[ccp4bb] Postdoctoral position available at University of Texas Southwestern Medical Center

[Diana Tomchick]

This message is posted for Eric Olson, Ph.D. (Chair of Molecular Biology), who 
is looking for a postdoctoral fellow to join his lab to work on a novel 
membrane protein (first described in Nature, in press). See project description 
below and if interested please contact him at:

Email: eric.ol...@utsouthwestern.edu

Eric N. Olson, Ph.D.
Chair and Professor
Department of Molecular Biology
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-9148
214-648-1187 phone
214-648-1196 fax
http://www4.utsouthwestern.edu/olsonlab/index.html

Project Description:
We have discovered a novel muscle-specific membrane protein that is necessary 
and sufficient to induce the fusion of muscle cells to form multinucleated 
muscle fibers.  The process of myoblast fusion has been the focus of intense 
interest for decades but, until now, no muscle-specific fusigen has been 
discovered.  This fusigenic protein is highly hydrophobic and localized to the 
plasma membrane.  One of our major goals is to understand at the structural 
level how such a protein can promote the merger of membranes between cells.  We 
hope to recruit a structural biologist to determine the crystal structure of 
this fusigenic protein and then to introduce mutations to perturb its structure 
to further understand the mechanistic basis of its actions.  This project has 
the potential to yield important new insights into general properties of 
membrane fusion.  This project will offer a unique opportunity for a young 
scientist to establish a reputation in an important area of cell biology and to 
independently extend this work in the future.

Facilities Description:
State-of-the-art equipment is shared between the members in the Structural 
Biology community at UT Southwestern and consists of one Rigaku FR-E 
SuperBright high brilliancy X-ray generator equipped with one set of 
high-resolution and one set of high-intensity X-ray optics, two imaging-plate 
X-ray detectors (one R-Axis IV++ and one R-Axis IV), two X-Stream crystal 
cooling devices, and one automated sample-mounting device (ACTOR) for the 
unattended screening of crystals; a Phoenix crystallization robot, plus two 
Desktop Minstrel imaging systems and a Gallery-160 Plate Hotel; 30 days per 
year of beamtime at beamlines 19ID at the Advanced Photon Source (APS), 
Argonne, IL; several NMR spectrometers (one 800 MHz, three 600 MHz, two 500 
MHz), cryo-probes and robotic sample changer.  These facilities are 
supplemented by a variety of biophysical instruments supporting the study of 
macromolecules using CD, dynamic light scattering, analytical 
ultracentrifugation, stopped-flow kinetics, isothermal titration calorimetry, 
microscale thermophoresis and mass spectrometry. Several investigators in the 
UT Southwestern Structural Biology community are expert membrane protein 
crystallographers, and have access to specific equipment and expertise related 
to construct optimization, crystallization and structure solution of membrane 
proteins.

Diana

* * * * * * * * * * * * * * * * * * * * * * * * * * * *
Diana R. Tomchick
Professor
University of Texas Southwestern Medical Center
Department of Biophysics
5323 Harry Hines Blvd.
Rm. ND10.136EB (until the end of July)
Dallas, TX 75390-8816, U.S.A.
Email: 
diana.tomch...@utsouthwestern.edu
214-645-6383 (phone)
214-645-6353 (fax)









UT Southwestern Medical Center
The future of medicine, today.

[ccp4bb] Rigaku Crystallization Webinar announcement

[Jian Xu]

Dear Colleagues,

On behalf of Rigaku, I'm very pleased to introduce a new Rigaku Crystallization 
Webinar series. As crystallization of biological molecules continues to remain 
the bottleneck in structural biology, we would like to provide the community 
educational materials and a discussion forum on scientific methodology 
development and applications in this field. This Webinar series will cover a 
broad range of subjects in crystallization, from theoretical to practical 
methods of crystallization, high-throughput to high output, manual to robotic 
setup, and soluble proteins to membrane proteins.  We are inviting world 
leading scientists in protein crystallization to present the latest and 
greatest technology and methods.

Rigaku is also focused on education in support of macromolecular 
crystallization. With this in mind, we would like to encourage graduate 
students and postdocs to present short talks in this forum, sharing your 
successes or challenges with your peers attending the webinar. The short 
presentation will be around 20 minute long and all presenters will receive a 
gift card of $50. In addition, student and postdoc presentations will be 
periodically reviewed by a panel of judges and the top presenters will be 
awarded a travel grant of $500, supporting the attendance of a scientific 
conference of their choice. Interested parties should contact Dr. Jian Xu at 
jian...@rigaku.com.

It is my honor to announce that the following speakers will be presenting in 
our future webinar series (not in sequence):
Dr. Bernhard Rupp  Innsbruck Medical University, Austria, and k.-k. 
Hofkristallamt, USA
Dr. Allan D'Arcy Novartis Institute of Biomedical Research, 
Switzerland
Dr. Edward Snell   Hauptman-Woodward Medical Research Institute, USA
Dr. Jose Gavira  CSIC-Universidad de Granada, Spain
Dr. Janet Newman  CSIRO, Australia
Dr. Jeroen Mesters University of Lubeck, Germany
Dr. Yvonne Thielmann   Max Planck Institute, Germany
Dr. Marc ElsligerThe Joint Center for Structural Genomics 
(JCSG), USA

Our first webinar will be given on August 6th, presented by Dr. Bernhard Rupp, 
Marie Curie Incoming International Fellow, Innsbruck Medical University, 
Austria, and Dept. of Forensic Crystallography, k.-k. Hofkristallamt, USA. The 
detailed information about each of these presentations will be sent out 
multiple times prior to the webinar. Please also go to 
http://www.rigakuautomation.com/webinars to find out the updated webinar 
information. We invite anyone to submit topic suggestions for future webinars 
and hope that you will provide feedback for previous webinars.

We are excited about this Webinar series and looking forward to seeing you 
there!

Jian Xu, Ph.D.
Rigaku Automation, Inc.
5999 Avenida Encinas, Suite 150
Carlsbad, CA 92008
USA
T:  760-438-5282 x130
C:  760-576-7167
jian...@rigaku.com
www.rigakuautomation.com
www.rigaku.com

Rigaku Automation, Inc. is an ISO 9001 registered company

Re: [ccp4bb] Off-topic: NMR and crystallography

[El Arnaout, Toufic]

Hi Theresa,

Here is a comparison between both methods (Table under "6-Summary"): http://www.cryst.bbk.ac.uk/pps97/assignments/projects/ambrus/html.htm

If you would like to have an idea about structures of membrane proteins (why was NMR used and what answers they got etc) solved by NMR to date please check: http://www.drorlist.com/nmr/MPNMR.html

; for solid-state NMR: http://www.drorlist.com/nmr/SPNMR.html

I'm sure any lab would be happy to solve their structures using both methods (if they can) + publish high impact papers. Even if structural differences exist, why not.. more to discuss :)

Sometimes large differences are more related to the detergent/environment or many other factors that affect memb proteins.

Regards




toufic el arnaout

School of Medicine - 660 S Euclid Ave
Washington University in St. Louis
St Louis, MO 63110








> Date: Sun, 9 Jun 2013 16:36:15 +0100
> From: theresah...@live.com
> Subject: [ccp4bb] Off-topic: NMR and crystallography
> To: CCP4BB@JISCMAIL.AC.UK
> 
> Dear all
> 
> A question for the cross-trained members of this forum - for small sized proteins, is NMR better than crystallography in terms of data collection (having crystals in the first place) and data processing? How about membrane proteins?
> 
> I would appreciate replies to the board, instead of off-board, to allow for a good discussion.
> 
> Thank you.
> 
> Theresa
> 

[ccp4bb] Cryo-Xe-Siter looking for new home

[Chris Richardson]

We have an MSC Cryo-Xe-Siter that won't fit in our refurbished X-ray 
laboratory.  If it can't find a new home it will be disposed of.  We're 
offering it free of charge to any interested UK organisations on the condition 
that the recipient pays for its transport.  It's currently in central London.

The Cryo-Xe-Siter is used for preparing xenon derivates of protein crystals.  A 
quick web search reveals a review in Nature Structural & Molecular Biology from 
1998.

  http://www.nature.com/nsmb/journal/v5/n12/full/nsb1298_1107.html

If you're interested, please email nora.cro...@icr.ac.uk.  If we don't have any 
interest before this Friday it will be scrapped.

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.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.

Re: [ccp4bb] PISA and ligands with non-natural amino acids

[Eugene Krissinel]

Dear Herman,

I am looking at protein complexes with ligands containing non-natural amino 
acids. When I run PISA, I get the total area of the ligand, as well as the area 
of the ligand-protein interface, but hydrogen bonds and salt links are not 
recognized. I therefore do not think the calculated DeltaG values can be 
trusted. Is there a way to specify non-natural ligands for PISA, or does it 
only work for amino acids which have been calibrated with help of a large 
number pdb structures?

- this is exactly the case at the moment.

Eugene



-- 
Scanned by iCritical.

[ccp4bb] PISA and ligands with non-natural amino acids

[Herman . Schreuder]

Dear Bulletin board,

I am looking at protein complexes with ligands containing non-natural amino 
acids. When I run PISA, I get the total area of the ligand, as well as the area 
of the ligand-protein interface, but hydrogen bonds and salt links are not 
recognized. I therefore do not think the calculated DeltaG values can be 
trusted. Is there a way to specify non-natural ligands for PISA, or does it 
only work for amino acids which have been calibrated with help of a large 
number pdb structures?

Thank you for your help!
Herman

Re: [ccp4bb] Protein concentration for crystallization

[Patrick Shaw Stewart]

Bernhard,

I'm often amazed at how forgiving protein crystallization is, or to put it
another way, how efficient screens are at picking up crystallization hits
even when you do everything wrong.

However if you do go down to 20 + 20 nl drops you have to remember that
probably 3/4 of your protein will be lost by sticking to the plastic of the
plate or forming a skin at the air interface.

You generally get roughly the same number of hits from 1 + 1 ul drops
(where most of the protein is still in solution) as from 100 + 100 nl drops
(roughly half the protein is lost), although the hits will be in different
places.  This implies that, within broad limits, things like protein
concentration don't matter too much.

My view of crystallization is that there's a group of proteins (lysozyme
and many others) where all you have to do is gently push the protein out of
solution, while taking care of nucleation (think microseeding).  For these
proteins it's a matter of *not *adding something that interferes with
crystallization.  Then there are others where you have to add something to
the mix that stabilizes the crystal lattice.  A smaller group requires 2
additives, a few may need 3   At the end there's a bunch that will
never crystallize no matter what you do.

It seems that protein concentration is of secondary importance in screening
- although I accept that it may be crucial in optimization.

Patrick



On 11 June 2013 08:48, Bernhard Rupp  wrote:

> H….the real message from figure 3.  The protein concentration…
>
> seems to be that >70% of proteins do NOT crystallize in the 10-12.5 mg bin,
> 
>
> i.e. the ‘right’ concentration is an individual protein-in-that-buffer
> property - and
>
> all one can say is that the concentration needs to be high enough so that
> the crystallization 
>
> conditions (either right away in case of batch, or vapor-diffusion
> assisted) can drive
>
> the system across the solubility limit into supersaturation. 
>
> Most people actually working with their protein have already a reasonably
> developed idea what
>
> their protein can take in various buffer systems (valuable parameter!)
>
> … once they have scraped if off a centricon membrane, for example…
>
> The pre-screening originated from structural genomics when one had no idea
> what
>
> the ‘customer’ actually sent to the facility. If one knows the material it
> might be more
>
> efficient (i.e. more information from the same precious material) to set
> up a plate of 
>
> 96 20+20 nl nanodrops than spending 2 ul on prescreening.
>
> ** **
>
> Just an opinion sans statistics, BR
>
> ** **
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of 
> *Debasish
> Chattopadhyay
> *Sent:* Tuesday, June 11, 2013 1:02 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Protein concentration for crystallization
>
> ** **
>
> Perhaps my question was not expressed well.  I wanted to know if proteins
> crystallize more frequently when the protein concentration is in the range
> 5-30mg/ml.
>
> The answer pointed out by my colleague Todd Green is on the page
>
> http://www.douglas.co.uk/PDB_data.htm
>
> ** **
>
> Thanks for your inputs.
>
> ** **
>
> Debasish
>
> ** **
>
> *From:* Orru, Roberto [mailto:roberto.o...@emory.edu]
>
> *Sent:* Monday, June 10, 2013 5:04 PM
> *To:* Debasish Chattopadhyay
> *Subject:* RE: Protein concentration for crystallization
>
> ** **
>
> Dear Debasish,
>
> On my memory there are 2 way (but I cannot say that are the only 2!)
> First: if you have the structure and you know the water content, you can
> guess the amount of protein crystallized in your drop by calculating the
> volume of the crystals.
> Second (if you can waste your drops): Fish all the crytsals in any drop
> for a given concentration, load a sds page w/ silver staining developing
> and compare it with a calibration curve done with your same protein in the
> same gel.
>
> Best
> R.
> --
>
> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Debasish
> Chattopadhyay [debas...@uab.edu]
> *Sent:* Monday, June 10, 2013 10:49
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Protein concentration for crystallization
>
> What would be a convenient way to estimate what percentages of proteins
> have been crystallized in a concentration range, for example 5-30 mg?
>
>  
>
> Debasish Chattopadhyay
>
>  
>
> University of Alabama at Birmingham
>
> CBSE-250
>
> 1025 18th Street South, Birmingham, Al-35294
>
> USA
>
> Ph: (205)934-0124; Fax: (205)934-0480
>
>  
>
> ** **
> --
>
>
> This e-mail message (including any attachments) is for the sole use of
> the intended recipient(s) and may contain confidential and privileged
> information. If the reader of this message is not the intended
> recipient, you are hereby notified that any d

Re: [ccp4bb] Fwd: [ccp4bb] pdbset

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Swastik Phulera,

if your res-file sports negative U-values, your model has room for
improvement. You really should go back to the ins-file and make the
appropriate modifications in order to get rid of negative U-values
(the do not make chemical sense!).

Do you use RIGU? It might overcome your problem. Negative B-values (of
waters) could also mean that you placed an oxygen instead of a heavier
ion.

Best,
Tim

On 06/11/2013 11:42 AM, Swastik Phulera wrote:
> Dear Tim,Fred Negative B factors and occupancies higher than one
> came in from shelxl, Also getting rid of Ansiou at first would lead
> me to an additional step of placing them in their right place later
> on (is there a short cut that I may take).
> 
> 
> 
> On Tue, Jun 11, 2013 at 2:09 PM, Tim Gruene
>  wrote:
> 
> Dear Swastik Phulera,
> 
> unless you need the ANISOU cards, you can first remove them with
> e.g.
> 
> grep -v "^ANISOU" youfile.pdb > yournewfile.pdb
> 
> before running pdbset.
> 
> (I hope you don't work on a Windows machine, then you would
> probably first find a way to install 'grep', a command common on
> unixoid operating systems).
> 
> By the way: how did you get negative B-values into your PDB-file?
> 
> Best, Tim
> 
> On 06/11/2013 10:22 AM, Swastik Phulera wrote:
 -- Forwarded message -- From: Swastik
 Phulera  Date: Tue, Jun 11, 2013
 at 1:51 PM Subject: Re: [ccp4bb] pdbset To: Tim Gruene 
 
 
 
 Dear Tim, Miguel Thanks for your suggestions, the program
 does work now, but it seems that it cant handle AnsioU s . It
 gives an error:
 
 PDBSET:  *** AnisoU present: cannot reset B ***
 
 Is there any other program which would set minimum bfactors
 for me. Also I am looking for a program that would set the
 maximum occupancy to a desired value (It seems that pdbset
 can only play with the minimum values)..
 
 
 
 On Tue, Jun 11, 2013 at 12:11 PM, Tim Gruene 
 wrote:
 
 Dear Swastik Phulera,
 
 after the word 'output.pdb' you must first hit the Enter-key
 which takes you into the program pdbset. Then you type
 
 B_reset Minimum 0 END
 
 and the program runs. If you wish to do it without
 interaction, e.g. in a script, you can use the shell
 construct '<<':
 
 pdbset XYZIN input.pdb XYZOUT output.pdb << eof B_reset
 MINIMUM 0 eof
 
 Best, Tim
 
 On 06/11/2013 08:15 AM, Swastik Phulera wrote:
>>> Dear All, I am trying to use pdbset from the terminal
>>> and am constantly getting an error:
>>> 
>>> [XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT
>>> output.pdb B_reset MINIMUM 0
>>> 
> CCP4 library signal ccp4_general:Use:
>  
>>> (Error) raised in ccp4fyp << pdbset:  Use: >> name>  pdbset:  Use:  >> name> Times: User: 0.0s System:0.0s Elapsed:
>>> 0:00
>>> 
>>> Does any one have any idea what's wrong here?
>>> 
>>> 
>>> Swastik Phulera
 
> 
 
 
 
> 
>> 
> 
> 
> 

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

GPG Key ID = A46BEE1A

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Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFRtwdfUxlJ7aRr7hoRAsy/AKCI1LfMVm9XM8HQfYacV91pRqK/3ACgtcSY
LT/zS9Igbt0Q/EghhpU4LDw=
=MCpu
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Re: [ccp4bb] Fwd: [ccp4bb] pdbset

[Eleanor Dodson]

If you are resetting B factors you must recalculate the AniosUs later

But if you are getting negative B values something in your procedure is
less than optimal!

Are you refining aniso Us with too limited data? You need high resolution
data to attempt this.

Are you trying to refine B factors and occupancies at the same time? You
need superb data to do this, and as a rule it isnt recommended. (Maybe for
metal atoms, or some special ligand, but not a good general practice..)

Or have you set occupancies too low, and the B factor is trying to
compensate for that?

Eleanor





On 11 June 2013 10:42, Swastik Phulera  wrote:

> Dear Tim,Fred
> Negative B factors and occupancies higher than one came in from shelxl,
> Also getting rid of Ansiou at first would lead me to an additional step of
> placing them in their right place later on (is there a short cut that I may
> take).
>
>
>
> On Tue, Jun 11, 2013 at 2:09 PM, Tim Gruene wrote:
>
>> -BEGIN PGP SIGNED MESSAGE-
>> Hash: SHA1
>>
>> Dear Swastik Phulera,
>>
>> unless you need the ANISOU cards, you can first remove them with e.g.
>>
>> grep -v "^ANISOU" youfile.pdb > yournewfile.pdb
>>
>> before running pdbset.
>>
>> (I hope you don't work on a Windows machine, then you would probably
>> first find a way to install 'grep', a command common on unixoid
>> operating systems).
>>
>> By the way: how did you get negative B-values into your PDB-file?
>>
>> Best,
>> Tim
>>
>> On 06/11/2013 10:22 AM, Swastik Phulera wrote:
>> > -- Forwarded message -- From: Swastik Phulera
>> >  Date: Tue, Jun 11, 2013 at 1:51 PM
>> > Subject: Re: [ccp4bb] pdbset To: Tim Gruene
>> > 
>> >
>> >
>> > Dear Tim, Miguel Thanks for your suggestions, the program does work
>> > now, but it seems that it cant handle AnsioU s . It gives an
>> > error:
>> >
>> > PDBSET:  *** AnisoU present: cannot reset B ***
>> >
>> > Is there any other program which would set minimum bfactors for
>> > me. Also I am looking for a program that would set the maximum
>> > occupancy to a desired value (It seems that pdbset can only play
>> > with the minimum values)..
>> >
>> >
>> >
>> > On Tue, Jun 11, 2013 at 12:11 PM, Tim Gruene
>> > wrote:
>> >
>> > Dear Swastik Phulera,
>> >
>> > after the word 'output.pdb' you must first hit the Enter-key which
>> > takes you into the program pdbset. Then you type
>> >
>> > B_reset Minimum 0 END
>> >
>> > and the program runs. If you wish to do it without interaction,
>> > e.g. in a script, you can use the shell construct '<<':
>> >
>> > pdbset XYZIN input.pdb XYZOUT output.pdb << eof B_reset MINIMUM 0
>> > eof
>> >
>> > Best, Tim
>> >
>> > On 06/11/2013 08:15 AM, Swastik Phulera wrote:
>>  Dear All, I am trying to use pdbset from the terminal and am
>>  constantly getting an error:
>> 
>>  [XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb
>>  B_reset MINIMUM 0
>> 
>> >> CCP4 library signal ccp4_general:Use: > >> name> 
>>  (Error) raised in ccp4fyp << pdbset:  Use: 
>>   pdbset:  Use:   Times:
>>  User: 0.0s System:0.0s Elapsed: 0:00
>> 
>>  Does any one have any idea what's wrong here?
>> 
>> 
>>  Swastik Phulera
>> >
>> >>
>> >
>> >
>> >
>>
>> - --
>> - --
>> Dr Tim Gruene
>> Institut fuer anorganische Chemie
>> Tammannstr. 4
>> D-37077 Goettingen
>>
>> GPG Key ID = A46BEE1A
>>
>> -BEGIN PGP SIGNATURE-
>> Version: GnuPG v1.4.12 (GNU/Linux)
>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>>
>> iD8DBQFRtuJQUxlJ7aRr7hoRAhcWAKDGPXBS3iJhzzbaYBK4GnJGjijyngCgqYZI
>> B26VKBDFO5FQNJJQd6plsc8=
>> =mDut
>> -END PGP SIGNATURE-
>>
>
>
>
> --
> --
> स्वस्तिक फुलेरा
> वरिष्ठ अनुसंधान कर्ता
> संरचनात्मक जीवविज्ञान प्रयोगशाला
> डी. एन. ए. फिंगरप्रिंटिंग एवं निदान केंद्र
> हैदराबाद, ५००, ००१
>
> और
>
> राष्ट्रीय कोशिका विज्ञान केंद्र
> पुणे विश्वविद्यालय परिसर,
> गणेशखिंड
> पुना,  ४११,००७
>

[ccp4bb] Two postdoctoral opportunities in X-ray crystallography at Umeå University, Sweden

[Karina Persson]

Two postdoctoral research opportunities in X-ray crystallography at Umeå 
University, Sweden

Several positions are open for postdoctoral candidates interested in doing 
research in the highly interactive and multidisciplinary research environment 
UCMR - Umeå Centre for Microbial Research at Umeå University. UCMR includes The 
Laboratory for Molecular Infection Medicine Sweden (MIMS) - the Swedish node of 
the Nordic EMBL Partnership for Molecular Medicine.

The number of positions that will be filled is not predetermined but can be a 
maximum of seven.

Two of the project ideas focus on structure determination of bacterial proteins 
important for infection, as described by Karina Persson and Elisabeth 
Sauer-Eriksson (karina.pers...@chem.umu.se 
and 
elisabeth.sauer-eriks...@chem.umu.se).

See the complete announcement including the project ideas:
http://www8.umu.se/umu/aktuellt/arkiv/lediga_tjanster/315-560-13.html#eng
Informal enquires may be made to Karina Persson and Elisabeth Sauer-Eriksson

[ccp4bb] Postdoctoral position in Oxford

[Ivan Ahel]

Postdoctoral Research Assistant
Sir William Dunn School of Pathology, South Parks Road, Oxford, UK
Salary Grade 7: £29,541 - £36,298 p.a.

A position is available in the DNA Damage Response group led by Dr Ivan Ahel 
investigating DNA damage response mechanisms. This post is for up to 36 months 
in the first instance and will be based in new laboratory space housing state 
of the art facilities at the Sir William Dunn School of Pathology in the centre 
of Oxford.

The successful candidate will study the structure and function of several novel 
DNA repair enzymes we have identified recently (Ahel et al, Nature, 2008; Slade 
et al, Nature, 2011; Sharifi et al, EMBO J, 2013).

Applicants should have a PhD in Biology or Biochemistry or a related subject, a 
high level of competence in protein X-ray crystallography, basic molecular 
biology and biochemistry, and relevant experience demonstrated by peer-reviewed 
publications. The ideal candidate should be organised, highly motivated and 
able to work independently as well as part of a team.

Enquiries should be directed to Dr Ivan Ahel at: 
ivan.a...@path.ox.ac.uk

Applications must be received by 8 July 2013.


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Re: [ccp4bb] Fwd: [ccp4bb] pdbset

[Swastik Phulera]

Dear Tim,Fred
Negative B factors and occupancies higher than one came in from shelxl,
Also getting rid of Ansiou at first would lead me to an additional step of
placing them in their right place later on (is there a short cut that I may
take).



On Tue, Jun 11, 2013 at 2:09 PM, Tim Gruene  wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Swastik Phulera,
>
> unless you need the ANISOU cards, you can first remove them with e.g.
>
> grep -v "^ANISOU" youfile.pdb > yournewfile.pdb
>
> before running pdbset.
>
> (I hope you don't work on a Windows machine, then you would probably
> first find a way to install 'grep', a command common on unixoid
> operating systems).
>
> By the way: how did you get negative B-values into your PDB-file?
>
> Best,
> Tim
>
> On 06/11/2013 10:22 AM, Swastik Phulera wrote:
> > -- Forwarded message -- From: Swastik Phulera
> >  Date: Tue, Jun 11, 2013 at 1:51 PM
> > Subject: Re: [ccp4bb] pdbset To: Tim Gruene
> > 
> >
> >
> > Dear Tim, Miguel Thanks for your suggestions, the program does work
> > now, but it seems that it cant handle AnsioU s . It gives an
> > error:
> >
> > PDBSET:  *** AnisoU present: cannot reset B ***
> >
> > Is there any other program which would set minimum bfactors for
> > me. Also I am looking for a program that would set the maximum
> > occupancy to a desired value (It seems that pdbset can only play
> > with the minimum values)..
> >
> >
> >
> > On Tue, Jun 11, 2013 at 12:11 PM, Tim Gruene
> > wrote:
> >
> > Dear Swastik Phulera,
> >
> > after the word 'output.pdb' you must first hit the Enter-key which
> > takes you into the program pdbset. Then you type
> >
> > B_reset Minimum 0 END
> >
> > and the program runs. If you wish to do it without interaction,
> > e.g. in a script, you can use the shell construct '<<':
> >
> > pdbset XYZIN input.pdb XYZOUT output.pdb << eof B_reset MINIMUM 0
> > eof
> >
> > Best, Tim
> >
> > On 06/11/2013 08:15 AM, Swastik Phulera wrote:
>  Dear All, I am trying to use pdbset from the terminal and am
>  constantly getting an error:
> 
>  [XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb
>  B_reset MINIMUM 0
> 
> >> CCP4 library signal ccp4_general:Use:  >> name> 
>  (Error) raised in ccp4fyp << pdbset:  Use: 
>   pdbset:  Use:   Times:
>  User: 0.0s System:0.0s Elapsed: 0:00
> 
>  Does any one have any idea what's wrong here?
> 
> 
>  Swastik Phulera
> >
> >>
> >
> >
> >
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.12 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>
> iD8DBQFRtuJQUxlJ7aRr7hoRAhcWAKDGPXBS3iJhzzbaYBK4GnJGjijyngCgqYZI
> B26VKBDFO5FQNJJQd6plsc8=
> =mDut
> -END PGP SIGNATURE-
>



-- 
--
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वरिष्ठ अनुसंधान कर्ता
संरचनात्मक जीवविज्ञान प्रयोगशाला
डी. एन. ए. फिंगरप्रिंटिंग एवं निदान केंद्र
हैदराबाद, ५००, ००१

और

राष्ट्रीय कोशिका विज्ञान केंद्र
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Re: [ccp4bb] Fwd: [ccp4bb] pdbset

[Robbie Joosten]

In Windows:

findstr /b /v ANISOU input.pdb > output.pdb


Cheers,
Robbie


> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Tim Gruene
> Sent: Tuesday, June 11, 2013 10:40
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Fwd: [ccp4bb] pdbset
> 
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Dear Swastik Phulera,
> 
> unless you need the ANISOU cards, you can first remove them with e.g.
> 
> grep -v "^ANISOU" youfile.pdb > yournewfile.pdb
> 
> before running pdbset.
> 
> (I hope you don't work on a Windows machine, then you would probably first
> find a way to install 'grep', a command common on unixoid operating
> systems).
> 
> By the way: how did you get negative B-values into your PDB-file?
> 
> Best,
> Tim
> 
> On 06/11/2013 10:22 AM, Swastik Phulera wrote:
> > -- Forwarded message -- From: Swastik Phulera
> >  Date: Tue, Jun 11, 2013 at 1:51 PM
> > Subject: Re: [ccp4bb] pdbset To: Tim Gruene 
> >
> >
> > Dear Tim, Miguel Thanks for your suggestions, the program does work
> > now, but it seems that it cant handle AnsioU s . It gives an
> > error:
> >
> > PDBSET:  *** AnisoU present: cannot reset B ***
> >
> > Is there any other program which would set minimum bfactors for me.
> > Also I am looking for a program that would set the maximum occupancy
> > to a desired value (It seems that pdbset can only play with the
> > minimum values)..
> >
> >
> >
> > On Tue, Jun 11, 2013 at 12:11 PM, Tim Gruene
> > wrote:
> >
> > Dear Swastik Phulera,
> >
> > after the word 'output.pdb' you must first hit the Enter-key which
> > takes you into the program pdbset. Then you type
> >
> > B_reset Minimum 0 END
> >
> > and the program runs. If you wish to do it without interaction, e.g.
> > in a script, you can use the shell construct '<<':
> >
> > pdbset XYZIN input.pdb XYZOUT output.pdb << eof B_reset MINIMUM 0
> eof
> >
> > Best, Tim
> >
> > On 06/11/2013 08:15 AM, Swastik Phulera wrote:
>  Dear All, I am trying to use pdbset from the terminal and am
>  constantly getting an error:
> 
>  [XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb
>  B_reset MINIMUM 0
> 
> >> CCP4 library signal ccp4_general:Use:  >> name> 
>  (Error) raised in ccp4fyp << pdbset:  Use:    name> pdbset:  Use:   Times:
>  User: 0.0s System:0.0s Elapsed: 0:00
> 
>  Does any one have any idea what's wrong here?
> 
> 
>  Swastik Phulera
> >
> >>
> >
> >
> >
> 
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> 
> GPG Key ID = A46BEE1A
> 
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.12 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
> 
> iD8DBQFRtuJQUxlJ7aRr7hoRAhcWAKDGPXBS3iJhzzbaYBK4GnJGjijyngCgqYZI
> B26VKBDFO5FQNJJQd6plsc8=
> =mDut
> -END PGP SIGNATURE-

Re: [ccp4bb] Fwd: [ccp4bb] pdbset

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Swastik Phulera,

unless you need the ANISOU cards, you can first remove them with e.g.

grep -v "^ANISOU" youfile.pdb > yournewfile.pdb

before running pdbset.

(I hope you don't work on a Windows machine, then you would probably
first find a way to install 'grep', a command common on unixoid
operating systems).

By the way: how did you get negative B-values into your PDB-file?

Best,
Tim

On 06/11/2013 10:22 AM, Swastik Phulera wrote:
> -- Forwarded message -- From: Swastik Phulera
>  Date: Tue, Jun 11, 2013 at 1:51 PM 
> Subject: Re: [ccp4bb] pdbset To: Tim Gruene
> 
> 
> 
> Dear Tim, Miguel Thanks for your suggestions, the program does work
> now, but it seems that it cant handle AnsioU s . It gives an
> error:
> 
> PDBSET:  *** AnisoU present: cannot reset B ***
> 
> Is there any other program which would set minimum bfactors for
> me. Also I am looking for a program that would set the maximum
> occupancy to a desired value (It seems that pdbset can only play
> with the minimum values)..
> 
> 
> 
> On Tue, Jun 11, 2013 at 12:11 PM, Tim Gruene
> wrote:
> 
> Dear Swastik Phulera,
> 
> after the word 'output.pdb' you must first hit the Enter-key which 
> takes you into the program pdbset. Then you type
> 
> B_reset Minimum 0 END
> 
> and the program runs. If you wish to do it without interaction,
> e.g. in a script, you can use the shell construct '<<':
> 
> pdbset XYZIN input.pdb XYZOUT output.pdb << eof B_reset MINIMUM 0 
> eof
> 
> Best, Tim
> 
> On 06/11/2013 08:15 AM, Swastik Phulera wrote:
 Dear All, I am trying to use pdbset from the terminal and am 
 constantly getting an error:
 
 [XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb 
 B_reset MINIMUM 0
 
>> CCP4 library signal ccp4_general:Use: > name> 
 (Error) raised in ccp4fyp << pdbset:  Use: 
  pdbset:  Use:   Times:
 User: 0.0s System:0.0s Elapsed: 0:00
 
 Does any one have any idea what's wrong here?
 
 
 Swastik Phulera
> 
>> 
> 
> 
> 

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

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFRtuJQUxlJ7aRr7hoRAhcWAKDGPXBS3iJhzzbaYBK4GnJGjijyngCgqYZI
B26VKBDFO5FQNJJQd6plsc8=
=mDut
-END PGP SIGNATURE-

Re: [ccp4bb] Fwd: [ccp4bb] pdbset

[vellieux]

What about getting rid of the ANISOU records before processing the pdb 
file, with


grep -v ANISOU input.pdb > output.pdb

?

If a program complains about ANISOU records then you use the isotropic 
approximation...


That's what I would do as a quick and dirty fix.

Fred.

On 11/06/13 10:22, Swastik Phulera wrote:



-- Forwarded message --
From: *Swastik Phulera* >

Date: Tue, Jun 11, 2013 at 1:51 PM
Subject: Re: [ccp4bb] pdbset
To: Tim Gruene mailto:t...@shelx.uni-ac.gwdg.de>>


Dear Tim, Miguel
Thanks for your suggestions, the program does work now, but it seems 
that it cant handle AnsioU s . It gives an error:


PDBSET:  *** AnisoU present: cannot reset B ***

Is there any other program which would set minimum bfactors for me.
Also I am looking for a program that would set the maximum occupancy 
to a desired value (It seems that pdbset can only play with the 
minimum values)..




On Tue, Jun 11, 2013 at 12:11 PM, Tim Gruene > wrote:


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Swastik Phulera,

after the word 'output.pdb' you must first hit the Enter-key which
takes you into the program pdbset.
Then you type

B_reset Minimum 0
END

and the program runs.
If you wish to do it without interaction, e.g. in a script, you can
use the shell construct '<<':

pdbset XYZIN input.pdb XYZOUT output.pdb << eof
B_reset MINIMUM 0
eof

Best,
Tim

On 06/11/2013 08:15 AM, Swastik Phulera wrote:
> Dear All, I am trying to use pdbset from the terminal and am
> constantly getting an error:
>
> [XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb
> B_reset MINIMUM 0
>
>>> CCP4 library signal ccp4_general:Use: 
>>> 
> (Error) raised in ccp4fyp << pdbset:  Use:   name> pdbset:  Use:   Times: User:
> 0.0s System:0.0s Elapsed: 0:00
>
> Does any one have any idea what's wrong here?
>
>
> Swastik Phulera

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

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFRtsaJUxlJ7aRr7hoRAiAsAKCuDDip6GFczecze/Y18+YaD4+SqACdGnSU
fG1/zzDml0ynkX8uOBN7S+o=
=2I5+
-END PGP SIGNATURE-




--
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हैदराबाद, ५००, ००१

और


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पुणे विश्वविद्यालय परिसर,
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--
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वरिष्ठ अनुसंधान कर्ता
संरचनात्मक जीवविज्ञान प्रयोगशाला
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हैदराबाद, ५००, ००१

और

राष्ट्रीय कोशिका विज्ञान केंद्र
पुणे विश्वविद्यालय परिसर,
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--
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ouvrier de la recherche
IBS / ELMA
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Tel: +33 438789605
Fax: +33 438785494

[ccp4bb] Fwd: [ccp4bb] pdbset

[Swastik Phulera]

-- Forwarded message --
From: Swastik Phulera 
Date: Tue, Jun 11, 2013 at 1:51 PM
Subject: Re: [ccp4bb] pdbset
To: Tim Gruene 


Dear Tim, Miguel
Thanks for your suggestions, the program does work now, but it seems that
it cant handle AnsioU s . It gives an error:

PDBSET:  *** AnisoU present: cannot reset B ***

Is there any other program which would set minimum bfactors for me.
Also I am looking for a program that would set the maximum occupancy to a
desired value (It seems that pdbset can only play with the minimum values)..



On Tue, Jun 11, 2013 at 12:11 PM, Tim Gruene wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Swastik Phulera,
>
> after the word 'output.pdb' you must first hit the Enter-key which
> takes you into the program pdbset.
> Then you type
>
> B_reset Minimum 0
> END
>
> and the program runs.
> If you wish to do it without interaction, e.g. in a script, you can
> use the shell construct '<<':
>
> pdbset XYZIN input.pdb XYZOUT output.pdb << eof
> B_reset MINIMUM 0
> eof
>
> Best,
> Tim
>
> On 06/11/2013 08:15 AM, Swastik Phulera wrote:
> > Dear All, I am trying to use pdbset from the terminal and am
> > constantly getting an error:
> >
> > [XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb
> > B_reset MINIMUM 0
> >
> >>> CCP4 library signal ccp4_general:Use: 
> >>> 
> > (Error) raised in ccp4fyp << pdbset:  Use:   > name> pdbset:  Use:   Times: User:
> > 0.0s System:0.0s Elapsed: 0:00
> >
> > Does any one have any idea what's wrong here?
> >
> >
> > Swastik Phulera
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.12 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>
> iD8DBQFRtsaJUxlJ7aRr7hoRAiAsAKCuDDip6GFczecze/Y18+YaD4+SqACdGnSU
> fG1/zzDml0ynkX8uOBN7S+o=
> =2I5+
> -END PGP SIGNATURE-
>



-- 
--
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संरचनात्मक जीवविज्ञान प्रयोगशाला
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हैदराबाद, ५००, ००१

और


राष्ट्रीय कोशिका विज्ञान केंद्र
पुणे विश्वविद्यालय परिसर,
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पुना,  ४११,००७



-- 
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वरिष्ठ अनुसंधान कर्ता
संरचनात्मक जीवविज्ञान प्रयोगशाला
डी. एन. ए. फिंगरप्रिंटिंग एवं निदान केंद्र
हैदराबाद, ५००, ००१

और

राष्ट्रीय कोशिका विज्ञान केंद्र
पुणे विश्वविद्यालय परिसर,
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Re: [ccp4bb] Protein concentration for crystallization

[Bernhard Rupp]

H..the real message from figure 3.  The protein concentration.

seems to be that >70% of proteins do NOT crystallize in the 10-12.5 mg bin,

i.e. the 'right' concentration is an individual protein-in-that-buffer
property - and

all one can say is that the concentration needs to be high enough so that
the crystallization 

conditions (either right away in case of batch, or vapor-diffusion assisted)
can drive

the system across the solubility limit into supersaturation. 

Most people actually working with their protein have already a reasonably
developed idea what

their protein can take in various buffer systems (valuable parameter!)

. once they have scraped if off a centricon membrane, for example.

The pre-screening originated from structural genomics when one had no idea
what

the 'customer' actually sent to the facility. If one knows the material it
might be more

efficient (i.e. more information from the same precious material) to set up
a plate of 

96 20+20 nl nanodrops than spending 2 ul on prescreening.

 

Just an opinion sans statistics, BR

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Debasish Chattopadhyay
Sent: Tuesday, June 11, 2013 1:02 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Protein concentration for crystallization

 

Perhaps my question was not expressed well.  I wanted to know if proteins
crystallize more frequently when the protein concentration is in the range
5-30mg/ml.

The answer pointed out by my colleague Todd Green is on the page

http://www.douglas.co.uk/PDB_data.htm

 

Thanks for your inputs.

 

Debasish

 

From: Orru, Roberto [mailto:roberto.o...@emory.edu] 
Sent: Monday, June 10, 2013 5:04 PM
To: Debasish Chattopadhyay
Subject: RE: Protein concentration for crystallization

 

Dear Debasish,

On my memory there are 2 way (but I cannot say that are the only 2!)
First: if you have the structure and you know the water content, you can
guess the amount of protein crystallized in your drop by calculating the
volume of the crystals.
Second (if you can waste your drops): Fish all the crytsals in any drop for
a given concentration, load a sds page w/ silver staining developing and
compare it with a calibration curve done with your same protein in the same
gel.

Best
R.

  _  

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Debasish
Chattopadhyay [debas...@uab.edu]
Sent: Monday, June 10, 2013 10:49
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Protein concentration for crystallization

What would be a convenient way to estimate what percentages of proteins have
been crystallized in a concentration range, for example 5-30 mg?

 

Debasish Chattopadhyay

 

University of Alabama at Birmingham

CBSE-250

1025 18th Street South, Birmingham, Al-35294

USA

Ph: (205)934-0124; Fax: (205)934-0480

 

 

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