[ccp4bb] ICCBM12 in Cancun, Mexico

[mesters]

This year, the ICCBM conference will take place in Cancun Mexico, May 
6-9 (http://www.iccbm12.com.mx/) and a 3-day workshop (about 30-36
participants) will precede this conference on the crystallization of 
biological macromolecules.


For information regarding workshop/school and conference, please visit 
http://www.iccbm12.com.mx/


See you there!

Jeroen.

--
Jeroen Raymundus Mesters, Ph.D.
Institut fuer Biochemie, Universitaet zu Luebeck
Zentrum fuer Medizinische Struktur und Zellbiologie
Ratzeburger Allee 160, D-23538 Luebeck
Tel: +49-451-5004070, Fax: +49-451-5004068
E-mail: [EMAIL PROTECTED]
Http://www.biochem.uni-luebeck.de
Http://www.iobcr.org
Http://www.opticryst.org
--
If you can look into the seeds of time and say
which grain will grow and which will not - speak then to me  (Macbeth)
--

[ccp4bb] Gastroeneterology position, Metro Tennessee area.

[Jessica Martin]

To all those interested, 

We have a 2 current openings in the same facility for a Gastroenterology 
specialist in Tennessee. Consultation status with the health system and will 
follow up with patients in the hospital after they are admitted.
?

Benefits include


NO call

Endoscopy procedure lab (suite) available

Highly competitive salary

Excellent benefits, CME, Malpractice

Moving expenses provided


?

Please fax CV/Resume attention: Jessica Martin to fax number 206-666-4501. Any 
questions may be directed [EMAIL PROTECTED] Thank you!



?Jessica Martin
Deb Bailey Recruiting
206-666-4501
203 Red Fern Pl
Hot Springs, AR 71901







More new features than ever.  Check out the new AOL Mail ! - 
http://webmail.aol.com

[ccp4bb] Opening for Dermapathologist in Delaware

[Jessica Martin]

To all those interested:

One other position available for a Dermapathologist in Delaware.

This position is for a BC or BE physician. Only candidates from Dermatology 
(not Pathology) will be considered. Position is Monday thru Friday, daytime, 
call rotates every 7th week. Residency on up. Will be? hospital consultant. 
Work for private practice with 7 physicians and 5 PAs. Pay dependant upon 
experience. 

?

For consideration, please submit your CV/Resume via fax attn: Jessica Martin 
206-666-4501. Questions may be submitted via email to [EMAIL PROTECTED] Thank 
you. ?



?Jessica Martin
Deb Bailey Recruiting
206-666-4501
203 Red Fern Pl
Hot Springs, AR 71901







More new features than ever.  Check out the new AOL Mail ! - 
http://webmail.aol.com

[ccp4bb] Application Scientist position available

[Angela Criswell]

Dear all,

Rigaku, the world's largest analytical X-ray company, is seeking an 
application scientist to work with our ACTOR team. ACTOR, Automated 
Crystal Transport, Orientation and Retrieval, is the most popular 
automated sample changer for X-ray crystallography. You will help 
install, maintain, train and support ACTOR users worldwide. You will 
also develop new features and help support internal users of the robot 
and other advanced projects at Rigaku. You will work with experts in the 
field of x-ray crystallography, automation, cryogenics and software 
development at Rigaku as well some of the world’s leading scientists in 
the field. You will need excellent communication skills and a desire to 
travel.


This position is located at our North American headquarters in The 
Woodlands, TX, just north of Houston. Rigaku offers a rewarding work 
environment and excellent benefits. Rigaku offers a full line of 
instrumentation and automation hardware and software products that cover 
the entire crystallographic pipeline from crystal growth through 
structure solution.


Please send resumes by mail to Rigaku Americas, 9009 New Trails Dr., The 
Woodlands, TX 77381-5209, Attention: Human Resources, by fax to 
281-364-3628 or email to [EMAIL PROTECTED] Please paste the resume in 
the body of the email. Email containing attachments will not be 
accepted. Rigaku Americas is an EEO/AA Employer M/F/D/V.

[ccp4bb] ACA 2008, Abstracts for Structural Enzymology

[Allen M. Orville]

2008 American Crystallographic Association Meeting
01.04   Structural Enzymology
Tuesday afternoon, June 3, 2008
Organized by Drs. Allen M. Orville and Carrie M. Wilmot
  
The abstract deadline for the 2008 ACA meeting in Knoxville, TN,
including our Structural Enzymology session, was extended to Jan 12,
2008 (this Saturday).  If you have not submitted your abstract,
then please submit it to the ACA web site by the deadline. This will help
greatly with the accelerated schedule required to prepare the meeting
materials. 
Our session will feature talks and posters that describe crystal
structures of reactive intermediates, and/or which use techniques that
provide strong correlation(s) to the proposed reaction mechanism. The
speakers will describe methods and structures of macromolecular catalysts
that are poised, trapped or stalled along the reaction coordinate, rather
than ground-state structures of resting systems that are more typical of
macromolecular crystal structures. These studies tend to provide a more
detailed, insightful, and complete picture of the particular reaction
mechanism. 
 
Our session code is: 01.04   Structural Enzymology
 
The guidelines for the abstracts can be found by following the links
from: 
 

http://neutrons.ornl.gov/conf/aca2008/abstracts.shtml
 
Briefly, some of the important metrics are:
 
“The entire abstract, including title, authors and their affiliations,
footnotes, references, tables, equations, etc., should be a maximum of
2000 characters (including spaces) using Times font with 10 point
size.”
 
“One image per abstract is allowed, and it must be black & white and
must fit into area no larger than 1.5” high x 3.5” wide.”
Sincerely,
AMO & CMW

**
Allen M. Orville, Ph.D.
Biology Department
Brookhaven National Laboratory
Upton, NY  11973-5000
e-mail: [EMAIL PROTECTED] 
phone 631-344-4739
fax 631-344-2741

www.biology.bnl.gov/structure/orville.html
**
Carrie Wilmot, Ph.D.
Associate Professor & Director of the Kahlert Structural Biology
Lab
Department of Biochemistry, Molecular Biology & Biophysics
University of Minnesota 
6-155 Jackson Hall, 321 Church St SE,
Minneapolis, MN 55455-0215, USA
 
e-mail: [EMAIL PROTECTED]
Tel: +1-612-624-2406
Fax: +1-612-624-5121
WWW:

http://biosci.cbs.umn.edu/BMBB/faculty/Wilmot.C.html

[ccp4bb] Post-Doc: Ion Channel Biochem & Struct Biol. Oxford UK

[Dr Stephen J. Tucker]

Post Doctoral Research Assistant in Ion Channel Biochemistry & Structural
Biology

Grade 7: £26,666 - £32,796 pa

An experienced post doctoral research assistant is required to work on
structural studies of an exciting new class of prokaryotic ion channels. 
The successful applicant will join the Potassium Channel Research Group
headed by Dr Stephen J. Tucker which will shortly be transferring to new
custom built laboratories in the Biological Physics Unit, based in the
Department of Physics.

The ideal candidate will have significant experience of protein expression
and purification, protein crystallisation and a particular interest in
membrane proteins. The project is at a fairly advanced stage and therefore
additional experience in X-ray structure determination would also be an
advantage.  The position would ideally suit graduates with a PhD degree in
biochemistry, crystallography, biophysics, or related subjects, and with
relevant research experience.  This post is available immediately and is
funded by the BBSRC for a maximum of three years.

Letters of application including a CV and names and addresses of 2 referees
should be sent to The Personnel Officer, Department of Physics, Clarendon
Laboratory, Parks Road, Oxford OX1 3PU or by email:
[EMAIL PROTECTED] by 12th February, 2008, quoting reference number
DK08-002. Informal enquiries may be addressed to
[EMAIL PROTECTED] Further Particulars are available from
www.physics.ox.ac.uk/cm/vacancies.htm

Re: [ccp4bb] Gastroeneterology position, Metro Tennessee area.

[William Scott]

Hi Jessica:

Thanks for posting these gastroeneterology and dermatology adverts to the CCP4 
bulletin board.  Many of in macromolecular X-ray crystallography are 
contemplating just such a career change, and although the retraining procedure 
may take 7 to 10 years, I am sure you would be willing to hold the position 
open given the flood of applications you will doubtless receive to your 
thoughtful and well-targetted email.

The gastroeneterology position is one that is truly near and dear to my heart 
right now, and as an extra bonus, my whole family, including the dog, appear to 
have live cultures of norovirus at the moment. This has made me rue the 
decision to install a white carpet several years ago, which now possesses an 
interesting patina. Please let me know if I should post pictures.

If, on the other hand, you were to decide that advertising for physician 
positions on a macromolecular crystallography email list was not an efficient 
means of getting the word out on behalf of your clients, I am sure those of us 
receiving these emails and contemplating just such a lucrative career change, 
complete with an endoscopy chamber in Tennesee, would somehow endure the trauma.

Peace and joy in a prosperous new year,

Bill




On Mon, 7 Jan 2008 09:27:21 -0500
Jessica Martin <[EMAIL PROTECTED]> wrote:

 To all those interested, 
 
 We have a 2 current openings in the same facility for a Gastroenterology 
specialist in Tennessee. Consultation status with the health system and will 
follow up with patients in the hospital after they are admitted.
 ?
 
 Benefits include
 
 
 NO call
 
 Endoscopy procedure lab (suite) available
 
 Highly competitive salary
 
 Excellent benefits, CME, Malpractice
 
 Moving expenses provided
 
 
 ?
 
 Please fax CV/Resume attention: Jessica Martin to fax number 206-666-4501. 
Any questions may be directed [EMAIL PROTECTED] Thank you!
 
 
 
 ?Jessica Martin
 Deb Bailey Recruiting
 206-666-4501
 203 Red Fern Pl
 Hot Springs, AR 71901
 
 
 
 
 
 
 
 More new features than ever.  Check out the new AOL Mail ! - 
http://webmail.aol.com
 

[ccp4bb] Scientist Position in Protein Crystallography - LNLS

[Selma Tsuda]

Scientist Position in Protein Crystallography - Brazilian Synchrotron Light
Laboratory (LNLS)

 

LNLS is a 1.37 GeV synchrotron source located in Campinas, Brazil, at 90 km
NW from São Paulo. It is the only synchrotron laboratory in Latin America
and has two beam lines dedicated to Macromolecular Crystallography. Modern
facilities for recombinant protein production, crystallization and
spectroscopy are also available at the LNLS campus. 

 

A scientific position to be part of LNLS staff is now available in the
Protein Crystallography group. The LNLS is seeking a motivated scientist
with a strong background in macromolecular crystallography and an interest
in instrumentation and/or methodology. The successful candidate is expected
to conduct independent research and to supervise PhD students and post
doctoral fellows. The scientist will also work on the MX beam lines to
provide support to external users and to contribute to the continuous
improvement and upgrade of the beam lines. 

 

QUALIFICATIONS

Candidates should have a PhD degree in structural biology, biochemistry or
related disciplines plus a post-doctoral experience in protein
crystallography. Candidates should be able to demonstrate their interest in
instrumentation and/or methodology related to macromolecular
crystallographic data collection and analysis. Experience of synchrotron
radiation beam lines (as an experienced user or beam line operator) is
desirable. Knowledge of crystallization techniques is an asset. 

 

Application letter and CV including the contacts of three referees should be
sent by email to   [EMAIL PROTECTED]

Deadline for application: January 15th, 2008.

 

--

Selma Tsuda

Brazilian Synchrotron Light Laboratory  - LNLS

 

[ccp4bb] How to override the use of NCS in Molrep?

[Pietro Roversi]

Dear all,
  I am working on a multidomain structure in P31 with two
copies in the asymmetric unit and pseudo-P3121 symmetry - the NCS is a
twofold relating most of copy A to copy B but one domain violates the
higher symmetry. I have placed all the NCS-obeying domains of A and B,
plus copy A of the NCS-violating domain, and am looking for the second
copy of the latter using molecular replacement. I am using all the
programs I know of including Molrep.

Now, the Molrep binary I downloaded from
http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp is far too clever: it
autodetects the NCS-twofold in the self rotation function and switches
the NCS on - which is not what I want:


INFO:Relations between peaks see in molrep.doc
  NCS_model (from Model Self rotation Function): 1
  Program will use NCS =: 1

 Does anyone know how to turn this off?

Thanks!

Pietro 
-- 
Pietro Roversi
Sir William Dunn School of Pathology, Oxford University
South Parks Road, Oxford OX1 3ER, England UK
Tel. 0044-1865-275385

Re: [ccp4bb] Have a happy new year with your very own crystallography system!

[David J. Schuller]

On Mon, 2008-01-07 at 18:22 +, Erin Curry wrote:

> Tired of embarrassing incidents at the beamline?...



Alright, who's been telling stories?

-  
===
With the single exception of Cornell, there is not a college in the
United States where truth has ever been a welcome guest - R.G. Ingersoll
===
  David J. Schuller
  modern man in a post-modern world
  MacCHESS, Cornell University
  [EMAIL PROTECTED]

[ccp4bb] Crystallographically perplexing article in Feb 2008 AMS Notices

[Ethan Merritt]

The Feb issue of AMS Notices  (American Mathematical Society)
contains an article of possible interest to crystallographers.

   http://www.ams.org/notices/200802/
   "Crystals That Nature Might Miss Creating" - Toshikazu Sunada

I confess myself perplexed as to what is actually being 
described in this article.  In particular, I cannot figure out
whether the "K_4 lattice" being described is truly a lattice in
the sense that crystallographers understand the term.
If so then what does it correspond to in our usual nomenclature?


-- 
Ethan A Merritt

[ccp4bb] ACA Microcrystals Session: deadline approaching

[Richard Gillilan]

Just a final reminder. The deadline for submitting abstracts (posters  
and talks) has been extended to January 12 (this Saturday). Students  
are strongly encouraged to submit abstracts and will be considered  
for the Etter Student Lecturer Award if invited to speak. There is  
still room in the schedule for new contributions.


Submit your abstract online at this link: www.amercrystalassn.org/ 
AbsSubmit/


Microcrystallography Session ACA 2008, Knoxville TN
(Session 13.14, Thursday June 5)

Organizers: Richard Gillilan, Ruslan Sanishvili

Frontiers of structural biology are continuously expanding. Membrane  
proteins, hetero-molecular assemblies, multi-domain proteins, and  
many other important biological systems only produce microcrystals.  
Increasingly, synchrotron beamlines are evolving to meet the  
challenges of obtaining good diffraction data from samples of ever  
decreasing size. While x-ray optics, background scattering reduction,  
beam stability, and mechanical design innovations continue to  
improve, this session will focus on supporting technologies, data  
collection strategies, and important biophysical questions  
surrounding the occurrence of microcrystals. What causes crystals to  
be small?  Within larger crystals, how much does diffraction quality  
vary from spot to spot and how can x-ray microbeam be effectively  
used to collect the best data? How can we avoid or mitigate radiation  
damage as a consequence of higher flux densities used with smaller  
diffracting volumes? The session will also touch upon recent advances  
in microcrystal recognition, manipulation, and harvesting, especially  
within the context of high-throughput screening.

[ccp4bb] FW: alignment

[Heidi Schubert]

Hi,

I'm looking for a program to improve a low homology sequence alignment using 
the known (but unpublished) structure of one of the sequences. Programs like 
Verify3D and CPROF (Eisenberg's lab) generate the environmental profile of a 
structure, but then how do I apply that to other sequences to improve an 
alignment. 

This request is compounded by the structural size of the sequence, 2100 amino 
acids containing some 70 helices (very repetative).  Hence using a starting 
alignment is a good idea.

THREADER won't build a TDB file (target file) for something this big. I guess 
we could do it in sections and then thread small portions of the weak homologs 
individually. We've hit a variety of errors with the TDB server. Other 
"threader" servers only use PDB archives, not new structures. 

any ideas.
Heidi

[ccp4bb] How to refine large moleculars?

[Yongchao Li]

I have a large molecule to refine.There are about three thousand residues in  
one asymmetric unit. 
Except for the lack of electron densities in several places, where the 
loops have been deleted, the rest parts fits well with density. But the R free 
and R work are all beyond 0.30 (R free = 0.35, R work = 0.30).
I don't know how to reduce them. 
Can anyone give me some ideas?

Thank you!


   
-
Looking for last minute shopping deals?  Find them fast with Yahoo! Search.

[ccp4bb] complement on how to refine large moleculars.

[Yongchao Li]

The space group is P212121

There are four chains in one asymmetric unit: two A chains and two B chains.

   
-
Never miss a thing.   Make Yahoo your homepage.

Re: [ccp4bb] How to refine large moleculars?

[Tim Gruene]

Depending on your data quality and the nature of the crystal it might be 
that you cannot reduce R/Rfree any further.
Low R/Rfree is not the goal of refinement and model building - at least 
not for the humans doing it. The goal is to get as good a model as 
possible, and if your data are not very good, or also for various other 
possibilities you might not be able to improve the statistical guidelines.


I am not suggesting you should stop refining now - but without knowing you 
data/ resolution/ data statistics it is very difficult to give an answer.


Cheers, Tim

--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A


On Mon, 7 Jan 2008, Yongchao Li wrote:


I have a large molecule to refine.There are about three thousand residues in  
one asymmetric unit.
Except for the lack of electron densities in several places, where the
loops have been deleted, the rest parts fits well with density. But the R free 
and R work are all beyond 0.30 (R free = 0.35, R work = 0.30).
I don't know how to reduce them.
Can anyone give me some ideas?

Thank you!



-
Looking for last minute shopping deals?  Find them fast with Yahoo! Search.

Re: [ccp4bb] how to model this density?

[Artem Evdokimov]

You should check if this residue is a part of a glycosylation pattern
(either via crude computational sequence analysis, or if you're lucky - by
digest and peptide MS).

 

The density *looks like* a disordered sugar but at 2.6A this is a very tough
call.

 

Artem

  _  

From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jiamu
Du
Sent: Monday, January 07, 2008 10:20 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] how to model this density?

 

Dear All:
I am refining a structure at 2.6 A reslution. The protein is expressed in
CHO cell, so it might be glycosylated.
While refining an Asn residue as shown in the figure of the attachment, I
found some strange density extended beyond the side chain of Asn. The sigma
level for the fofc map of the figure in the attachment is as high as 3.0. My
protein buffer is Tris and NaCl, and the reservior is PEG and NH4Cl. I
believe this is not water mlecules. Considering the residue is Asn, I guess
it might be carbohydrate. 
Is this density like a carbohydrate molecule? How to model this density? 
Thanks and Happy New Year.

-- 
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 model this density?

[Jiamu Du]

Dear Jeff:
The sequence here is NYT. I think it is glycosylated here, isn't it?
Thanks a lot.

On Jan 8, 2008 11:37 AM, Jeff Lee <[EMAIL PROTECTED]> wrote:

> Hi,
> Do you know what is the protein sequence in this region.  If it is
> glycosylated, it should have a distinctive motif (N-X-S/T).  You might have
> the first NAG attached to the Asn if the motif is there.
>
> Jeff
>
>
> On Jan 7, 2008, at 7:19 PM, Jiamu Du wrote:
>
> Dear All:
> I am refining a structure at 2.6 A reslution. The protein is expressed in
> CHO cell, so it might be glycosylated.
> While refining an Asn residue as shown in the figure of the attachment, I
> found some strange density extended beyond the side chain of Asn. The sigma
> level for the fofc map of the figure in the attachment is as high as 3.0.
> My protein buffer is Tris and NaCl, and the reservior is PEG and NH4Cl. I
> believe this is not water mlecules. Considering the residue is Asn, I guess
> it might be carbohydrate.
> Is this density like a carbohydrate molecule? How to model this density?
> Thanks and Happy New Year.
>
> --
> Jiamu Du
> State Key Laboratory of Molecular Biology
> Institute of Biochemistry and Cell Biology Shanghai Institutes for
> Biological Sciences
> Chinese Academy of Sciences (CAS)
>
>
>


-- 
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 refine large moleculars?

[Lari Lehtio]

Without knowing the resolution, you could try to use TLS refinement (if you 
haven't done it 
already)  and see if the maps improve and allow you to build more/better. If 
the resolution is 
reasonable and you can not lower the R & Rfree you should check whether 
twinning is 
possible. It is common AFAIK that in twin cases the R-factors get stuck above 
30 %.

~L~

___

 Lari Lehtiö
 Structural Genomics Consortium
 Medical Biochemistry & Biophysics Dept.   
 Karolinska Institute
 Stockholm, Sweden
___

- Original Message -
From: Yongchao Li <[EMAIL PROTECTED]>
Date: Tuesday, January 8, 2008 1:51 am
Subject: [ccp4bb] How to refine large moleculars?
To: CCP4BB@JISCMAIL.AC.UK

> I have a large molecule to refine.There are about three thousand 
> residues in  one asymmetric unit. 
> Except for the lack of electron densities in several places, where 
> the 
> loops have been deleted, the rest parts fits well with density. But 
> the R free and R work are all beyond 0.30 (R free = 0.35, R work = 
> 0.30).I don't know how to reduce them. 
> Can anyone give me some ideas?
> 
> Thank you!
> 
> 
>   
> -
> Looking for last minute shopping deals?  Find them fast with Yahoo! Search.