[ccp4bb] PDB Crazy or Me?

[James Stroud]

Hello All,

I noticed some things different about the PDB today causing me to rub  
my eyes vigorously and to put my nose right on my monitor in disbelief:


* -> ' for nucleic acid sugars
  O#P -> OP# for the phosphate oxygens
  C5A -> C7 for thymidine exocyclic methyl (didn't it used to be C5A?)

And who knows what else. In fact, my real question *is* "who knows  
what else?" I looked at the RCSB site and googled PDB changes, etc,  
but really couldn't find the low-down. Another question is how long  
before it all changes again? I noticed some threads here with PDB in  
the title recently, but didn't read them because I thought they  
discussed esoteric and philosophical issues that do not affect us  
common folk.


James

--
James Stroud
UCLA-DOE Institute for Genomics and Proteomics
Box 951570
Los Angeles, CA 90095

http://www.jamesstroud.com

Re: [ccp4bb] How to number atoms in a ligand

[Artem Evdokimov]

If you want to be 'by the book' on it, you should follow IUPAC rules for
atomic numbering of chemical compounds. Unless you're an organic chemist,
these rules are pretty hard to follow, so most people number at will.

 

If you're dealing with a 'known' series of compounds, such as analogous
inhibitors developed in the course of a research project (say, in pharma
industry) then typically you will see people refer to specific locations by
number, and try to keep numbering consistent.

 

Artem

 

  _  

From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Zheng
Zhou
Sent: Monday, October 08, 2007 9:01 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] How to number atoms in a ligand

 

Hi, all


I am a rookie in crystallography. I know this may be a little bit off topic.
I have cocrystallized several compounds with my favorite protein. I found
crystal structures for some of these chemicals. But the numbering systems
are different in those original papers for the small molecules. Some
numbering system has all the atoms from 1 to the end (C1-O3-O8-N9-C15),
while others have numbers for each individual element. (C1-C12, O1-O2, N1).
I was trying to search a unified theme for ligands in pdb. I even emailed
[EMAIL PROTECTED], but so far I haven't heard anything back. Could
anyone give me some suggestions? Any help would be greatly appreciated. 

 

Thanks,

Sorry to bother others 

Joe 

Re: [ccp4bb] How to number atoms in a ligand

[Dale Tronrud]

Dear Joe,

   Atom labels are, in principle, arbitrary.  The molecule doesn't case
what we call its atoms.  To make the PDB more useful, it is handy if
all the people working with a particular compound use the same names for
their atoms.  If you find that someone has already deposited a structure
containing your compound you are expected to use the same names they did.
There are lists of compounds and naming conventions on the PDB web site.

   The small molecule literature doesn't count as precedence for naming
conventions, only what is in the PDB.  No one will hold you to the names
used in the small molecule structure paper.

   If you are the first to work with this compound in the macromolecular
world you are free to choose whatever names you want.  Please choose
something sensible as the rest of use will be stuck with your choice
forever.  Consistency is king here.  If a similar compound is in the
PDB, using atom names based on it would simplify comparisons.

Dale Tronrud


Zheng Zhou wrote:

Hi, all

I am a rookie in crystallography. I know this may be a little bit off 
topic. I have cocrystallized several compounds with my favorite protein. 
I found crystal structures for some of these chemicals. But the 
numbering systems are different in those original papers for the small 
molecules. Some numbering system has all the atoms from 1 to the end 
(C1-O3-O8-N9-C15), while others have numbers for each individual 
element. (C1-C12, O1-O2, N1). I was trying to search a unified theme for 
ligands in pdb. I even emailed [EMAIL PROTECTED] 
, but so far I haven't heard anything 
back. Could anyone give me some suggestions? Any help would be greatly 
appreciated.
 
Thanks,


Sorry to bother others

Joe

[ccp4bb] Reminder, Oct 15, Deadline SLS PX Proposals

[Heinz J Weyer]

Dear SLS users,

 Reminder, Call for Proposals: SLS PX Beamlines
 ==

 Call is open for proposals for the following
 beamlines of the Swiss Light Source, SLS:

 PX (X06SA and X10SA), Protein Crystallography

 Periods:
 ===
 January 1, 2008 - April 30, 2008 (normal, test)
 January 1, 2008 - December 31, 2009 (long term)

 Deadline:
 
 for submission is Monday, October 15, 2007





2) Submission:
   ===
All submissions will be handled by the SLS Digital Users
Office (DUO).

Notes:
==


a) For the proposal evaluation by the Proposal Review
   Committee, DUO Experimental Reports on previous
   experiments represent a very important input, and
   a missing experimental report may seriously affect
   the chances of acceptance. Proposers are asked to
   supply a separate experimental report for each
   experiment performed. Note that now also a co-proposer
   can input an experimental report.

b) The SLS is part of the EU I3 initiative and we will
   be able to provide travel and accommodation support.
   Proposers interested in this support are asked to mark
   the corresponding box in the proposal. For further
   details please go to:

   http://sls.web.psi.ch/view.php/users/experiments/eusupport


Info:

For further information about proposal and / or experimental
report submission please go to
http://sls.web.psi.ch/view.php/users/experiments/proposals/opencalls

For further information about the SLS beamlines please go to
report submission, please go to
http://sls.web.psi.ch/view.php/beamlines


Help:

In case of questions, please contact the Users' Office at

[EMAIL PROTECTED] 


For the SLS Team
Heinz J. Weyer



--
PD Dr. Heinz J. WeyerEmail:  [EMAIL PROTECTED]
Paul-Scherrer Institut   Phone:  +41 (56) 310 3494
CH-5232 Villigen PSI Fax :   +41 (56) 310 3151
Switzerland  Url:http://www.psi.ch/sls

[ccp4bb] CCP4 winter web-newsletter contributions

[Remacle, F (Francois)]

Dear developers and users,

This is just a reminder for anyone who wishes to contribute to the next
issue of the web-based CCP4 newsletter. The current deadline is 1st week
of December, so more or less in two months.

Articles may cover any topic of interest to macromolecular
crystallographers, on software or methodology. Short items of news are
also very welcome (help put the news back into Newsletter!).

Thanks to all past, present and future contributors.

Francois Remacle
CCP4

[ccp4bb] Issue of IEEE Software on developing scientific software

[Morris, C (Chris)]

Hi,

I would like to invite you to submit articles for a special issue of
IEEE Software on
"Developing Scientific Software". The call for articles is below, and
also at:
http://www.computer.org/portal/site/software/menuitem.538c87f5131e262449
55a4108bcd45f3/index.jsp?&pName=software_level1&path=software/content&fi
le=cfp2.xml&xsl=article.xsl&

I should mention that as a guest editor I can recommend an article
to the editorial board, but cannot guarantee publication!

regards,
Chris

Chris Morris 
[EMAIL PROTECTED]  
Tel: +44 1925 603689  Fax: +44 1925 603825
Mobile: 07921-717915
http://www.pims-lims.org/
Daresbury Lab,  Daresbury,  Warrington,  UK,  WA4 4AD




Call for Articles

Developing Scientific Software


Publication date: July/August 2008
Submission deadline: 9 January 2008

IEEE Software seeks submissions for a special issue on the topic of
scientific software development. Many of the recent advances in science
have been dependent on software, such as that embedded in instruments or
simulating complex or physically unsafe situations or facilitating
collaboration among a dispersed scientific community. Because of the
complex nature of the science underlying the software, much scientific
software is written either by scientists themselves or by
multi-disciplinary teams of software engineers and scientists.  In the
former case, scientists face the challenge of knowing little about
software engineering beyond coding (they thus fall into the category of
'professional end-user developers'); in the latter, the
multi-disciplinary teams face the challenges of clashing cultures
(science and software development) and communication. The aim of this
issue is to explore the particular challenges facing scientific software
development and the ways by which these challenges might be addressed.

Topics of interest include, but are not limited to

*   Case studies of scientific software development 
*   Analyses, grounded in practice, of the 
*   

*   particular characteristics of, and problems facing,
scientists as professional end-user developers 
*   particular characteristics of scientific software
development 
*   the particular characteristics of, and problems facing,
multi-disciplinary development teams comprising software engineers and
scientists.

*   Discussions of tools, techniques, strategies specifically
designed to support scientific software development. 
*   Discussion of how tools, techniques and strategies commonly
deployed by software engineers might be usefully deployed, perhaps with
some modification, by professional end-user developers.

We are particularly interested in papers grounded in practice.

Manuscripts must not exceed 5,400 words including figures and tables,
which count for 200 words each. Submissions in excess of these limits
may be rejected without refereeing. The articles we deem within the
theme's scope will be peer-reviewed and are subject to editing for
magazine style, clarity, organization, and space. We reserve the right
to edit the title of all submissions.

For author guidelines and submission details, please visit our Author
Center   or contact the
publications coordinator  . Submit your
article via the Computer Society's Electronic Submission System
  by 9 January 2008. Only
Postscript or PDF files can be submitted for review. Specify that you
are submitting it for the "Developing Scientific Software" special
issue.

For more information, contact the Guest Editors:

Judith Segal  
The Open University


Chris Morris  
Daresbury Lab

[ccp4bb] How to number atoms in a ligand

[Zheng Zhou]

Hi, all

I am a rookie in crystallography. I know this may be a little bit off topic.
I have cocrystallized several compounds with my favorite protein. I found
crystal structures for some of these chemicals. But the numbering systems
are different in those original papers for the small molecules. Some
numbering system has all the atoms from 1 to the end (C1-O3-O8-N9-C15),
while others have numbers for each individual element. (C1-C12, O1-O2, N1).
I was trying to search a unified theme for ligands in pdb. I even emailed
[EMAIL PROTECTED], but so far I haven't heard anything back. Could
anyone give me some suggestions? Any help would be greatly appreciated.

Thanks,

Sorry to bother others

Joe

Re: [ccp4bb] Rfree statistics in SHELXL

[Oliv Eidam]

It is actually possible to calculate R(free) with SHELXL for the outer 
most resolution shell. Gabor Bunkoczi indicated the solution and I 
forward it here to the public:

- Rename the .res file of the last refinement run to .ins
- adjust the CGLS parameter in the .ins file to 0 -1 (Zero refinement 
cycles, selection of reference set with the flag -1):

 CGLS 0 -1
- Set the resolution limits to the ones of the outer most resolution 
shell (in my case 1.39-1.34 Angstroem):

 SHEL 1.39 1.34
- re-run the job with the modified .ins file
- the R1(Free) values in the output .res file correspond to those of the 
highest resolution shell.


Gabor, thank you very much for this great suggestion!

 Oliv


Dr G. Bunkoczi schrieb:

Hi Oliv,

you can include a SHELL command (set to the highest resolution shell), 
and CGLS 0 -1 and re-run the job. The R-factors you get are those of 
the highest resolution shell.


BW, Gabor

On Oct 8 2007, Oliv Eidam wrote:


Dear all,

I used SHELXL for anisotropic structure refinement of high-resolution 
data (1.3 Angstroem) and a reviewer asked me to include refinement 
statistics for the outer most resolution shell in the 
crystallographic table. While R-factors for the outer most resolution 
shell belong to the standard output in REFMAC or CNS, it seems to me 
that SHELXL calculates R-factors only for reflections of the work 
set. I also noticed that test reflections are missing in the 
structure factor file (.fcf file) generated by shelxpro, preventing 
me to use the [S] or [L] options in shelxpro to calculate R(free) 
statistics.
Is it simply not possible to calculate the R(free) factor for the 
outer most shell after SHELX refinement? Or is there a problem with 
my SHELX program?


Many thanks for your answers and suggestions,

Oliv








--
Oliv Eidam

Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
8057 Zurich, Switzerland

Phone: 0041-44-635-6563
Email: [EMAIL PROTECTED]
Web:   http://www.bioc.uzh.ch/gruetter
NCCR:  http://www.structuralbiology.ethz.ch

[ccp4bb] CCP4 needs your help, part 2 a reminder

[Jim Naismith]

Dear Colleagues,
So far there have been over 30 letters of support
for CCP4. There is a further 14 days for you to send your letter of support.

I know many labs do not use CCP4BB or at least many lab heads do not.
Perhaps you can ask them to read the message below?  This is very important
to CCP4, your support will weigh heavily with the BBSRC committee.

The full letter is at the end.

In summary, what we would like is a letter to me on headed note paper (sent
by email to [EMAIL PROTECTED]). This letter should be personal to you,
however to help CCP4 it might comment on how CCP4 has helped and how its
future plans will help your research.

I stress companies, Research Insts and academic labs are equally as
important. Letters from overseas are as wellcome as those from the UK.

If you are a student or post-doc using CCP4, I would be grateful if you ask
the lab head.

Best
Jim
Chair of CCP4


 Dear Colleagues,
CCP4 derives its core financial support from the
BBSRC (UK). We are now in the process of attempting to renew our grant
funding. The grant proposal has four sections
(1) New methods for working with low resolution and difficult structures
(2) Improvements in data processing, dealing with new detectors, split
crystals etc
(3) A new database to provide intelligent decision making for new to
moderately experienced users (that is, the programs will make sensible
choices in order to avoid mistakes and automate the work flow). Where no
such clear choice exists, the program will provide clear and sensible
one-click suggestions to proceed based on analysis of your data to this
point.
(4) Continuing support of workshops, bulletin board, installation, etc.

The choice of these areas was made by Working group 1 in January. I am
writing to you to ask for your help. The BMS grant committee of BBSRC will
probably have, at most, one person who has used CCP4.  It is therefore
important that we can show evidence of its success in the past and,
crucially, its continuing importance in the future. Our proposal will have
to compete against high quality project grants in a normal funding round
and, if we fail to demonstrate its importance, CCP4 may fail to be funded,
just like any other grant. International and national support will be very
useful in making the case. Commercial organization support is extremely
welcome.

If you feel (and only if) you can support CCP4, it would greatly help to
have letters of support (as attached PDF format letters with your letter
head addressed to me), "Jim Naismith, Chair of CCP4". Please email these to
[EMAIL PROTECTED], marked CCP4.

If the letter is to be useful, you should explain who you are, what your lab
does and what it comprises, please list your publications in the last five
years that have used CCP4 (please remember PISA at the EBI is funded by the
current CCP4 grant). Any personal highlighting would be very welcome. In
this letter, if you were able to say how any or all the aims of the new
proposal (1-4 above) will help you, that will be absolutely crucially
important. Words like step change and paradigm shift, are useful if you
relate them to new capabilities, since this is the rubric of BMS committee.

Other things that you might like to mention are how important the training
and support aspects of CCP4 are to your lab (any specific instance welcome).

It is important that colleagues who use CCP4 (say jointly supervise a
student, post-doc, collaborate, etc.) but do not see themselves as
crystallographers support us, again only if they feel able to. The support
of people who are not crystallographers will be extremely important and will
no doubt heavily with the committee. 

If you are a student or post-doc using CCP4 as a non-expert, your support
would be helpful (although check with the PI first). If you think an
"automated expert system" for tough problems would help you, please say so.
If you have found a CCP4 sponsored workshop or training to be good, again
please say so. If the PI in your lab does not read the CCP4BB, show them
this message.

Can I stress, that what will not help at all is a letter saying "CCP4 is
great - fund it!". What will help immensely is an explanation of the role
that CCP4 has played, and will continue to play, in aiding you in achieving
your scientific goals. In that regard, if there are five PI's in your
department one letter from each one of you is better than a single letter on
behalf of all five.

The pre-proposal for the grant has just been accepted (submitted months
ago), but we now have only four weeks to submit the full application. (Who
would have figured it was a government organization?) This is my priority, I
cannot promise to reply to emails in good time. If you could send your
letters in the next two weeks, it would be great. Your letters will be
treated in confidence, no lists put up. I will send them by post to the
committee.

I thank you in advance for any support you might be ab

[ccp4bb] shutdown of ccp4 website

[Charles Ballard]

Dear All

the ccp4 website and ftp site will be "off air" from 4pm BST on  
Friday 12 October until Monday 15 October.  This is to allow  
necessary maintenance on the server room.


Happily, the ccp4bb mailing list and ccp4 e-mail address will not be  
affected


Charles Ballard
CCP4

Re: [ccp4bb] Rfree statistics in SHELXL

[George M. Sheldrick]

Boaz,

If you had used the U option in SHELXPRO to update from .res to .ins the 
free R should have been included in the deposition PDB file by the B 
option!

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry, 
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582


On Mon, 8 Oct 2007, Boaz Shaanan wrote:

> A related but somewhat easier problem to fix, I would think, is the report of 
> overall-R-free value in the B option in shelxpro. The R-free value is 
> reported in the .lst and other o/p files but is not transmitted to the output 
> pdb. Here is an example:
> 
> REMARK   3 DATA USED IN REFINEMENT.
> REMARK   3  RESOLUTION RANGE HIGH (ANGSTROMS) :  1.35
> REMARK   3  RESOLUTION RANGE LOW  (ANGSTROMS) : 10.00
> REMARK   3  DATA CUTOFF(SIGMA(F)) :  0.0
> REMARK   3  COMPLETENESS FOR RANGE(%) :  93.2
> REMARK   3  CROSS-VALIDATION METHOD   :  FREE R
> REMARK   3  FREE R VALUE TEST SET SELECTION   :  RANDOM
> REMARK   3  
> REMARK   3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
> REMARK   3  R VALUE   (WORKING + TEST SET, NO CUTOFF) :  0.1749
> REMARK   3  R VALUE  (WORKING SET, NO CUTOFF) :
> REMARK   3  FREE R VALUE  (NO CUTOFF) :
> REMARK   3  FREE R VALUE TEST SET SIZE (%, NO CUTOFF) :
> REMARK   3  FREE R VALUE TEST SET COUNT   (NO CUTOFF) :
> REMARK   3  TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) :   44691
> REMARK   3  
> REMARK   3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
> REMARK   3  R VALUE   (WORKING + TEST SET, F>4SIG(F)) :  0.1635
> REMARK   3  R VALUE  (WORKING SET, F>4SIG(F)) :
> REMARK   3  FREE R VALUE  (F>4SIG(F)) :
> REMARK   3  FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) :
> REMARK   3  FREE R VALUE TEST SET COUNT   (F>4SIG(F)) :
> REMARK   3  TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) :   35043
> 
>  Best wishes,
> 
> Boaz
> - Original Message -
> From: "George M. Sheldrick" <[EMAIL PROTECTED]>
> Date: Monday, October 8, 2007 11:16
> Subject: Re: [ccp4bb] Rfree statistics in SHELXL
> To: CCP4BB@JISCMAIL.AC.UK
> 
> > SHELX is much older than the free R so this was added as an 
> > afterthought, 
> > and unfortunately I did not think of calculating R-free for just 
> > the outer 
> > resolution shell. There isn't an easy way of doing this without 
> > some 
> > programmeing effort. I also think that it is NOT a good idea, in 
> > the outer 
> > resolution shell you may only about 100 reflections in your free 
> > R set, so 
> > the free R value will have a very large esd and so could be 
> > misleading.
> > George 
> > 
> > Prof. George M. Sheldrick FRS
> > Dept. Structural Chemistry, 
> > University of Goettingen,
> > Tammannstr. 4,
> > D37077 Goettingen, Germany
> > Tel. +49-551-39-3021 or -3068
> > Fax. +49-551-39-2582
> > 
> > 
> > On Mon, 8 Oct 2007, Oliv Eidam wrote:
> > 
> > > Dear all,
> > > 
> > > I used SHELXL for anisotropic structure refinement of high-
> > resolution data
> > > (1.3 Angstroem) and a reviewer asked me to include refinement 
> > statistics for
> > > the outer most resolution shell in the crystallographic table. 
> > While R-factors
> > > for the outer most resolution shell belong to the standard 
> > output in REFMAC or
> > > CNS, it seems to me that SHELXL calculates R-factors only for 
> > reflections of
> > > the work set. I also noticed that test reflections are missing 
> > in the
> > > structure factor file (.fcf file) generated by shelxpro, 
> > preventing me to use
> > > the [S] or [L] options in shelxpro to calculate R(free) statistics.
> > > Is it simply not possible to calculate the R(free) factor for 
> > the outer most
> > > shell after SHELX refinement? Or is there a problem with my 
> > SHELX program?
> > > 
> > > Many thanks for your answers and suggestions,
> > > 
> > > Oliv
> > > 
> > > 
> > > -- 
> > > Oliv Eidam
> > > 
> > > Department of Biochemistry
> > > University of Zurich
> > > Winterthurerstrasse 190
> > > 8057 Zurich, Switzerland
> > > 
> > > Phone: 0041-44-635-6563
> > > Email: [EMAIL PROTECTED]
> > > Web:   http://www.bioc.uzh.ch/gruetter
> > > NCCR:  http://www.structuralbiology.ethz.ch
> > > 
> > > 
> > 
> 
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
> Phone: 972-8-647-2220 ; Fax: 646-1710
> Skype: boaz.shaanan‎
> 

Re: [ccp4bb] Rfree statistics in SHELXL

[George M. Sheldrick]

SHELX is much older than the free R so this was added as an afterthought, 
and unfortunately I did not think of calculating R-free for just the outer 
resolution shell. There isn't an easy way of doing this without some 
programmeing effort. I also think that it is NOT a good idea, in the outer 
resolution shell you may only about 100 reflections in your free R set, so 
the free R value will have a very large esd and so could be misleading.

George 

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry, 
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582


On Mon, 8 Oct 2007, Oliv Eidam wrote:

> Dear all,
> 
> I used SHELXL for anisotropic structure refinement of high-resolution data
> (1.3 Angstroem) and a reviewer asked me to include refinement statistics for
> the outer most resolution shell in the crystallographic table. While R-factors
> for the outer most resolution shell belong to the standard output in REFMAC or
> CNS, it seems to me that SHELXL calculates R-factors only for reflections of
> the work set. I also noticed that test reflections are missing in the
> structure factor file (.fcf file) generated by shelxpro, preventing me to use
> the [S] or [L] options in shelxpro to calculate R(free) statistics.
> Is it simply not possible to calculate the R(free) factor for the outer most
> shell after SHELX refinement? Or is there a problem with my SHELX program?
> 
> Many thanks for your answers and suggestions,
> 
> Oliv
> 
> 
> -- 
> Oliv Eidam
> 
> Department of Biochemistry
> University of Zurich
> Winterthurerstrasse 190
> 8057 Zurich, Switzerland
> 
> Phone: 0041-44-635-6563
> Email: [EMAIL PROTECTED]
> Web:   http://www.bioc.uzh.ch/gruetter
> NCCR:  http://www.structuralbiology.ethz.ch
> 
> 

[ccp4bb] Rfree statistics in SHELXL

[Oliv Eidam]

Dear all,

I used SHELXL for anisotropic structure refinement of high-resolution 
data (1.3 Angstroem) and a reviewer asked me to include refinement 
statistics for the outer most resolution shell in the crystallographic 
table. While R-factors for the outer most resolution shell belong to the 
standard output in REFMAC or CNS, it seems to me that SHELXL calculates 
R-factors only for reflections of the work set. I also noticed that test 
reflections are missing in the structure factor file (.fcf file) 
generated by shelxpro, preventing me to use the [S] or [L] options in 
shelxpro to calculate R(free) statistics.
Is it simply not possible to calculate the R(free) factor for the outer 
most shell after SHELX refinement? Or is there a problem with my SHELX 
program?


Many thanks for your answers and suggestions,

Oliv


--
Oliv Eidam

Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
8057 Zurich, Switzerland

Phone: 0041-44-635-6563
Email: [EMAIL PROTECTED]
Web:   http://www.bioc.uzh.ch/gruetter
NCCR:  http://www.structuralbiology.ethz.ch

[ccp4bb] Job offer: Postdoctoral Scientist in Protein Crystallography

[Prof. Dr. Arne Skerra]

Postdoctoral Scientist in Protein Crystallography

A postdoctoral staff position is available at the Institute of 
Biological Chemistry of the Technical University Munich starting as 
soon as possible for initially three years, with the option for 
prolongation.


Projects are focused at aspects of rational and combinatorial protein 
design and at the structural study of plant proteins, either with 
regulatory functions or with interesting enzymatic activities. 
Applicants should have experience in protein crystallization and 
diffraction data collection as well as in molecular biology 
techniques.


The in-house X-ray facility includes a Rigaku rotating anode 
generator with Osmic confocal layer optics, MAR imaging plate 
detector and an Oxford cryostream liquid nitrogen cooling device. In 
addition, there is robotic crystallisation and imaging equipment.


The position will also involve teaching activities, especially in 
conjunction with our new BSc/MSc curriculum Molecular Biotechnology, 
and there may be an opportunity to apply for the academic degree of 
'Habilitation'.


Our research group provides a fruitful environment with strong 
background and state of the art equipment for protein engineering, 
biochemistry, and recombinant gene expression. The institute is 
located at the biological sciences campus of TUM in 
Freising-Weihenstephan, north of Munich and close to the 
international airport. Our laboratory is member of the recently 
established Cluster of Excellence 'Munich Center for integrated 
Protein Science - CIPSM'.


Applications including CV and two letters of recommendation or 
addresses of references should be sent to: Prof. Dr. Arne Skerra, 
Lehrstuhl f. Biologische Chemie, TU Muenchen, 85350 
Freising-Weihenstephan, Germany, phone: +49 8161 714351, eMail: 
[EMAIL PROTECTED]; http://www.wzw.tum.de/bc


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Prof. Dr. Arne Skerra  [EMAIL PROTECTED]
Lehrstuhl f. Biologische Chemie   Phone: +49 (0)8161 71-4351
Technische Universitaet MuenchenFax:   -4352
85350 Freising-Weihenstephan
Germany http://www.wzw.tum.de/bc