Re: [ccp4bb] balbes run

[Dr. F Long]

Sorry Ed,

We will add that function to the server in a few days.

Fei 

On Wed, 27 Apr 2011 13:49:17 -0400, Ed Pozharski 
wrote:
> Is there any way to download all of the files produced by a BALBES run
> on YSBL server at once (as opposed to going through every item
> individually)?  
> 
> A related question is what is a minimal set of files I will actually
> need to analyze the solution?  refmac_final_result.* and summary.log -
> is that all I actually need?
> 
> Thanks,
> 
> Ed.

[ccp4bb] PhD student position at Univ. of Milan

[stefano ricagno]

Dear BB readers,
at the University of Milan we are currently looking for a motivated candidate 
for a PhD student position in the lab of Prof. Bolognesi, under Bolognesi's and 
my supervision.


The project will be focusing on crystallographic and biophysical studies of 
Beta-2 microglobulin, an amyloid prone human protein. Some background in 
biochemistry/biophysics/crystallography is expected and some experience in 
protein expression and purification would be very welcome.


For more details about the project, you can check 
http://users.unimi.it/stericagno/default.html
and/or contact me directly


Any interested candidate should send a short CV and two references to 
this address ciciu...@hotmail.com


all the best 


Stefano Ricagno

Dept. of Biomolecular Sciences & Biotechnology
University of Milano
Via Celoria, 26. I-20133 Milano (Italy)
Tel. +39 02 5031 4894
Fax. +39 02 5031 4895http://users.unimi.it/stericagno/default.html
http://whc.unesco.org/en/list/1287

[ccp4bb] DNA oligonucleotide purification

[Wallen, Jamie]

Title: DNA oligonucleotide purification



All,

Our laboratory is looking for a new column to purify short (40mers or less) DNA oligonucleotides that will be used for crystallization setups. I wanted to ask if anyone has suggestions of a column that will give excellent separation of N and N-1 products. We have a Shimadzu HPLC system. We are considering Dionex columns as well as Oligonucleotide Separation C18 columns from Waters, but if there are others that are better we would like to know. Any suggestions will be greatly appreciated. Thank you!

Jamie Wallen

Re: [ccp4bb] DNA oligonucleotide purification

[Kushol Gupta]

 

Hi Jamie - 

 

We've had good success with these columns from Dionex (the DNAPac PA-100 and
the DNAPac PA200 (Analytical 4x250mm and Semi-Prep 9x250mm,)).  We use them
precisely for the application you describe.

 

http://www.dionex.com/en-us/products/columns/bio/nucleic-acid/dnapac-pa100/l
p-73370.html

http://www.dionex.com/en-us/products/columns/bio/nucleic-acid/dnapac-pa200/l
p-73371.html

 

cheers,

 

Kushol

 

Kushol Gupta, Ph.D.

Research Associate

Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School of Medicine

 mailto:kgu...@stwing.upenn.edu> kgu...@mail.med.upenn.edu

215-573-7260 / 267-259-0082

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Wallen, Jamie
Sent: Thursday, April 28, 2011 9:32 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] DNA oligonucleotide purification

 

All,

Our laboratory is looking for a new column to purify short (40mers or less)
DNA oligonucleotides that will be used for crystallization setups. I wanted
to ask if anyone has suggestions of a column that will give excellent
separation of N and N-1 products. We have a Shimadzu HPLC system. We are
considering Dionex columns as well as Oligonucleotide Separation C18 columns
from Waters, but if there are others that are better we would like to know.
Any suggestions will be greatly appreciated. Thank you!

Jamie Wallen 

[ccp4bb] GST tag digestion conditions

[gauri misra]

Hi everyone,
This is although an off topic question but I would certainly seek expert
advices on the following query:



I have a GST-tagged protein that is purified in presence of the steroids. I
carry out an in column digestion using thrombin. Digestion buffer
compositin:
50mM Tris pH: 8.0,
 150mM NaCl,
 10% glycerol,
 100micro Molar steroid,
 0.15 n-octyl-beta glucoside,
1mM DTT,
3mM CaCl2,
12units thrombin/ml of protein

Problem:  Protein when purified in presence of steroid like testosterone
gets around 85% digested on incubating at 4 degree C for 24 hours with the
above specified thrombin quantity.
However, when the steroid is replaced by some plant steroids like
phytoestrogen there is no GST digestion under the same conditions?

Can someone provide some inputs for achieving the perfect GST-digestion?
Whether a change in some of the constituents of the buffer or some other
factor could be effective?

Thanks in advance for any suggestions.

Cheers

Gauri

Re: [ccp4bb] DNA oligonucleotide purification

[Wallen, Jamie]

Title: Re: [ccp4bb] DNA oligonucleotide purification



Kushol,

Thank you for the reply. Might I ask what kind of HPLC system you have? Our HPLC is old and has stainless steel pumps, and to our knowledge this is not compatible with the Dionex columns (due to metal leaching). Dionex has recommended either a titanium or peek system. As our HPLC is still running well, we were hoping to find a column that can tolerate the stainless steel. 

Jamie


On 4/28/11 9:11 AM, "Kushol Gupta"  wrote:

 
Hi Jamie – 
 
We’ve had good success with these columns from Dionex (the DNAPac PA-100 and the DNAPac PA200 (Analytical 4x250mm and Semi-Prep 9x250mm,)).  We use them precisely for the application you describe.
 
http://www.dionex.com/en-us/products/columns/bio/nucleic-acid/dnapac-pa100/lp-73370.html
http://www.dionex.com/en-us/products/columns/bio/nucleic-acid/dnapac-pa200/lp-73371.html
 
cheers,
 
Kushol
 

Kushol Gupta, Ph.D.
Research Associate
Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School of Medicine
kgu...@mail.med.upenn.edu mailto:kgu...@stwing.upenn.edu> 
215-573-7260 / 267-259-0082
 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Wallen, Jamie
Sent: Thursday, April 28, 2011 9:32 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] DNA oligonucleotide purification
 
All,

Our laboratory is looking for a new column to purify short (40mers or less) DNA oligonucleotides that will be used for crystallization setups. I wanted to ask if anyone has suggestions of a column that will give excellent separation of N and N-1 products. We have a Shimadzu HPLC system. We are considering Dionex columns as well as Oligonucleotide Separation C18 columns from Waters, but if there are others that are better we would like to know. Any suggestions will be greatly appreciated. Thank you!

Jamie Wallen 

Re: [ccp4bb] DNA oligonucleotide purification

[Kushol Gupta]

We're using an older Dynamax system that is outfitted with PEEK throughout.


 

Cheers,

Kushol

 

From: Wallen, Jamie [mailto:jwal...@biochem.wustl.edu] 
Sent: Thursday, April 28, 2011 10:17 AM
To: Kushol Gupta; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] DNA oligonucleotide purification

 

Kushol,

Thank you for the reply. Might I ask what kind of HPLC system you have? Our
HPLC is old and has stainless steel pumps, and to our knowledge this is not
compatible with the Dionex columns (due to metal leaching). Dionex has
recommended either a titanium or peek system. As our HPLC is still running
well, we were hoping to find a column that can tolerate the stainless steel.


Jamie


On 4/28/11 9:11 AM, "Kushol Gupta"  wrote:


Hi Jamie - 
 
We've had good success with these columns from Dionex (the DNAPac PA-100 and
the DNAPac PA200 (Analytical 4x250mm and Semi-Prep 9x250mm,)).  We use them
precisely for the application you describe.
 
http://www.dionex.com/en-us/products/columns/bio/nucleic-acid/dnapac-pa100/l
p-73370.html
http://www.dionex.com/en-us/products/columns/bio/nucleic-acid/dnapac-pa200/l
p-73371.html

cheers,
 
Kushol
 

Kushol Gupta, Ph.D.
Research Associate
Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School of Medicine
kgu...@mail.med.upenn.edu mailto:kgu...@stwing.upenn.edu> 
215-573-7260 / 267-259-0082


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Wallen, Jamie
Sent: Thursday, April 28, 2011 9:32 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] DNA oligonucleotide purification

All,

Our laboratory is looking for a new column to purify short (40mers or less)
DNA oligonucleotides that will be used for crystallization setups. I wanted
to ask if anyone has suggestions of a column that will give excellent
separation of N and N-1 products. We have a Shimadzu HPLC system. We are
considering Dionex columns as well as Oligonucleotide Separation C18 columns
from Waters, but if there are others that are better we would like to know.
Any suggestions will be greatly appreciated. Thank you!

Jamie Wallen 

Re: [ccp4bb] DNA oligonucleotide purification

[Phoebe Rice]

  We actually screen with unpurified oligos (up to just over 30nt) and it works 
just fine.  Saves lots of time & $$.
  If we get hopefull crystals, we pay for purification or do it ourselves by 
gel.  Sometimes it makes the crystals better and sometimes it doesn't. 
  Phoebe

=
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: Thu, 28 Apr 2011 08:32:23 -0500
>From: CCP4 bulletin board  (on behalf of "Wallen, 
>Jamie" )
>Subject: [ccp4bb] DNA oligonucleotide purification  
>To: CCP4BB@JISCMAIL.AC.UK
>
>   All,
>
>   Our laboratory is looking for a new column to purify
>   short (40mers or less) DNA oligonucleotides that
>   will be used for crystallization setups. I wanted to
>   ask if anyone has suggestions of a column that will
>   give excellent separation of N and N-1 products. We
>   have a Shimadzu HPLC system. We are considering
>   Dionex columns as well as Oligonucleotide Separation
>   C18 columns from Waters, but if there are others
>   that are better we would like to know. Any
>   suggestions will be greatly appreciated. Thank you!
>
>   Jamie Wallen

Re: [ccp4bb] AMoRe fails to use model coordinates

[Eleanor Dodson]

Hmm - I use this quite a bit.
ifier.
You cant start Autoamore for a particular model until that has been 
entered into the model database - the first Q you are asked from the GUI 
is "Which model?"   But you can certainly close the model database once 
you have entered the model name with a unique identifier.


The orde of operations is:
sortfun to reformat the observed data
tabfun to generate SFs from the model

rotfun
trafun
fitfun



However if you have already run sortfun or tabfun with that input the 
gui will not repeat the steps.
Could you have used the same name for different models perhaps - that 
will get the software well confused!


 Eleanor


On 04/27/2011 04:26 PM, Chris Richards: on wrote:

On 27 Apr 2011, at 15:02, Edward A. Berry wrote:


No, that would be the TABFUN step. You are running SORTFUN which takes your
experimental data and puts in the the .tab format required by the subsequent
routines. And with the HKLIN command line variable you are telling it to
get data from AmoreModel_MR_trial.mtz . Does that file exist, is it
readable, and path name correct?


The file doesn't exist, it's a figment of the GUI's imagination.  After some 
poking around, I've now got it to work properly.

The problem seems to be that the GUI is very sensitive to the order in which 
you enter data.  When you choose to run AMoRe, it pops up an AMoRe window and a 
Model Database window.  If you enter data into these in the order specified in 
the tutorial, it will run the scripts for a model in the form of SFs from an 
MTZ, even though the Model Database window claims to be using a model in the 
form of coordinates.

The trick to getting it to work seems to be:

1) Open the Model Database window.  Enter your pdb filename.  Don't even think about clicking "Close", 
despite what the tutorial says.  Click "Save&Exit", and never open the window again.  If you do 
have to open it again, "Restore Default Parameters" and start from scratch.

2) Open the AMoRe window, set up the job parameters and run the job.

Doing this will get it to run TABFUN on your pdb file rather than SORTFUN on a 
non-existent mtz file.  Most of the time.

Thanks to Stefano Trapani and Jorge Navaza for pointing us in the direction of 
the standalone AMoRe.

Chris
--
Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk


The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

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[ccp4bb] Error in LABIN

[Jason Porta]

I installed a fresh copy of FC14 at home and am having problems with my CCP4 
installation. When I try to input an mtz file into any CCP4i program, I get the 
following errors:

Error in LABIN: label Unassigned not found in file!
MOLREP(ccp4):  Error in label assignments in LABIN

MOLREP(ccp4):  Error in label assignments in LABIN

In a previous post, it was suggested that the the tcl/tk location may need to 
be changed in ccp4.setup, though I check this and it is pointing to the right 
directory. 

Any suggestions?

Jason Porta