[ccp4bb] CALL CCPFYP: Segmentation fault: 11 (macOS Sierra Version 10.12.4)

[Wei Ding]

Dear all,
I want to CALL CCPFYP in my fortran script, but after compile, the binary file 
can not be run (macOS Sierra Version 10.12.4).
E.G.
1. :
  PROGRAM example_MTZ
  CALL CCPFYP
  stop
  end
2. gfortran-5  -O2  -o test test.f -L${CLIB} -lccp4f -lccp4c -lmmdb2 -lstdc++ 
-lgcc_s.10.5 -lSystem -lm
3. ./test
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x104287502
#1  0x104286820
#2  0x7fffbcb9bb39
#3  0x103dc5aca
#4  0x103da9aa2
#5  0x10588d506
#6  0x103d91f40
Segmentation fault: 11

I try gfortran-4/5 to compile this script，but error information is the same.
But the script can complie and run successfully in linux system, such as ubuntu 
and centos.

and if I use ifort to compile the script in macOS, everything seems ok.


Dose anyone can help me solve this problem? Thanks for your time.

--

Wei Ding
P.O.Box 603
The Institute of Physics,Chinese Academy of Sciences
Beijing,China
100190
Tel: +86-10-82649083
E-mail: ding...@iphy.ac.cn

Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

[Murpholino Peligro]

That's more like a tutorial for XDS :P (thanks though)

The problems:
1) It uses autorickshaw (which is a black box ...guess I'll read the paper
today) ...
 and
2) my files were not recognized  (MTZ with proper labels ...even the
XDS_ASCII.HKL files ).

Is it working? Guess I'll try to contact the developers.


Thanks again

2017-04-28 11:29 GMT-05:00 Christian Roth :

> There was a tutorial for MX including UV RIP available from the HZB in
> Berlin (BESSY MX group). Have a look at there website. I'm sure it is still
> available, or maybe they can send you the files on request.
>
> Cheers
>
> Christian
>
>
>
> Am 28.04.2017 um 17:12 schrieb Murpholino Peligro:
>
> Hi lads...
> Do you know if there is a good tutorial for doing RIP somewhere on the
> internet?
> What programs can do RIP?
> -SHELX
> -AutoRickShaw
> -?
>
> Thanks
>
>
>

Re: [ccp4bb] CH-bond length discrepancies

[Pavel Afonine]

Note, Molprobity has an option to use longer (neutron) X-H distances.
Pavel

On Fri, Apr 28, 2017 at 11:46 AM, Tristan Croll  wrote:

> I believe the reason for the discrepancy here is that MolProbity by
> default places the hydrogens according to the centroid of the electron
> cloud (most relevant to x-ray crystallographic data) rather than the
> nuclear position. In a polar bond like N-H the difference can be quite
> substantial.
>
> Cheers,
>
> Tristan
>
>
>
> Tristan Croll
> Research Fellow
> Cambridge Institute for Medical Research
> University of Cambridge CB2 0XY
>
>
>
>
> On 28 Apr 2017, at 18:33, Bernhard Rupp  wrote:
>
> Dear Fellows of the Bond,
>
>
>
> when validating a QM refined homology model with Molprobity, I noticed
> various 8 sigma deviations in the carbon-hydrogen bond distances.
>
> Out of curiosity, I then used refmac to calculate riding Hs for the same
> model, and at least in one instance (N-H backbone) there are
>
> significant differences between Molprobity and Refmac H bond distances
> (differences to the QM distances in other
>
> instances I find interesting, but less relevant for us).
>
>
>
> The riding H vs Molprobity presumably should be consistent, because if we
> use them in VDW restraints but
>
> they differ from the validation target, systematic bias will occur. I have
> no feel how significant that effect
>
> might be – maybe someone more erudite can comment.
>
>
>
> Examples
>
>
>
> distance  MP   REF QM
>
> backbone N-H   0.861.011.00
>
> phenyl C-H 0.930.931.09
>
>
>
> Best, BR
>
>
>
> PS: If someone has accurate experimental values for CH distances I’d
> appreciate a link.
>
> No access to CSD.
>
>
>
> --
>
> Bernhard Rupp
>
> Crystallographiae Vindicis Militum Ordo
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429 <(925)%20209-7429>
>
> +43 767 571 0536 <+43%207675%20710536>
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
>

Re: [ccp4bb] CH-bond length discrepancies

[Tristan Croll]

I believe the reason for the discrepancy here is that MolProbity by default 
places the hydrogens according to the centroid of the electron cloud (most 
relevant to x-ray crystallographic data) rather than the nuclear position. In a 
polar bond like N-H the difference can be quite substantial.

Cheers,

Tristan

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

> On 28 Apr 2017, at 18:33, Bernhard Rupp  wrote:
> 
> Dear Fellows of the Bond,
>  
> when validating a QM refined homology model with Molprobity, I noticed 
> various 8 sigma deviations in the carbon-hydrogen bond distances.
> Out of curiosity, I then used refmac to calculate riding Hs for the same 
> model, and at least in one instance (N-H backbone) there are
> significant differences between Molprobity and Refmac H bond distances 
> (differences to the QM distances in other
> instances I find interesting, but less relevant for us).
>  
> The riding H vs Molprobity presumably should be consistent, because if we use 
> them in VDW restraints but
> they differ from the validation target, systematic bias will occur. I have no 
> feel how significant that effect
> might be – maybe someone more erudite can comment.
>  
> Examples
>  
> distance  MP   REF QM
> backbone N-H   0.861.011.00  
> phenyl C-H 0.930.931.09
>  
> Best, BR
>  
> PS: If someone has accurate experimental values for CH distances I’d 
> appreciate a link.
> No access to CSD.
>  
> --
> Bernhard Rupp
> Crystallographiae Vindicis Militum Ordo
> http://www.hofkristallamt.org/
> b...@hofkristallamt.org
> +1 925 209 7429
> +43 767 571 0536
> --
> Many plausible ideas vanish
> at the presence of thought
> --
>  

[ccp4bb] CH-bond length discrepancies

[Bernhard Rupp]

Dear Fellows of the Bond,

 

when validating a QM refined homology model with Molprobity, I noticed
various 8 sigma deviations in the carbon-hydrogen bond distances.

Out of curiosity, I then used refmac to calculate riding Hs for the same
model, and at least in one instance (N-H backbone) there are 

significant differences between Molprobity and Refmac H bond distances
(differences to the QM distances in other 

instances I find interesting, but less relevant for us).

 

The riding H vs Molprobity presumably should be consistent, because if we
use them in VDW restraints but

they differ from the validation target, systematic bias will occur. I have
no feel how significant that effect

might be - maybe someone more erudite can comment.

 

Examples

 

distance  MP   REF QM

backbone N-H   0.861.011.00   

phenyl C-H 0.930.931.09

 

Best, BR

 

PS: If someone has accurate experimental values for CH distances I'd
appreciate a link.

No access to CSD.

 

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

  http://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 767 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

[Christian Roth]

There was a tutorial for MX including UV RIP available from the HZB in 
Berlin (BESSY MX group). Have a look at there website. I'm sure it is 
still available, or maybe they can send you the files on request.


Cheers

Christian



Am 28.04.2017 um 17:12 schrieb Murpholino Peligro:

Hi lads...
Do you know if there is a good tutorial for doing RIP somewhere on the 
internet?

What programs can do RIP?
-SHELX
-AutoRickShaw
-?

Thanks

[ccp4bb] radiation damage-induced phasing (RIP) tutorial

[Murpholino Peligro]

Hi lads...
Do you know if there is a good tutorial for doing RIP somewhere on the
internet?
What programs can do RIP?
-SHELX
-AutoRickShaw
-?

Thanks

[ccp4bb] SECOND ANNOUNCEMENT: Cryo-EM Symposium, 6-7 July 2017, European Photon & Neutron Campus, Grenoble, France

[Montse SOLER LOPEZ]

Dear all,

This is the second announcement to the Cryo-Electron Microscopy 
Symposium that will take place from 6-7th July, 2017 in Grenoble, France.


The aim of this symposium is to promote the exciting opportunities in 
structural biology opened by the advances in cryo-electron microscopy 
and by the integration of structural biology approaches at 
multi-resolution level.


This symposium will celebrate the establishment of a new cryo-EM 
platform on the EPN campus. The platform will offer access to the 
international structural biology community to a new Titan Krios equipped 
with a Quantum LS filter and phase plate. Such microscope will be 
installed as a user facility at the ESRF and will reinforce the ongoing 
EM activity at the IBS and at the EMBL. The new facility will thus be 
open to the user community based on peer-review of scientific merit and 
technical feasibility. Scientists from ESRF, IBS and EMBL will support 
user operation.


The symposium will bring together leading experts, junior researchers 
and representatives of industrial partners to present and discuss the 
latest developments and the future trends in cryo-EM as well as their 
applications in addressing biological challenges.


It will also provide a forum for discussion among both established and 
junior scientists from different disciplines. We encourage participants 
to present their scientific results in a poster session, with the 
possibility of being selected for a short talk.


Poster Abstract submission deadline: 30 April 2017; Notification of 
acceptance: 15 May 2017

*Deadline for registration: 22 May 2017*

You can find more information at: http://www.esrf.fr/cryo-em.fr

We look forward to seeing you in Grenoble!

On behalf of the Organising committee: Stephen Cusack (EMBL), Trevor 
Forsyth (ILL/Keele), Wojciech Galej (EMBL), Gordon Leonard (ESRF), Marco 
Marcia (EMBL), Christoph Mueller-Dieckmann (ESRF), Hugues Nury (IBS), 
Guy Schoehn (IBS), Montserrat Soler-Lopez (ESRF), Jean Susini (ESRF) and 
Winfried Weissenhorn (IBS).


--

MontseSOLER LOPEZ

European Synchrotron Radiation Facility

Structural Biology Group

Carl-Ivar Branden Building - office 114

71 Avenue des Martyrs – CS 40220

F-38043 Grenoble Cedex 09

Phone: +33 (0)47688 1770

Fax:+33 (0)47620 9400

[ccp4bb] GRAL MASTER 2 RESEARCH SCHOLARSHIPS in Grenoble/France - Launch of the call for application 2016

[Wim Burmeister]

  
  
in case if you are in contact with
Master students:

for this list the most relevant speciality is the Master 2 of 
"Integrative Structural Biology (ISB)".

Wim Burmeister
 
  Dear

colleagues,
   
   
   
  The

call for application 2017 for the GRAL Master 2 scholarships
is open and we decided to push the fence to  May 31th 2017.
   
   
   
  Here

is the link to the dedicated page on the GRAL website : http://www.labex-gral.fr/master-2-research-scolarship-program/
   
   
   
  Thank

you in advance for your kind collaboration.
   
   
   
  My

best regards .
   
  -
   
   
  GRAL
MASTER 2 RESEARCH SCHOLARSHIPS IN GRENOBLE - ACADEMIC YEAR
2017 – 2018
   
   
   
   
  The Labex GRAL program in collaboration with the University of Grenoble seeks applications for Master 2 scholarships. The candidates should be interested in any of the research topics proposed below by the groups associated with the GRAL program at IBS (http://www.ibs.fr) and BIG (http://irtsv.cea.fr/dsv/irtsv) and should enter one of the 10 Grenoble Master 2 program also indicated below.
   
  The successful candidates will receive from the GRAL Labex a scholarship of 8 000 € in order to cover the academic year from September to June, which includes 4 month of courses and 6 month of laboratory training. A maximum of 10 scholarships are available this year.
   
  Please note that the candidates must deposit a file to the University from May 2017 
   
   
  The file you send to the GRAL LABEX is only dedicated to the scholarship.
   
  You should at least send us a letter of acceptance from the head of the M2 Program 
   
  Candidates to the Master 2 research scholarships
  must present a Master 1 diploma or any equivalent. If you are
  not registered and accepted in one of the dedicated M2
  program, you can’t obtain the GRAL scholarship.
   
   
  Contact :  manel.boumego...@cea.fr
   
  
List of the UGA Master 2 available in this program
  
   
  
1.   Masters in biology (Taught in English): 
  
-  Integrative Structural Biology (ISB)
  
-  Physiology, Epigenetics Development, Cell
Differentiation (PHEDD)
  
-  Neurosciences,


  Neurobiology (NN)
  
-  Immunology, Microbiology, Infectious Diseases
(IMID)
   
    
  
2.   Masters in Biodiversity, Ecology, Evolution
(Taught in French):
  
-  Dynamique


  et Modélisation de la Biodiversité
  
-  Gestion


  de l’Environnement
    
    
    
  
3.   Masters in Physics (Taught in English and
French): 
  
-  Matière


  complexe, matière vivante (MCMV)
   
    
  
4.   Masters in Nanosciences, nanotechnologies
(Taught in English):
  
-  Nano-chemistry
  
-  Nano-biosciences
  
-  Nano-physics

   
   
  ___
  Manel
BOUMEGOURA
  Chargée de
  valorisation et de transfert de technologie-LABEX-GRAL
  CEA / Institut de
  Biosciences & Biotechnologies de Grenoble
  17 rue des
  martyrs, F-38054 Grenoble Cedex 9
  Tel:  +33 (0)4 38
  78 05 78 / Mobile: +33 (0)6 47 91 62 75
  Manel.boumegoura@cea.fr 
  LABEX-GRAL-VALO
   
  
   
   
   
   

  

[ccp4bb] Postdoctoral Fellow Position at Rutgers University

[Vijay Parashar]

Postdoctoral Fellow Position


 
Parashar laboratory at Rutgers School of Dental Medicine iscurrently seeking a 
highly motivated, creative individual with strong interestin the 
structure-function studies of proteins regulating bacterial signaling.

 

Qualifications:

   
   - Ph.D. in Biochemistry, Molecular Biology,Structural Biology, or a related 
field   

   - Experience with cloning, proteinexpression, and protein purification 
methods   

   - Asound understanding of methods and approaches relating to 
macromolecularcrystallography preferred   

   - Ability to plan and carry out researchprojects independently   

   - Ability to work on own initiative andtake personal responsibility for 
delivery of work   

   - Excellent problem solving, interpersonal,communication and presentation 
skills   

   - A working knowledge of bacterial geneticsand computational modeling of 
protein-ligand interactions preferred   















 

Responsibilities:

   
   - Performing experiments for cloning,protein expression, and purification of 
proteins for biochemical and structuralstudies; robotic screens for 
crystallization; optimizing crystallizationconditions; and collecting and 
analyzing diffraction data.   

   - Performing model building and structurerefinement.   

   - Maintaining laboratory equipment to meetunique needs of the research 
activity   

   - Assisting with preparation of grantproposals, presentations and 
publications   

   - Actively seeking new collaborativeprojects within the department and 
externally   

   -     













The Rutgers University Newark campus is well equipped withstate-of-the-art 
equipment for molecular biology, protein purification, andcrystallography, 
including crystallization robot, crystal imaging system, andX-ray generator. 
Please visit Parashar Laboratory website for more information.Applicants should 
send a cover letter, a CV, a list of publications, a summary of research 
experience and interests as well as the names and contactinformation of three 
references. The information should be sent via e-mail to parasha...@gmail.com 
with the subjectline “Postdoctoral Position Applicant”. 


  
|  
|   |  
Home | PARASHAR LABORATORY
   |  |

  |

 

 
Rutgers University is an AA/EEO employer. All applicantswill receive 
consideration for employment without regard to race, color,religion, sex, 
sexual orientation, gender identity, national origin,citizenship, disability or 
protected veteran status.

Re: [ccp4bb] Sliconizing of cover-slips

[Jaydeep Paul]

Dear Praveen,

I always siliconize my cover slips before using them for crystallization.
Recipe is very simple. But make sure that you always use mask, gloves and
perform your experiment under a fume hood.

1. 95% toluene + 5% dichloromethylsilane  will give you a very good
siliconization solution.

2. Purchase thick cover slips ( because thin one is very fragile and can
break during the experiment)  and wash them with water to remove the dust.
Then wash them with acetone and keep them hot air oven for drying.

3. Then take a large glass petri dish and pore the siliconization solution.
Then put all cover slips into it and keep them for 30sec-1min.( do this
step inside the hood ). Make sure that all faces of cover slip can come to
the contact of siliconization solution.

4. Then take each cover slip one by one with tweezer and wash them with
toluene ( in other petri dish) then put them on water  ( They will float if
they are siliconized and it is a proof of hydrophobic coat on them).

5. Collect them and keep them for drying in hot air oven for few hours.

If you find any problem, I will happy to discus with you.

Best of luck!

Regards Jaydeep Paul.

Project fellow at NISER,Bhubaneswar,India
Dr. Rudresh Acharya's lab
ᐧ

On Thu, Apr 27, 2017 at 2:56 PM, Praveen Kumar Tripathi <
tripathipraveen.i...@gmail.com> wrote:

> Dear all,
>
> sorry for off topic question.
>
> May i know if anybody uses homemade silinization of coverslips for protein
> crystallization purposes?
>
> I have purchased Sigmacote SL2-100 ml for silanizing coverslips for
> hanging drop protein crystallization setup.
>
> Please share your methods to siliconize coverslip using Sigmacote SL2-100
> ml if anybody uses.
>
> Thanks in advance
>
> regards
> Praveen
>
>
>
> --
> *Praveen Kumar Tripathi*
> PhD Research Scholar
> Kusuma School of Biological Sciences
> Indian Institute of Technology Delhi-110016
> +91-9873625228
>

[ccp4bb] Senior Research Scientist Protein Crystallography

[Ingo Korndoerfer]

To add additional expertise and capacity to our drug discovery service team in 
Munich-Martinsried, we are immediately looking for a Senior Research Scientist, 
PhD in Protein Crystallography.

Protein Crystallographer

As a Senior Research Scientist, you will support our team with crystallization, 
data collection, processing and analysis of x-ray diffraction data and model 
building. You have a firm grasp of crystallographic theory to carry out or 
assist in the structure determination of more complex or larger quantities of 
structures from fragment screening campaigns, where established software fails 
or an individual processing through software GUIs is no longer feasible

You will be expected to assist or take over the further development and 
integration of our in-house LIMS and automated data processing pipeline. A firm 
knowledge of Linux operating systems, scripting and basic programming is 
indispensable, as you will likely have to interact with MySQL or Oracle servers 
and existing data mining routines.

As the ideal candidate, you will be highly organized and capable of handling a 
large number of projects including sharing and proper documentation of all your 
activities. You appreciate contributing to your colleague’s work, with ideas or 
hands-on, as well as integrating the insights of your colleagues into your own 
line of work. You have a problem-solving attitude and an innovative mind to 
help us in further developing this position as well as our company. And you 
enjoy communicating the results of your work to our clients all over the world, 
representing CRELUX as part of the WuXi AppTec family and as a global leader 
for structure based drug discovery solutions. 

CRELUX offers structure based drug discovery service and supports its clients 
from Pharma, Biotech and Research Institutes with expertise and an external 
work force. We are operating as a part of WuXi AppTec - one of the leading 
Contract Research Organizations worldwide. 

WuXi AppTec operates from over 20 research sites and employs over 14.000 people 
in China, the US and Europe. Within WuXi AppTec’s Research Service Division 
(RSD) we act as the global center of excellence in hit finding, validation and 
confirmation projects. As such CRELUX’s biophysical assay, screening and 
crystallography departments are forming a pivot service platform for all 
integrated drug discovery programs WuXi AppTec executes for clients.

Are you interested in becoming a CRELUX employee? 

We offer competitive salaries and a work environment that is science-based, 
collaborative and inspiring. The success of our company is based on a “clients 
first” attitude and cooperative efforts - which make excellent organizational 
and communication skills essential. We benefit from the diversity of our 
workforce and are proud to be an equal opportunity employer. 

For additional information visit our website, www.crelux.com. Please send your 
complete application for this position as a single .pdf file to: 

CRELUX GmbH
Am Klopferspitz 19a
82152 Martinsried 

Dr. Michael Schaeffer
michael_schaef...@wuxiapptec.com
+49 89 700760-170 

[ccp4bb] AW: [ccp4bb] Sliconizing of cover-slips

[Hughes, Jon]

anyone tried rainex (if it's still on sale)? for us it works 1000x better than 
anything else: rugged, extremely water repellent, and cheap (one bottle lasts a 
lifetime). in the '90s at least you could get it in auto stores in the USA.
cheers
jon

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Tristan 
Croll
Gesendet: Freitag, 28. April 2017 13:36
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Sliconizing of cover-slips

Ahh, this brings back memories of a former life, preparing hydrophobic 
coverslips for my surface chemistry experiments. I used chlorotrimethylsilane, 
and what I remember best is that the secret to a good coating is making sure 
your coverslips are utterly clean and dry. I used to clean them by boiling in 
base piranha (concentrated ammonia and hydrogen peroxide - need I say this 
stuff should be treated with extreme respect?) before rinsing thoroughly in 
milli-Q water and baking under vacuum. Then essentially as David said: dump 
them in the silane solution (again, it helps to make sure to keep your solvent 
dry), then fish them out one-by-one, rinse and dump them into a beaker of fresh 
solvent (acetone, I think I used). Then once they're all done, take them out of 
that, dry in a nitrogen stream and store. Painful & fiddly, but you can easily 
do a hundred or so in an afternoon.


Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY




On 27 Apr 2017, at 10:26, Praveen Kumar Tripathi 
mailto:tripathipraveen.i...@gmail.com>> wrote:
Dear all,

sorry for off topic question.

May i know if anybody uses homemade silinization of coverslips for protein 
crystallization purposes?

I have purchased Sigmacote SL2-100 ml for silanizing coverslips for hanging 
drop protein crystallization setup.

Please share your methods to siliconize coverslip using Sigmacote SL2-100 ml if 
anybody uses.

Thanks in advance

regards
Praveen



--
Praveen Kumar Tripathi
PhD Research Scholar
Kusuma School of Biological Sciences
Indian Institute of Technology Delhi-110016
+91-9873625228

Re: [ccp4bb] Sliconizing of cover-slips

[Bert Van-Den-Berg]

To me this begs the question: why do this at all? A cost issue?

The Hampton coverslips work pretty well even with detergents that drastically 
lower surface tension like C8E4. Those of a UK competitor that i shall not name 
are not as good, in our humble experience.


Bert



From: CCP4 bulletin board  on behalf of Tristan Croll 

Sent: 28 April 2017 12:36
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Sliconizing of cover-slips

Ahh, this brings back memories of a former life, preparing hydrophobic 
coverslips for my surface chemistry experiments. I used chlorotrimethylsilane, 
and what I remember best is that the secret to a good coating is making sure 
your coverslips are utterly clean and dry. I used to clean them by boiling in 
base piranha (concentrated ammonia and hydrogen peroxide - need I say this 
stuff should be treated with extreme respect?) before rinsing thoroughly in 
milli-Q water and baking under vacuum. Then essentially as David said: dump 
them in the silane solution (again, it helps to make sure to keep your solvent 
dry), then fish them out one-by-one, rinse and dump them into a beaker of fresh 
solvent (acetone, I think I used). Then once they're all done, take them out of 
that, dry in a nitrogen stream and store. Painful & fiddly, but you can easily 
do a hundred or so in an afternoon.



Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY




On 27 Apr 2017, at 10:26, Praveen Kumar Tripathi 
mailto:tripathipraveen.i...@gmail.com>> wrote:

Dear all,

sorry for off topic question.

May i know if anybody uses homemade silinization of coverslips for protein 
crystallization purposes?

I have purchased Sigmacote SL2-100 ml for silanizing coverslips for hanging 
drop protein crystallization setup.

Please share your methods to siliconize coverslip using Sigmacote SL2-100 ml if 
anybody uses.

Thanks in advance

regards
Praveen



--
Praveen Kumar Tripathi
PhD Research Scholar
Kusuma School of Biological Sciences
Indian Institute of Technology Delhi-110016
+91-9873625228

Re: [ccp4bb] Sliconizing of cover-slips

[Tristan Croll]

Ahh, this brings back memories of a former life, preparing hydrophobic 
coverslips for my surface chemistry experiments. I used chlorotrimethylsilane, 
and what I remember best is that the secret to a good coating is making sure 
your coverslips are utterly clean and dry. I used to clean them by boiling in 
base piranha (concentrated ammonia and hydrogen peroxide - need I say this 
stuff should be treated with extreme respect?) before rinsing thoroughly in 
milli-Q water and baking under vacuum. Then essentially as David said: dump 
them in the silane solution (again, it helps to make sure to keep your solvent 
dry), then fish them out one-by-one, rinse and dump them into a beaker of fresh 
solvent (acetone, I think I used). Then once they're all done, take them out of 
that, dry in a nitrogen stream and store. Painful & fiddly, but you can easily 
do a hundred or so in an afternoon.

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

> On 27 Apr 2017, at 10:26, Praveen Kumar Tripathi 
>  wrote:
> 
> Dear all,
> 
> sorry for off topic question.
> 
> May i know if anybody uses homemade silinization of coverslips for protein 
> crystallization purposes?
> 
> I have purchased Sigmacote SL2-100 ml for silanizing coverslips for hanging 
> drop protein crystallization setup.
> 
> Please share your methods to siliconize coverslip using Sigmacote SL2-100 ml 
> if anybody uses.
> 
> Thanks in advance
> 
> regards
> Praveen
> 
> 
> 
> -- 
> Praveen Kumar Tripathi
> PhD Research Scholar
> Kusuma School of Biological Sciences
> Indian Institute of Technology Delhi-110016
> +91-9873625228

Re: [ccp4bb] Sliconizing of cover-slips

[Hargreaves, David]

Hi Praveen,

20 years ago I seemed to spend more time siliconising cover slips than setting 
up the Magic 50. We had special jigs to hold a couple of dozen slips for 
washing, drying and finally immersion in silane solution. This method was very, 
very tedious. An alternative method was to pull a vacuum over the slips 
scattered on a glass Petri dish in a desiccator containing around 50mls of 
silane solution in a beaker. The dish sat on top of the beaker and the vacuum 
from a water tap pump would make the silane solvent boil. This was marginally 
quicker and used less silane solution. Either way, each slip was then 
individually polished using lens tissue and the dust blown away using 
compressed air before storage.
My own “quick and dirty” method was to fill a tall plastic measuring cylinder 
with solution and drop the slips in serially and let them tumble through the 
solution as they sank. The cylinder should be tall and have a diameter 
comparable to that of the cover slip. I’d do around 300 at a time like this. 
All methods require scattering the slips onto aluminium foil and giving them a 
quick bake at around 100DegC to get rid of excess silane solution and HCl 
immediately after treatment. I gave up polishing them and just used to wash the 
slips in HPLC grade ethanol before drying in the oven and storing (hiding) 
them.  Whichever way you choose, you do need to do the siliconising in a fume 
cupboard.

Best wishes,

David


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Praveen 
Kumar Tripathi
Sent: 27 April 2017 10:26
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Sliconizing of cover-slips

Dear all,

sorry for off topic question.

May i know if anybody uses homemade silinization of coverslips for protein 
crystallization purposes?

I have purchased Sigmacote SL2-100 ml for silanizing coverslips for hanging 
drop protein crystallization setup.

Please share your methods to siliconize coverslip using Sigmacote SL2-100 ml if 
anybody uses.

Thanks in advance

regards
Praveen



--
Praveen Kumar Tripathi
PhD Research Scholar
Kusuma School of Biological Sciences
Indian Institute of Technology Delhi-110016
+91-9873625228


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Re: [ccp4bb] shadow at the edge

[Colin Nave]

Abhishek

The fun thing to do in these circumstances is to move the detector a known 
distance and see how much a point on the shadow expands (or contracts) from the 
centre of the detector. One can then ray trace (a simple diagram) to find the 
position of the object creating the shadow. In your case, the diffraction from 
the crystal is being shadowed so you know an origin. For diffuse background 
being shadowed you might need 3 positions for the detector as you have to find 
both the origin of the scatter (it could be near the slit system) and the 
position of the shadowing object.

Of course this does take a bit of time which  isn’t always available.

Good luck

Colin

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dr A.A. 
Jalan
Sent: 27 April 2017 21:49
To: ccp4bb
Subject: [ccp4bb] shadow at the edge


Dear all,

The attached diffraction image has a shadow at the right edge. It moves from 
the top to the bottom right corner. I was wondering if anyone knows what it 
could be and whether it would affect data processing?

Thank you

Abhishek






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[ccp4bb] Post-doctoral research fellow positions available at Monash university

[Jennifer Huynh]

Dear All

Post-doctoral research fellows: Lipid -mediated immunity 
 
MONASH UNIVERSITY
Infection and Immunity Program, Biomedicine Discovery Institute
Faculty of Medicine, Nursing and Health Sciences
 
Prof. Jamie Rossjohn FAA FLSW, ARC Australian Laureate Fellow & Head, Infection 
and Immunity Program, Monash Biomedicine Discovery Institute, seeks 
postdoctoral researchers to join his research group to work in the area of 
structural biology centered on T-cell mediated immunity to lipid antigens, at 
Monash University, Clayton campus. 
 
The Rossjohn laboratory has provided profound insight into the molecular bases 
underpinning lipid-mediated immunity (e.g. Nature 2007, Immunity 2009, 2011, 
Nature Immunol. 2012, 2015 & 2016), and seeks to build upon these initial 
findings in the context of protective, tumour and aberrant immunity. The 
laboratory is funded by grants from the NHMRC and ARC. 
 
For more details on the research themes, fellowships awarded and publication 
outputs see, http://research.med.monash.edu.au/rossjohn/
 
The applicants should hold a PhD, have a proven track record in the field of 
protein chemistry, and be sufficiently self-motivated to pioneer new areas of 
Immunity. 

Candidates with a promising track record in the relevant areas and a proven 
publication record in international journals are encouraged to apply.
 
Appointment will be made at a level appropriate to the successful applicant’s 
qualifications, experience and in accordance with classification standards for 
each level. 
Salary range: Level A $81,486 - $87,471 or
Level B $92,074 - $109,339, 
Duration: ​Position  - up to 3 years.​​
Location:​Clayton Campus
 
Closing Date: 1st June 2017
 
Please direct all enquires to Jennifer Huynh (jennifer.hu...@monash.edu) 
 
Sent from my iPhone ➰

[ccp4bb]

[Vipul Panchal]

Provided your protein is >90 pure as per 15% SDS-PAGE analysis, you should
try seeding.

On 28-Apr-2017 12:43 PM, "李霞"  wrote:

Dear all:

My protein is a demethylase,has failed to obtain protein crystals,then
adopt the method of in situ enzyme and get protein crystals,but the crystal
is still very very small,how to optimize can get diffraction
crystal,please?


Best

X. L

[ccp4bb]

[李霞]

Dear all:

My protein is a demethylase,has failed to obtain protein crystals,then adopt 
the method of in situ enzyme and get protein crystals,but the crystal is still 
very very small,how to optimize can get diffraction crystal,please? 




Best

X. L