[ccp4bb] Detergents

[anita p]

Hi,
I had set up crystallization with a bicine  as buffer and peg 400 as
precipitant. I used the detergent DDAO/LDAO as an additive to the
crystallization drop (one of the hampton additive screen condition, it says
5% on the vial)
I have a clear drop and in the centre there is a shiny precipitate (looks
like granules attached to eah other).
Then I opened the drop to touch those granules with a needle, but
suprisingly its like a skin and the skin surrounded my needle, and then some
how I was able to but back the skin in the ppt.
orelse the drop is clear if I remove the skin from the drop.
I couldnot see the same on the control drop with no protein and just buffer.
Does anyone have any experience with  such kind of of shiny skins on
crystallization drops??

Is it protein? Can I go forward and use it for seeding??

Please suggest
with regards
Rashmi

Re: [ccp4bb] mtz2various command line R-free label?

[Eleanor Dodson]

I dont know - it works for me..


That is under Fedora x


Eleanor
mtz2various HKLIN "./ins_pig_zn_T2_hex-unique_refmac1.mtz" HKLOUT 
"./ins_pig_zn_T2_hex-unique_refmac1.hkl"

 OUTPUT CNS
labin  FP=FP SIGFP=SDFP PHIB=PHIC FREE=FreeR_flag
end




On 04/27/2011 07:26 PM, Kelly Daughtry wrote:

Yes, you are correct, mtz_to_cns is calling up mtz2various.

I have tried many alternatives for the label for Rfree flag with no success.
I have also tried just asking for F and SIGF, and the output does not
contain Rfree.
The next step would be to use make_cv.inp to generate a test test.
I want to ensure I have my original test set carried over and do it simply
from the command line.
The program works perfectly fine within the CCP4 GUI.

If no command line option is found, that is ok.
I just want to ask everyone to see if it was do-able.

Thanks again!
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
***


2011/4/27 Bjørn Panyella Pedersen


mtz_to_cns calls mtz2various as far as I know.
If mtz2various works for you then you can use it directly. It too can be
run from the commandline. Look for the 'View Files from Job' -->  'View
Command Script' in the GUI to get help on syntax or look at the website
under examples (http://www.ccp4.ac.uk/html/mtz2various.html).

hth
-Bjørn

--
Bjørn Panyella Pedersen
Macromolecular Structure Group
Dept. of Biochemistry and Biophysics
University of California, San Francisco



On 2011-04-27 09:58, Kelly Daughtry wrote:


Hello all,
I am been unsuccessful in converting my mtz file into cns format and
bringing along my R-free reflections.

The interwebs tells me that the label should be FREE=label

So, on the command line I type:
mtz_to_cns hklin hklout F=F-obs SIGF=SIGF-obs FREE=R-free-flags

Yet I am always returned with an error that the label FREE is not
recognized.

I am able to run mtz2various in ccp4 using the GUI just fine with
selecting my R-free flag. The log file of that shows that the R-free
label is indeed FREE.

Thus, I am confused. How can I get this to run from the command line (so
I don't always have to open the GUI for one task).

Thanks in advance for any help you can provide!

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
***

Re: [ccp4bb] Map correlation coefficient

[Eleanor Dodson]

I guess one way would be to seperate coordinates..
But doesnt overlapmap do that by default?

Eleanor



On 04/21/2011 10:25 PM, Maher Alayyoubi wrote:

Hi Everybody, I posted a question earlier on the bulletin regarding
how to calculate the map correlation coefficient using Overlapamp or
any other program? My follow up question is, does anybody know how to
calculate the map correlation coefficient for the main chain and side
chain separately?


Thank you


Maher




On Wed, Feb 23, 2011 at 11:40 PM, Maher Alayyoubi
  wrote:

Hi Everybody, I am a new user on the ccp4 bulletin, I have a question on how
to calculate the map correlation coefficient using Overlapamp or any other
program?
Thank You,

Maher

Re: [ccp4bb] Detergents

[Enrico Stura]

Rashmi,

Yes, you should use the needle for seeding.
The first thing to do is to seed your control drop to make sure that the  
needles
are not bicine, as this buffer can give needles at certain pH at high  
PEG400

concentrations.
Next (or at the same time) also seed other protein drops that you have  
already set up
under similar conditions. I recommend streak seeding, so that even if  
crystal growth

is slow you will see the streak line early on.

Enrico.

On Fri, 29 Apr 2011 12:43:21 +0200, anita p  wrote:


Hi,
I had set up crystallization with a bicine  as buffer and peg 400 as
precipitant. I used the detergent DDAO/LDAO as an additive to the
crystallization drop (one of the hampton additive screen condition, it  
says

5% on the vial)
I have a clear drop and in the centre there is a shiny precipitate (looks
like granules attached to eah other).
Then I opened the drop to touch those granules with a needle, but
suprisingly its like a skin and the skin surrounded my needle, and then  
some

how I was able to but back the skin in the ppt.
orelse the drop is clear if I remove the skin from the drop.
I couldnot see the same on the control drop with no protein and just  
buffer.

Does anyone have any experience with  such kind of of shiny skins on
crystallization drops??

Is it protein? Can I go forward and use it for seeding??

Please suggest
with regards
Rashmi



--
Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office
Room 19, Bat.152,   Tel: 33 (0)1 69 08 9449Lab
LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette,   FRANCE
http://www-dsv.cea.fr/en/institutes/institute-of-biology-and-technology-saclay-ibitec-s/unites-de-recherche/department-of-molecular-engineering-of-proteins-simopro/molecular-toxinology-and-biotechnology-laboratory-ltmb/crystallogenesis-e.-stura
http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html
e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71

[ccp4bb] database search within the PDB

[Tobias Beck]

Dear all,

I would like to search the PDB for protein structures with the
conditions that the biological unit consists of a homo-tetramer and
that the monomers are related by a fourfold rotation, i.e. point group
4.

The rcsb.org server allows to specify the number of chains in the
biological unit, but no symmetry operation can be given.

The PISA search from the PDBe allows to search for the multimeric
state and the symmetry number. This returns however also structures
that are not related by fourfold symmetry, e.g. point group 222.

I assume that an elegant way to carry out the search would be to take
advantage of the REMARK 350 generated by PISA (or the author). Any
suggestions how to exploit this, also without downloading the whole
PDB (or pointers to other web servers that can do the job) would be
greatly appreciated.

Thanks, Tobias.

-- 
___

Dr. Tobias Beck
Dept. Structural Chemistry
Georg-August University Goettingen
Tammannstr. 4
37077 Goettingen, Germany
phone:   +49 551 39-3075
fax:       +49 551 39-22582
web:      http://shelx.uni-ac.gwdg.de/tbeck/
___

[ccp4bb] Staff scientist for the Core Facility ,Structural Biology (protein expression) in Vienna

[Kristina Djinovic Carugo]

  
  

The Campus Science
Support Facilities (CSF) are looking for a

 
Staff
  scientist for the Core Facility 
Structural
  Biology (protein _expression_)
 
Campus
  Science Support Facilities (CSF) were
established to provide scientific infrastructure, which will
be operated and constantly further developed by highly qualified
experts. Founded
in 2010, we are a non-profit organization funded by the Austrian
Ministry of
Science and Research and the City of Vienna. We are situated at
the Campus
Vienna Biocenter, which is one of the leading multi-disciplinary
biomedical
research centers in Europe and the premier location for Life
Science in
Austria. 
One of the support
facilities offered is the Structural
  Biology Core Facility, which will provide services on
large scale protein
_expression_ in eukaryotic systems (baculovirus and mammalian
cells), and
macromolecular crystallography, covering biophysical
characterization and crystallization
of macromolecular samples. 
Job
  description: The staff scientist will
be involved in participating in as
well as overseeing all the facility activities related to protein _expression_, as well as supervising,
managing, and leading
the team, as well as in advising and training of users. The staff
scientist will be involved in (but not limited to) conducting
laboratory
experiments related to all aspects and steps of offered
services, in
communication with scientists and dissemination at external
events. S/he will
be encouraged to recruit external funding through own or
collaborative project
applications in the field of structural biology.
Qualifications
and
  experience: a
Ph.D. in biochemistry, molecular biology, physics, chemistry or
a related field is required. Minimum 4-5 years of post-doctoral
or staff scientist
experience in molecular biology, protein _expression_ in
prokaryotic and
eukaryotic _expression_ systems, protein purification, as well as
experience with
cell-lines and/or structural genomics is required. Experience in
macromolecular crystallography is a plus. Previous
experience with team-leading, grant writing and budget
management will be a
competitive advantage.
Good
communication skills, organizational ability, project management
experience with
multiple projects in parallel and capacity to interact with
other researchers
are essential as well as capacity for
strategic thinking and strong
leadership ability.


 Contract: A one year contract, that can be extended to an
unlimited time
period, will be offered to the successful candidate.
 
Closing
date:
  15th
  July 2011
 Further
  information can
be obtained from 
Kristina
Djinovic-Carugo
; tel.: + 43 1 4277 52203
and Tim Clausen
 tel.: +43 1 79730 3300
 Interviews
  planned for
mid August 2011
 
To apply
for this
position, please send:
·
  Letter of interest
·
  Detailed CV with
concise description of
research experience
·
  Three references 
To:
barbara.mik...@viennabiocenter.org, subject: “Application for
Staff
Scientist position of Structural Biology Core Facility”.
-- 

**
Department for Structural and Computational Biology
Max F. Perutz Laboratories
University of Vienna
Campus Vienna Biocenter 5
A-1030 Vienna
Austria

e-mail: kristina.djino...@univie.ac.at
Phone: +43-1-4277-52203/52201
Mobile: +43-664-602 77-522 03
Fax: +43-1-4277-9522



  

[ccp4bb] Staff scientist for the Core Facility ,Structural Biology (macromolecular crystallography) in Vienna

[Kristina Djinovic Carugo]

  
  

The Campus Science
Support Facilities (CSF) are looking for a

 
Staff
  scientist for the Core Facility 
Structural
  Biology (macromolecular crystallography)
 
Campus
  Science Support Facilities (CSF) were
established to provide scientific infrastructure, which will
be operated and constantly further developed by highly qualified
experts. Founded
in 2010, we are a non-profit organization funded by the Austrian
Ministry of
Science and Research and the City of Vienna. We are situated at
the Campus
Vienna Biocenter, which is one of the leading multi-disciplinary
biomedical
research centers in Europe and the premier location for Life
Science in
Austria. 
 One of the support
facilities offered is the Structural
  Biology Core Facility, which will provide services on
large scale protein
_expression_ in eukaryotic systems (baculovirus and mammalian
cells), and
macromolecular crystallography, covering biophysical
characterization and crystallization
of macromolecular samples. 
 Job
  description: The staff scientist will
be involved in participating in as
well as overseeing all the facility activities related to biophysical characterization and macromolecular
  crystallography, as
well as supervising, managing, and leading the team, as well as
in advising and
training of users. The
staff scientist will be involved in (but not limited to)
conducting laboratory experiments related to all aspects and
steps of offered
services, in communication with scientists and dissemination at
external
events. S/he will be encouraged to recruit external funding
through own or
collaborative project applications in the field of structural
biology.
 Qualifications
and
  experience: a
Ph.D. in biochemistry, molecular biology, physics, chemistry or
a related field is required. Minimum 4-5 years of post-doctoral
or staff
scientist experience in protein purification, crystallisation
with robotics and
macromolecular crystallography together with hands-on experience
with
biophysical techniques (e.g. dynamic light scattering, static
light scattering,
isothermal calorimetry, differential scanning fluorimetry,
differential
scanning calorimetry, circular dichroism) are a must. Previous
experience with
team-leading, grant writing and budget management will be a
competitive
advantage.
 Good
communication skills, organizational ability, project management
experience with
multiple projects in parallel and capacity to interact with
other researchers
are essential as well as capacity for
strategic thinking and strong
leadership ability.

  

Contract: A one year contract, that can be extended to an
unlimited time
period, will be offered to the successful candidate.
 Closing
  date:
15th
July 2011
 Further
  information can
be obtained from 
Kristina
Djinovic-Carugo
 ; tel.: + 43 1 4277 52203
and Tim Clausen
 tel.: +43 1 79730 3300
 Interviews
  planned for
mid August 2011
 To apply
for this
position, please send:
·
  Letter of interest
·
  Detailed CV with
concise description of
research experience
·
  Three references 
To:
barbara.mik...@viennabiocenter.org, subject: “Application for
Staff
Scientist position of Structural Biology Core Facility”.
 
  
-- 

**
Department for Structural and Computational Biology
Max F. Perutz Laboratories
University of Vienna
Campus Vienna Biocenter 5
A-1030 Vienna
Austria

e-mail: kristina.djino...@univie.ac.at
Phone: +43-1-4277-52203/52201
Mobile: +43-664-602 77-522 03
Fax: +43-1-4277-9522



  

Re: [ccp4bb] Using chaperones to boost expression in E. coli

[Kothe, Michael]

Hi,

 

I wanted to thank everyone for their responses to my inquiry. It's good
to see that there have been positive examples, and also that one should
not be discouraged from trying by initial negative results. 

 

Thanks again, and have a nice weekend,

Michael

 



From: Olga Kolaj [mailto:olga.ko...@gmail.com] 
Sent: Tuesday, April 26, 2011 5:17 AM
To: Kothe, Michael
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Using chaperones to boost expression in E. coli

 

Michael,

We have put together a review about use of folding modulators to improve
expression in E. coli some time ago which might be useful to you (Kolaj
et al Microb Cell Fact. 2009 Jan 27;8:9). Here is the link:

http://www.ncbi.nlm.nih.gov/pubmed/19173718

 

 Regards

On Fri, Apr 22, 2011 at 4:28 PM, Kothe, Michael
 wrote:

Dear ccp4bb,

 

I am curious to hear of examples where the expression of well-behaved
protein was achieved by the coexpression of chaperones in E. coli. I
know the appropriate strains and vectors exist, but I can't remember
hearing of a successful case. I have heard anecdotally of several cases
where it was tried without success (including one attempt I made
myself). I also heard of concerns that the chaperones might copurify
with the (now soluble) protein of interest and are difficult to remove.

 

Thanks,

Michael

 

[ccp4bb] Job opportunity

[ferrer]

Hi, 

Here is a position in a company in the
US for a protein crystallographer.

JL

-- 
Jean-Luc Ferrer
|---|
|Institut de Biologie Structurale J.P. Ebel CEA/CNRS/UJF|
|41 rue Jules Horowitz - 38027 Grenoble cedex 1 - FRANCE|
|tel.: +33 (0)4-38-78-59-10 - fax : +33 (0)4-38-78-51-22|
|---|


NatX-ray LLC (www.natx-ray.com),
a start-up company specializing in automated systems and consumable
products for crystallography laboratories has an opening for a
full-time Sales Position in San Diego, California.
For this position, a PhD in
Protein Crystallography or equivalent is preferred, as well as an
interest in marketing and sales.  Candidate must also have a
high level of enthusiasm, motivation and be able to work
independently.
Compensation: Base salary based on
experience, plus a pre-determined % commission on sales.
For further information (job
description) or for interested candidates please e-mail cover
letter/resume to: cont...@natx-ray.com

[ccp4bb] Phenix version 1.7.1 released

[Paul Adams]

The Phenix developers are pleased to announce that version 1.7.1 of Phenix is 
now available. Binary installers for Linux, and Mac OSX platforms are available 
at the download site:

http://phenix-online.org/download/

Some of the new features in this version are:

Graphical Interface
---
- New interfaces for: phenix.phase_and_build, phenix.mtz2map, 
phenix.french_wilson
- Updates to the Structure comparison GUI, which now allows use of 
non-identical sequences, 
  and results viewing in PyMol.
- A plugin for running multiple sequence alignment

Installers
--
- Graphical installers for Macintosh (installs in /Applications)
- Binary installer for 64-bit Mac Intel (OS 10.6 only)

New Commands

- phenix.french_wilson (new command):
  - Implements French & Wilson correction of negative and weak intensities (see
Acta Cryst A34:517 [1978])
  - outputs modified amplitudes in MTZ format
  - used internally by default in Phaser GUI and phenix.refine when intensities
are provided
- phenix.reciprocal_space_arrays (new command):
  - this tool takes a PDB model and a data file and outputs an MTZ file
containing a number of arrays that are typically used in various
crystallographic calculations, such as R-factors, maps, refinement targets, 
etc.
The output arrays include:
- Fmodel, Fcalc, Fmask, Fbulk, FOM, resolution, Hendrickson-Lattman
  coefficients (input original, computed from model and combined),
  FB_CART (overall anisotropic scale), input Fobs and Rfree-flags and more
- phaser.brunett (new command):
  - automated molecular replacement using incremental exploration, with support 
for parallelization
  - quick SSM-superposition-based LLG evaluation for alternative models for the 
same component
  - "puzzle"-assembly of solutions for a more complete solution
  - novel space group determination algorithm that retains possible space 
groups until they are 
significantly outperformed by others
  - handles custom models (used without modification), templates (a PDB 
template and an alignment, 
Sculptor is run to create models from it) and homology searches (PDB and 
alignment obtained from
homology search, currently HHPRED and BlastXML; data downloaded from EBI)

Structure refinement

- New output MTZ file that contains original data, amplitudes used in 
refinement, and map 
  coefficients (this replaces *_map_coeffs.mtz)
- French and Wilson procedure automatically applied if intensities are input to 
refinement
- Optional automatic rigid-body grouping by polymer chain 
(rigid_groups_mode=one_group_per_chain)
- Reference model uses a "top-out" restraint potential with a smooth cutoff
- Automatic determination of Saenger class for nucleic acid base pairs (if not 
provided by user)
- Ability to run phenix.find_tls_groups internally to obtain atom selections
- option: tls.find_automatically=True
- Automatic non-bonded distance correction for H-bonded atoms

Molecular Replacement
-
- phenix.mr_rosetta:
  - Bug fixes
  - Added web site with data used in Nature Rosetta+Phenix paper at:
http://www.phenix-online.org/phenix_data/terwilliger/rosetta_2011/
  - Added keyword include_solvation_energy=False to allow use of mr_rosetta for 
membrane proteins.
- phenix.automr:
  - bug fix in residue number input, now allows four-digit IDs

Ligands
---
- eLBOW:
  - Geometries can be generated using CSD Mogul substructure searches of
experimental geometries. Estimated standard deviations of the bonds
and angles are also included in the restraints file.

Visualization
-
- KiNG (phenix.king):
  - Improved opening multiple electron density maps: tiered windows, with
automatic deciphering of file name to preset sigma levels and colors.
  - Added -phenix command line option to preset map colors to be more like Coot.


For a full list of changes see:

http://www.phenix-online.org/documentation/CHANGES

Please note that this publication should be used to cite use of Phenix:

PHENIX: a comprehensive Python-based system for macromolecular structure 
solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. 
Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. 
McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. 
Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010).

Full documentation is available here:

http://www.phenix-online.org/documentation/

There is a Phenix bulletin board:

http://www.phenix-online.org/mailman/listinfo/phenixbb/

Please consult the installer README file or online documentation for
installation instructions.

Direct questions and problem reports to the bulletin board or:

h...@phenix-online.org and b...@phenix-online.org

Commercial users interested in obtaining access to Phenix should visit the
Phenix website for information about the Phe

Re: [ccp4bb] Error in LABIN

[Jason C Porta]

Here is more information on my problem:

I installed ccp4i in /usr/local as root using the automated install.sh script.

I then sourced the ccp4.setup and ccp4-others.setup for the proper shell, 
making sure the environment variables were pointing in the right direction. 

Now, if I run ccp4i as a normal user, and try to input an mtz file into any of 
the programs I get:

CCP4i encountered an error when trying to extract the data from 
/home/jcp/KAuCN/new_refine/sad.mtz
You can view the output from the mtzdump program which mayand so on.

file does not exist /tmp/jcp/sad.mtz

Now I think the problem might have to do with permissions. When I run ccp4i as 
root, I do not get this problem. 

Any suggestions?

Jason Porta


-CCP4 bulletin board  wrote: -

To: CCP4BB@JISCMAIL.AC.UK
From: Jason Porta 
Sent by: CCP4 bulletin board 
Date: 04/28/2011 07:09PM
Subject: [ccp4bb] Error in LABIN

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