convert matrix to angle
To: CCP4BB@JISCMAIL.AC.UK

Thanks a lot.
You are so kind.


 
On 7/7/07, *Kay Diederichs* <[EMAIL PROTECTED]

> wrote:

Jiamu Du schrieb:
> Dear all:
> I want to calculate the rotation angle between two similar
domains. By
> using Coot, I can superposr the two domain and get the
rotation matrix.
> But how to convert this matrix to an angle. Is there any
program can
> calculate this ?
> Thanks.
>
Jiamu Du,

If you have the rotation matrix
a11 a12 a13
a21 a22 a23
a31 a32 a33

then

(a11 + a22 + a33 - 1) / 2

is the cosine of the angle you're looking for.

HTH,

Kay
--
Kay Diederichs  
http://strucbio.biologie.uni-konstanz.de

email: [EMAIL PROTECTED]
  Tel +49 7531 88 4049
Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457
Konstanz





-- 
Jiamu Du

State Key Laboratory of Molecular Biology
Institute of Biochemistry and Cell Biology Shanghai Institutes for
Biological Sciences
Chinese Academy of Sciences (CAS) 




Local listings, incredible imagery, and driving directions - all in 
one place! Find it! 

Re: [ccp4bb] twin

[Eleanor Dodson]

Look at http://www.ccp4.ac.uk/dist/html/twinning.html for introduction..

Eleanor

Li Sheng wrote:
> Hi, Dear All,
>
> How could I know whether a crystal was twin or not from it's
> diffraction data?
> Thanx in advance.
>
>
>
>
> Sincerely,
> Li
> 07-08-2007 

[ccp4bb] freezing Ammonium Nitrate

[Gebhard Schertler]

I have obtained some promising X-tals in 2M Ammonium Nitrate. I am  
now looking for freezing conditions. Has anybody had experience in  
successfully freezing X-tals under similar conditions ? What was the  
best cryo-protectant and which concentration was optimal ?




Dr. Gebhard F. X. Schertler

Senior Scientist and Group Leader
MRC
Laboratory of Molecular Biology
Cambridge CB2 2QH

tel  0044 1223 402328
e-mail   [EMAIL PROTECTED]
web   http://www2.mrc-lmb.cam.ac.uk/SS/Schertler_G/

Re: [ccp4bb] freezing Ammonium Nitrate

[M T]

2007/7/12, Gebhard Schertler <[EMAIL PROTECTED]>:




 I have obtained some promising X-tals in 2M Ammonium Nitrate. I am now looking 
for freezing
conditions. Has anybody had experience in successfully freezing X-tals under 
similar conditions
? What was the best cryo-protectant and which concentration was optimal ?


Hi,

You have some informations in supplementary methods of this ref:

Structural insight into antibiotic fosfomycin biosynthesis by a
mononuclear iron enzyme
Luke J. Higgins, Feng Yan, Pinghua Liu, Hung-wen Liu and Catherine L. Drennan
Nature 437, 838-844 (1 October 2005)

Informations are in the first doc at this page:
http://www.nature.com/nature/journal/v437/n7060/suppinfo/nature03924.html
30% xylitol, 2.0M ammonium sulfate, and 100mM  Tris-HCl pH 8.0

Some other good cryoprotectants are small PEGs, glycerol, MPD...

Michel.

[ccp4bb] Answer concerning restraints for 2`-deoxyuridine in Refmac

[Kristina Lakomek]

Hello,

if anybody else needs the .cif file correctly describing a 2`-deoxyuridine its
bonds to the adjacent nucleotides in a DNA strand for Refmac  :  
in the attachment you can find the file I kindly received at my question.

Best regards,
 Kristina

Ud_cif.doc
Description: MS-Word document

Re: [ccp4bb] protein contacts

[Eleanor Dodson]

msd pisa does that

eleanor

[EMAIL PROTECTED] wrote:


Dear all,

I’m wondering anyone can recommend some programs or servers to 
evaluate protein-protein contacts. I’m currently have a homogeneous 
tetramer. However, the protein exists as a dimer in solution. I’m 
thinking where to cut the line to generate a dimer from the available 
structure.


Thanks for your time!

Regards,

Hua

___

Hua Yuan


Indiana University Bloomington
e-mail: [EMAIL PROTECTED]

Re: [ccp4bb] shelx HKLF4 to mtz conversion?

[Eleanor Dodson]

Is this a SHELX data set where the FreeR is flagged as -1?
There seems to be a variety of methods ..
But if you read in the FreeR flag from SHELX and ask to have a FreeRflag 
output  the convert -t o - mtz script under Reflection data utilities 
will output the SHELX value


Eleanor



Leonard Thomas wrote:
I have a Shelx HKLF4 formated reflection file that I would like to 
convert to a mtz file.  The primary reason is to transfer the freeR 
set.  I found a couple of convoluted ways of converting the reflection 
data, but no real way of getting the freeR set to transfer.


Any suggestions?

Cheers


Leonard M. Thomas Ph.D.
Director, Macromolecular Crystallography Laboratory
Howard Hughes Medical Institute
California Institute of Technology
Division of Biology
1200 E. California Blvd.  MC 114-96
Pasadena, CA 91125
626-395-2453
[EMAIL PROTECTED]
http://www.br.caltech.edu/cmclab

Re: [ccp4bb] Metal-ligand(s) positioning following refinement...

[Eleanor Dodson]

Yes there is a way to do something anyway.
Is your metal only linked to protein or are there extra atoms as part of 
the metal?


If there is protein lins you need to make a LINK record in your PDB and 
provide a dictionary description of your expected geometry.


 If you have more details I can be more specific.

On the GUI if you specify "review restraints" as your first REFMAC call 
it will make an attempt to produce such a dictionary entry - you will 
want to edit it, but it is a start


Eleanor


James Pauff wrote:

Good day all,

I have a metal center in my enzyme active site, in a
roughly square pyramidal coordination.  I know from
EXAFS and other work how this coordination sphere
should look, but following REFMAC the cofactor here
does not end up realistically coordinated/oriented. 
Although it is in the density and roughly in position,

the coordination sphere and ligands are not correct,
and not correctly connected.

Is there a means by which I can position this
cofactor, establish the connectivity I want, and then
specifically restrain this cofactor/center while
refining?  


Thank you,
Jim


   


Need a vacation? Get great deals
to amazing places on Yahoo! Travel.
http://travel.yahoo.com/


  

Re: [ccp4bb] modelling radiation damage of Asp/Glu (occ vs. B factor)

[Eleanor Dodson]

John Pak wrote:

Hi all, I was hoping to receive some guidance on the following subject.

I'm refining a structure using REFMAC that shows all the symptoms of 
radiation damage.  Namely partially broken disulphide bonds and 
decarboxylated Asp/Glu residues.  I have an idea of how to handle the 
partially broken disulphides.  I was wondering how people model 
decarboxylated Asp/Glu residues.  Do you adjust the occupancy of the 
carboxylic acid moiety until the negative Fo-Fc density goes away, or 
do you losen the side-chain B factor restraint in REFMAC to something 
higher, like 30 A^2.  I don't know which is more appropriate.


Thanks.





It is difficult because your merged data set will include some 
information from complete ASN etc and some from damaged ones..
Prob. all you can do is use the occupancy factor to partially model what 
has happened..

Eleanor

[ccp4bb] CCP4 at ACA 2007, Salt Lake City

[Charles Ballard]

Dear All,

We at CCP4 look forward to seeing you at this year's ACA in Salt Lake  
City.


Please drop by the CCP4 booth, #110, to learn about the latest  
developments in the suite, and have your queries answered (or at  
least forwarded onto someone who might know the answer.


CCP4 staff will be on hand to demonstrate some of the new and coming  
attraction, such as MrBUMP, BALBES, PISA, CCP4MG, etc.  Special Guest  
appearances by CCP4 Fellow Paul Emsley (Dr. Coot).


See you there (or in a watering hole nearby)

Charles Ballard
CCP4

Re: [ccp4bb] Program to 'visualize' the reciprocal space ?

[Sergei Strelkov]

Many thanks to good people who have responded
to my message! Apparently I have to apologize for not formulating
my question clearly enough. Here is more explanation.

According to Ewald construction, diffraction images
collected by oscillation method correspond to thin 'curved' slices of the
reciprocal space. What I am looking for is a program to generate the 
reciprocal

space (as a 3D map) from these 'slices' directly, *without* any indexing or
integration of I's. This is a simple purely geometrical calculation.

This is *not* anything routinely done for normal high-quality crystal data.
For a good dataset, such a conversion should simply yield a lattice
with distinct points. For our partially-ordered crystals, this should 
help us

visualizing the actual 'shapes' of our reflections (many of them
are smeared/overlapping).

My guess that folks working with semi-ordered systems, such as liquid 
crystals

or lipid bilayers, should have some programs like that...
any ideas?

Thank you again,
Sergei.



Dear All,

we are dealing with a difficult case of a 'partially ordered' protein 
crystal.

Here it would be very useful to view the reciprocal space
as a 3D map. Is anyone aware of a program that would convert
standard oscillation data (one-degree frames, mar225)
into such a map? What we need is a direct conversion.
There is a program in CCP4 that is able to 'visualize' the reciprocal
space, but it requires hkl's as input.

Thank you,
Sergei Strelkov




--
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Department of Pharmaceutical Sciences, Catholic University of Leuven
Campus Gasthuisberg, O&N2 Herestraat 49 bus 822, 3000 Leuven, Belgium
Work phone: +32 16 33 08 45  Fax: +32 16 32 34 69
Mobile: +32 486 29 41 32
E-mail:  [EMAIL PROTECTED] 



Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

Re: [ccp4bb] Program to 'visualize' the reciprocal space ?

[Winter, G (Graeme)]

Hi Sergei,

I don't think that there is a program available to do what you want, but
I think that the tools are there for you to make one. The biggest
challenge you will have is keeping the mathematics straight!

So, if you start off with something like the DiffractionImage library,
this will help with reading in the diffraction images - contact Francois
Remacle for this one ([EMAIL PROTECTED]) - you will need to know the
beam centre, wavelength and detector distance *exactly* for this to be
useful. Well, more exactly than is normal in image headers ;o)

Next you will need something which can render the 3D density that you
will generate - I would google "voxel" and see what you can come up
with. I vaguely remember some libraries for this kind of thing available
in C/C++. Common uses are medical imaging.

Now comes the tricky bit. You will need to work through each image and
for each pixel add the approptiate constant times the pixel value to the
"right" voxel given by the diffraction geometry. The calculations for
this appear in most crystallography texts, though I expect computing
said constant will be non-trivial. The constant will correct for the
"volume" of the pixel in reciprical space, determined by the position on
the detector face and the oscillation angle.

After that you should be about done.

Oh, and you might want to do this on rather a large computer if you
intend to get a high resolution representation of each reflection on all
of the images. If you are wanting a voxel cube 1000 pixels to a side
(say) as int*2 (say) this is a 2GB before you have read in your first
image. Without some kind of prediction and shoeboxing (as goes on inside
XDS, for instance) you won't be able to avoid this.

Good luck,

Graeme

 

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Sergei Strelkov
Sent: 12 July 2007 16:29
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Program to 'visualize' the reciprocal space ?

Many thanks to good people who have responded to my message! Apparently
I have to apologize for not formulating my question clearly enough. Here
is more explanation.

According to Ewald construction, diffraction images collected by
oscillation method correspond to thin 'curved' slices of the reciprocal
space. What I am looking for is a program to generate the reciprocal
space (as a 3D map) from these 'slices' directly, *without* any indexing
or integration of I's. This is a simple purely geometrical calculation.

This is *not* anything routinely done for normal high-quality crystal
data.
For a good dataset, such a conversion should simply yield a lattice with
distinct points. For our partially-ordered crystals, this should help us
visualizing the actual 'shapes' of our reflections (many of them are
smeared/overlapping).

My guess that folks working with semi-ordered systems, such as liquid
crystals or lipid bilayers, should have some programs like that...
any ideas?

Thank you again,
Sergei.


> Dear All,
>
> we are dealing with a difficult case of a 'partially ordered' protein 
> crystal.
> Here it would be very useful to view the reciprocal space as a 3D map.

> Is anyone aware of a program that would convert standard oscillation 
> data (one-degree frames, mar225) into such a map? What we need is a 
> direct conversion.
> There is a program in CCP4 that is able to 'visualize' the reciprocal 
> space, but it requires hkl's as input.
>
> Thank you,
> Sergei Strelkov
>


--
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Department of Pharmaceutical Sciences, Catholic University of Leuven
Campus Gasthuisberg, O&N2 Herestraat 49 bus 822, 3000 Leuven, Belgium
Work phone: +32 16 33 08 45  Fax: +32 16 32 34 69
Mobile: +32 486 29 41 32
E-mail:  [EMAIL PROTECTED] 


Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

Re: [ccp4bb] Program to 'visualize' the reciprocal space ?

[Peter Zwart]

I don't think that there is a program available to do what you want, but


What about APEX2 from Bruker?

P

Re: [ccp4bb] Program to 'visualize' the reciprocal space ?

[Jim Pflugrath]

What about CrystalClear from Rigaku?

-Original Message-
From: Peter Zwart <[EMAIL PROTECTED]>
Date: Thu, 12 Jul 2007 08:55:04 
To:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Program to 'visualize' the reciprocal space ?

> I don't think that there is a program available to do what you want, but

What about APEX2 from Bruker?

P

Re: [ccp4bb] Program to 'visualize' the reciprocal space ?

[Raji Edayathumangalam]

I am often receiving only responses to the original queries posted on CCP4BB 
but not the original
query itself. They are not going to my spam box either.

Has anyone else noticed the same?

Thanks.
Raji


-Included Message--
>Many thanks to good people who have responded
>to my message! Apparently I have to apologize for not formulating
>my question clearly enough. Here is more explanation.
>
>According to Ewald construction, diffraction images
>collected by oscillation method correspond to thin 'curved' slices of the
>reciprocal space. What I am looking for is a program to generate the 
>reciprocal
>space (as a 3D map) from these 'slices' directly, *without* any indexing or
>integration of I's. This is a simple purely geometrical calculation.
>
>This is *not* anything routinely done for normal high-quality crystal data.
>For a good dataset, such a conversion should simply yield a lattice
>with distinct points. For our partially-ordered crystals, this should 
>help us
>visualizing the actual 'shapes' of our reflections (many of them
>are smeared/overlapping).
>
>My guess that folks working with semi-ordered systems, such as liquid 
>crystals
>or lipid bilayers, should have some programs like that...
>any ideas?
>
>Thank you again,
>Sergei.
>
>
>> Dear All,
>>
>> we are dealing with a difficult case of a 'partially ordered' protein 
>> crystal.
>> Here it would be very useful to view the reciprocal space
>> as a 3D map. Is anyone aware of a program that would convert
>> standard oscillation data (one-degree frames, mar225)
>> into such a map? What we need is a direct conversion.
>> There is a program in CCP4 that is able to 'visualize' the reciprocal
>> space, but it requires hkl's as input.
>>
>> Thank you,
>> Sergei Strelkov
>>
>
>
>-- 
>Prof. Sergei V. Strelkov
>Laboratory for Biocrystallography
>Department of Pharmaceutical Sciences, Catholic University of Leuven
>Campus Gasthuisberg, O&N2 Herestraat 49 bus 822, 3000 Leuven, Belgium
>Work phone: +32 16 33 08 45  Fax: +32 16 32 34 69
>Mobile: +32 486 29 41 32
>E-mail:  [EMAIL PROTECTED] 
>
>
>Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
>
>
-End of Included Message--

[ccp4bb] Postdoctoral Opportunities

[Cheryl Kerfeld]

--
Cheryl A. Kerfeld Ph.D.
Education/Structural Genomics
DOE Joint Genome Institute
2800 Mitchell Drive
Walnut Creek, CA 94598
(925) 296-5691
[EMAIL PROTECTED]



postdoc2_ck.doc
Description: MS-Word document

[ccp4bb] Asking help about refmac5?

[zhongzhou chen]

Dear Sir or madam,

 I have some questions about refmac5.

 I am new to Refmac. I optimized the structure with CNS (Rwork: 23%, Rfree: 
25%).

Cell :71.48071.480   151.81390.00090.00090.000
Space group p43212
resolution 100 1.97

protein contain 350 amino acids.
Nmol/asym: 1

number of amino acids built: 330
number of  waters:330
three glycerols 
six sulfate ions.



My friends told me that refmac5 will get lower Rfree and Rfactor.
 
 I refined the pdb structure from CNS using restrained refinement.

  Ncyc   Rfact   Rfree FOM LLG  rmsBOND  rmsANGLE rmsCHIRAL $$
$$

using TLS:
 0   0.215   0.2210.763  165320.60.0061.2500.092
 1   0.189   0.2300.751  162623.70.0221.6800.116
 2   0.187   0.2330.751  162500.20.0221.7240.119
 3   0.185   0.2390.747  162269.00.0221.7900.123
 4   0.185   0.2410.748  162314.80.0221.8090.124
 5   0.185   0.2440.744  162248.10.0231.8310.126
 6   0.185   0.2450.744  162353.00.0231.8390.126
 7   0.185   0.2470.743  162226.20.0231.8580.128
 8   0.186   0.2480.741  162430.40.0231.8520.128
 9   0.185   0.2480.741  162300.20.0231.8570.128
10   0.185   0.2490.740  162317.20.0231.8610.129


without TLS:
  Ncyc   Rfact   Rfree FOM LLG  rmsBOND  rmsANGLE rmsCHIRAL $$
$$
 0   0.217   0.2230.764  166172.20.0061.2500.092
 1   0.192   0.2340.752  163514.50.0221.6760.116
 2   0.190   0.2370.752  163400.60.0221.7150.119
 3   0.188   0.2420.747  163218.20.0221.7830.124
 4   0.188   0.2440.747  163276.60.0221.8020.125
 5   0.188   0.2480.744  163167.90.0231.8280.127
 6   0.188   0.2480.744  163271.00.0231.8320.127
 7   0.188   0.2510.743  163144.50.0231.8490.128
 8   0.189   0.2510.742  163331.20.0231.8450.129
 9   0.188   0.2520.741  163209.30.0231.8500.129
10   0.188   0.2530.741  163249.60.0231.8540.129


May I ask some questions?

1. Can I use the structure in zero cycle to deposit in pdb bank?
   Because its rfree is lowest  and it just come from CNS result without any 
change of B 

factor?

2. Why Rfree increase during refinement?

3. Usually,   delta(Rwork,Rfree) is lower than 3.0 percent for a good structure.
 However,  there is 7%  if using the final refinement structure. 
 How can I do to reduce Rfree?

4. I use the TLS to refine during restrained refinement. Why the result 
structure show 

that there is no tls groups? 

 The TLS format 
RANGE  'A  11.' 'A  60.' ALL
ORIGIN   -5.756  -6.929  21.439
T-0.0229 -0.0472 -0.0103 -0.0487 -0.0019  0.0414
L 0.8419  0.3881  3.8499 -0.2446 -1.1643  0.8341
S-0.0615 -0.0707 -0.0949 -0.1532  0.1007  0.1020  0.2434 -0.2249



 The pdb output file is shown as below.

REMARK   3   TLS DETAILS
REMARK   3   NUMBER OF TLS GROUPS  : NULL



thanks


Best regards, 
  
zhong chen
[EMAIL PROTECTED]
2007-07-12



This communication is for the use of the intended recipient only.  It may 
contain information that is privileged and confidential.  If you are not the 
intended recipient of this communication, any disclosure, copying, further 
distribution or use thereof is prohibited.  If you have received this 
communication in error, please advise me by return e-mail or by telephone and 
delete/destroy it.

Re: [ccp4bb] Asking help about refmac5?

[Garib Murshudov]

1) Rfree in the first cycle seem to be more apparent than actual. You  
need to check you free reflection conversion. It may turn out that you

have more reflections for free than for working R.
2) You may need to use tighter restraints. For example by changing  
weight matrix value to smaller number or by using weight auto.


I would not deposit with 0 cycles.

regards
Garib


On 12 Jul 2007, at 21:38, zhongzhou chen wrote:


Dear Sir or madam,

 I have some questions about refmac5.

 I am new to Refmac. I optimized the structure with CNS (Rwork:  
23%, Rfree: 25%).


Cell :71.48071.480   151.81390.00090.00090.000
Space group p43212
resolution 100 1.97

protein contain 350 amino acids.
Nmol/asym: 1

number of amino acids built: 330
number of  waters:330
three glycerols
six sulfate ions.



My friends told me that refmac5 will get lower Rfree and Rfactor.

 I refined the pdb structure from CNS using restrained refinement.

  Ncyc   Rfact   Rfree FOM LLG  rmsBOND  rmsANGLE  
rmsCHIRAL $$

$$

using TLS:
 0   0.215   0.2210.763  165320.60.006 
1.2500.092
 1   0.189   0.2300.751  162623.70.022 
1.6800.116
 2   0.187   0.2330.751  162500.20.022 
1.7240.119
 3   0.185   0.2390.747  162269.00.022 
1.7900.123
 4   0.185   0.2410.748  162314.80.022 
1.8090.124
 5   0.185   0.2440.744  162248.10.023 
1.8310.126
 6   0.185   0.2450.744  162353.00.023 
1.8390.126
 7   0.185   0.2470.743  162226.20.023 
1.8580.128
 8   0.186   0.2480.741  162430.40.023 
1.8520.128
 9   0.185   0.2480.741  162300.20.023 
1.8570.128
10   0.185   0.2490.740  162317.20.023 
1.8610.129



without TLS:
  Ncyc   Rfact   Rfree FOM LLG  rmsBOND  rmsANGLE  
rmsCHIRAL $$

$$
 0   0.217   0.2230.764  166172.20.006 
1.2500.092
 1   0.192   0.2340.752  163514.50.022 
1.6760.116
 2   0.190   0.2370.752  163400.60.022 
1.7150.119
 3   0.188   0.2420.747  163218.20.022 
1.7830.124
 4   0.188   0.2440.747  163276.60.022 
1.8020.125
 5   0.188   0.2480.744  163167.90.023 
1.8280.127
 6   0.188   0.2480.744  163271.00.023 
1.8320.127
 7   0.188   0.2510.743  163144.50.023 
1.8490.128
 8   0.189   0.2510.742  163331.20.023 
1.8450.129
 9   0.188   0.2520.741  163209.30.023 
1.8500.129
10   0.188   0.2530.741  163249.60.023 
1.8540.129



May I ask some questions?

1. Can I use the structure in zero cycle to deposit in pdb bank?
   Because its rfree is lowest  and it just come from CNS result  
without any change of B


factor?

2. Why Rfree increase during refinement?

3. Usually,   delta(Rwork,Rfree) is lower than 3.0 percent for a  
good structure.

 However,  there is 7%  if using the final refinement structure.
 How can I do to reduce Rfree?

4. I use the TLS to refine during restrained refinement. Why the  
result structure show


that there is no tls groups?

 The TLS format
RANGE  'A  11.' 'A  60.' ALL
ORIGIN   -5.756  -6.929  21.439
T-0.0229 -0.0472 -0.0103 -0.0487 -0.0019  0.0414
L 0.8419  0.3881  3.8499 -0.2446 -1.1643  0.8341
S-0.0615 -0.0707 -0.0949 -0.1532  0.1007  0.1020  0.2434 -0.2249



 The pdb output file is shown as below.

REMARK   3   TLS DETAILS
REMARK   3   NUMBER OF TLS GROUPS  : NULL



thanks


Best regards,

zhong chen
[EMAIL PROTECTED]
2007-07-12



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[ccp4bb] NSLS II User Workshop - July 17-18,2007 - Last day to Register

[Stojanoff, Vivian]

NSLS-II USER WORKSHOP - Last day to register

https://www.bnl.gov/nsls2meeting

We would like to invite all members of the community to participate in
the NSLS-II user workshop hosted by Brookhaven National Laboratory on
July 17-18th. Following general sessions on the 17th several specific
Life Science workshops are planned on July 18th.

The aim of these sessions is to lay the ground stone for the needs of the Life 
Science
community.  For further information follow the link:  
https://www.bnl.gov/nsls2meeting
or contact one of the session organizers.

Vivian Stojanoff
for the MX session organizing committee

Robert Sweet & Vivian Stojanoff

Re: [ccp4bb] Program to 'visualize' the reciprocal space ?

[Jim Pflugrath]

Frank and everybody else ... I must apologize because the CrystalClear 
Reciprocal Space Viewer (click on the icon in the toolbar) uses a refln 
list file and does not convert pixel values in images to an undistorted 
view of reciprocal space.


Jim

On Thu, 12 Jul 2007, Frank von Delft wrote:


Really?  How?

Jim Pflugrath wrote:

What about CrystalClear from Rigaku?

[ccp4bb] Phaser question !!!

[john kryst]

Hi all !!!

  Is it possible to fix one domain and search for the second one in
phaser !!!  What are the keywords to use.
I have a protein with two domains. It i give both the domains together or as
two ensembles it is not finding the solution. If i give only one domain it
is giving the solution (R and Rfee is 28 and 33). But it is not finding the
second one.

Thanks in advance for your suggestions..

regards
John

Re: [ccp4bb] Phaser question !!!

[Fred. Vellieux]

On Fri, 13 Jul 2007, john kryst wrote:

> Hi all !!!
> 
>Is it possible to fix one domain and search for the second one in
> phaser !!!  What are the keywords to use.
> I have a protein with two domains. It i give both the domains together or as
> two ensembles it is not finding the solution. If i give only one domain it
> is giving the solution (R and Rfee is 28 and 33). But it is not finding the
> second one.
> 
> Thanks in advance for your suggestions..
> 
> regards
> John

Yes it is possible to do what you are trying to do within Phaser. I am
using scripts. What you need to do is to introduce within the Phaser
script a solution card, e.g.

SOLU 6DIM ENSE TET1 EULER 327.076 56.322 181. FRAC 0.12840 -0. 0.27387

The phaser script will look like:

#!/bin/csh -f

cd /homei/vellieux/mpb11a/phaser_trimer

time /home/prog/phaser/bin/phaser > phaser.out << EOI

MODE MR_AUTO

HKLIN rescut.mtz

LABIN F = FP SIGF = SIGFP

PACK 6

ENSEMBLE TET1 PDBFILE trimer.pdb IDENTITY 0.221

COMPOSITION PROTEIN MW 168960 NUM 2

SEARCH ENSEMBLE TET1 NUM 1 ROOT phaser_trimer

SOLU 6DIM ENSE TET1 EULER 327.076 56.322 181. FRAC 0.12840 -0. 0.27387

EOI



Fred.

-- 

 Fred. Vellieux, esq.

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