[ccp4bb] Upcoming SSRL Macromolecular Crystallography Proposal Deadlines

[Dunn, Lisa B.]

Dear All,



The next two deadlines for submitting Standard or Block Allocation Group (BAG) 
proposals for macromolecular crystallography (MC) beam time at the Stanford 
Synchrotron Radiation Lightsource (SSRL) are April 1, 2023 (for access 
beginning in May 2023) and July 1, 2023 (for access beginning fall 2023).  
Please visit our website<https://smb.slac.stanford.edu/> and user 
guide<https://smb.slac.stanford.edu/users_guide/index.shtml> to learn more 
about our beamline parameters, new developments and guidelines.



New or inexperienced users are welcome to contact one of our crystallography 
group leaders, Aina Cohen<mailto:aco...@slac.stanford.edu> and Mike 
Soltis<mailto:sol...@slac.stanford.edu> to discuss their proposals ahead of 
submission.  For administrative details related to access requirements, please 
contact Lisa Dunn<mailto:l...@slac.stanford.edu>.



If you are not currently a user of our facility the first step is to register 
in our user portal<https://userportal.slac.stanford.edu/> to submit a proposal. 
 Once your registration is accepted the next steps include:

  *   Log into the user portal and select the SSRL tab
  *   Click on Proposals Pull-Down Menu and Select "Submit SSRL PX Proposal"
  *   Select the radio button for "Macromolecular Crystallography Standard 
Proposal" or "MC Block Allocation Group (BAG)"


Note: Submitting a Rapid Access proposal is another option and can be submitted 
at any time. This proposal type is intended for short-term usage until a 
standard proposal can be submitted and reviewed.



Please reference proposal submittal 
guidelines<https://www-ssrl.slac.stanford.edu/content/user-resources/proposal-submittal-and-scheduling-procedures-macromolecular-crystallography>
 for more information.



Best regards,

Lisa Dunn

SSRL User Services

SLAC National Accelerator Laboratory




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Re: [ccp4bb] Running Refmac from WinCoot

[Mydy, Lisa]

Hi,
I haven’t encountered these issues, however I am routinely using CCP4i2 on 
Windows 10. A fresh install of  CCP4 Program Suite v8.0.009 + SHELX + COOT 
v0.9.8.1 (exe) has worked well. After Refmac5, I use the button “Coot” to 
launch a new task, then run WinCoot from there. When I use CCP4i, WinCoot has 
worked from the outpage of Refmac5.

Hope this helps, please let me know if you have any questions: lmydy at 
umich.edu
--Lisa

From: CCP4 bulletin board  On Behalf Of Kevin Cowtan
Sent: Wednesday, March 8, 2023 4:22 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Running Refmac from WinCoot

External Email - Use Caution
Hi all

I am using WinCoot with a number of final year project students, and they are 
having a miserable time.

They are installing CCP4 themselves (so that they get both WinCoot and refmac), 
I presume using all the defaults. We also have it on classroom machines across 
campus.

If they run WinCoot directly, then refmac doesn't work.

So what we do is tell them to launch a CCP4console, and type 'coot' in it. Then 
refmac works most of the time, but not all. And for some, refmac will work for 
a month or so, and then stop.

After that, our fallback is to teach them to launch CCP4i2, create a dummy 
project, and launch Coot from there. That is clumsy, but very seldom fails. But 
very occasionally even that fails.

Unfortunately I don't have very much in the way of debug information except for 
screenshots I get sent. Does anyone have WinCoot and refmac running reliably 
together please, or has anyone seen similar problems?



--
Professor Kevin (Kathryn) Cowtan
Email:  kevin.cow...@york.ac.uk<mailto:kevin.cow...@york.ac.uk>
Pronouns:   Please use they/them when referring to me in professional contexts
ORCiD:  -0002-0189-1437<https://orcid.org/-0002-0189-1437>
Disclaimer: 
http://w<http://www.york.ac.uk/docs/disclaimer/email.htm>ww.york.ac.uk/docs/disclaimer/email.htm<http://www.york.ac.uk/docs/disclaimer/email.htm>



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[ccp4bb] BAG Proposals for Macromolecular Crystallography Beam Time at SSRL

[Dunn, Lisa B.]

We are pleased to announce that we are introducing a Block Allocation Group 
(BAG) type proposal for our macromolecular crystallography beamlines at SSRL.



Block Allocation Groups (BAGs) are a mode of beam time access intended for 
groups of researchers that want to combine their short beam time requests into 
a single proposal in order to permit greater flexibility in beam time 
allocation and scheduling. BAG proposals may be submitted by groups working at 
a shared university or with a shared affiliation. Combining the beam time of 
individual groups permits greater flexibility in the choice of projects and 
samples during a given allocation period and offers the individuals in the BAGs 
the benefit of access to more regular allocation of beam time.  Currently, BAG 
proposals are accepted on SSRL BL14-1, BL9-2, BL12-2 and BL12-1. Only 
measurements based on existing, standard setups available at these beamlines 
will be considered for the BAG beam time.



Our next deadline for submitting BAG proposals is January 15, 2023.  Standard 
proposals for 2-year beam time eligibility are due on December 1, 2022, for 
beam time starting in March 2023, and April 1, 2023, for beam time starting in 
June 2023.  Rapid Access proposals can be submitted at any time.   All of these 
proposal types are submitted through our User 
Portal<https://userportal.slac.stanford.edu/>.



For more information see the following:

* Block Allocation Group 
Proposal<https://www-ssrl.slac.stanford.edu/content/user-resources/block-allocation-group-proposal>

* Proposal Submittal and Scheduling 
Procedures<https://www-ssrl.slac.stanford.edu/content/user-resources/proposal-submittal-and-scheduling-procedures-macromolecular-crystallography>

* User Guide<https://smb.slac.stanford.edu/users_guide/index.shtml>

* Beamline parameters<https://smb.slac.stanford.edu/>



We look forward to providing you with beam time soon!

Best Regards,

Lisa Dunn
SSRL Structural Molecular Biology
SLAC Linear Accelerator Laboratory



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[ccp4bb] Positions Open for Academic Staff Scientists in Stanford’s SyneRx Center’s Structural Biology Core

[Dunn, Lisa B.]

Academic Staff Scientist in Stanford’s SyneRx Center’s Structural Biology Core

Job Description:
The SyneRx Center at Stanford University is one of nine National Antiviral Drug 
Discovery Centers for Pathogens of Pandemic Concern (AViDD) recently funded by 
the National Institute for Allergy and Infectious Diseases. We are seeking to 
appoint two Ph.D. level scientists that will bring complementary research 
experience in cryoEM/ET and synchrotron-enabled x-ray techniques, primarily 
macromolecular crystallography. Stanford’s SyneRx Center includes a Structural 
Biology Core (SBC) to provide state-of-the-art tools and capabilities for 
structural determinations from RNA and proteins to virus and virus infected 
cells. This SBC is comprised of three Subcores including protein production (at 
Stanford University campus facilities and labs), x-ray crystallography and 
scattering (at the Stanford Synchrotron Radiation Lightsource), and cryogenic 
electron microscopy and tomography (cryoEM/ET at facilities located at SLAC 
National Accelerator Laboratory).
As a staff scientist, you would work collaboratively to drive all aspects of 
the three Subcores in the SBC, specifically through interacting with scientists 
in the research teams and providing coordination in areas that include sample 
preparation and characterization, data acquisition, modeling and structure 
determination and validation, pipe-line organization and feedback.  You would 
also assist and train the SyneRx Center’s Project scientists in performing the 
structure characterizations to facilitate and accelerate the design of novel 
and effective antivirals against SARS-CoV-2 and other RNA viruses of pandemic 
potential.  Driving new developments in innovative approaches to obtaining and 
applying high throughput structure-based cryoEM/ET and x-ray methods would also 
be a goal of your research. You would be interacting with other staff 
scientists in the vibrant research organization that comprises the structural 
biology programs for x-rays (SSRL) and cryoEM at SLAC and Stanford, and also 
have a strong role within the SyneRx Center to provide knowledge and services 
as well as bridge and coordinate between the many entities.  You would be 
cross-trained in the structural methods.  The work will require being 
accessible occasionally outside of regular working hours.

Qualifications:

A Ph.D. degree in biophysics, structural biology, biochemistry or a related 
field and post-doctoral experience in the use of x-ray macromolecular 
crystallography, and/or cryoEM/ET.  Other required qualifications include:

· Experience in biochemical purification and sample preparation.

· Experience in data collection, processing and analysis of 
macromolecular crystallography and/or cryoEM data up to structural solutions 
and validation of results.

· Excellent communications and organizational skills.

· The ability to work both independently and collaboratively in a team.
Desired Qualifications/Skills:

· Experience with biological small angle x-ray scattering/diffraction 
is desirable as applicable.

· A track record of scientific productivity through publications in 
relevant fields.

· Experience with computer tools in data management and image analysis.

· Strong communication skills demonstrated through teaching roles 
and/or invited lectures at conferences.
Stanford is an equal employment opportunity and affirmative action employer.  
All qualified applicants will receive consideration for employment without 
regard to race, color, religion, sex, sexual orientation, gender identity, 
national origin, disability, protected veteran status, or any other 
characteristic protected by law. Stanford welcomes applications from all who 
would bring additional dimensions to the University's research mission.

For additional information on our research activities, please visit
https://www.nih.gov/news-events/news-releases/nih-announces-antiviral-drug-development-awards
https://med.stanford.edu/news/all-news/2022/06/jeffrey-glenn-grant.html 
https://cryoem.slac.stanford.edu/
http://smb.slac.stanford.edu/
Please send your application, CV and the names of three references with contact 
information to Ms. Evelyn Castaneda, 
evel...@slac.stanford.edu.




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[ccp4bb] DMMULTI replacement in CCP4i2?

[Mydy, Lisa]

Hi all,

 I read that Parrot is a replacement for DM based on CCP4i2 documentation 
and am curious if Parrot has the same capabilities as DMMULTI for phase 
extension?


Is DMMULTI by command line only? I see DM in CCP4i GUI.


I'm trying to figure out best path forward with phase extension including 
2-fold averaging, solvent flattening, and extending phases from 4 A to 2.9 A 
for SeMet SAD.



Thank you kindly,

--Lisa Mydy



lm...@med.umich.edu<mailto:lm...@umich.edu>

Postdoctoral Fellow

University of Michigan
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[ccp4bb] Stanford Electron Microscopy-X (EM-X) Seminar - November 1, 2021

[Dunn, Lisa B.]

We are pleased to invite you to our new academic year Stanford Electron 
Microscopy-X (EM-X) Symposium series on November 1, 2021, 8:00-9:30 a.m. 
(Pacific Time).



Speakers:

Prof. Roger D. Kornberg

Mrs. George A. Winzer Professor of Medicine

Stanford University

Talk title: Chromosome Structure



Prof. Hamish L. Fraser

Ohio Regents Scholar and Professor

The Ohio State University

Talk title: Applications of Aberration-Corrected TEM for Alloy Design



We expect a large attendance, and the occupancy is limited. Please register 
soon at:

https://stanford.zoom.us/webinar/register/WN_0djYtBHSSOuA5RXQV86ssA
and visit our official website at https://emx.stanford.edu/
Best,
Wah Chiu
Wallenberg-Bienenstock Professor
Department of Bioengineering
Division of CryoEM and Bioimaging, SLAC National Accelerator Laboratory
Stanford University





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[ccp4bb] Protein Crystallisation Position at Vernalis Research, Cambridge, UK (full-time, permanent)

[Lisa Baker]

Protein Crystallisation Position at Vernalis Research, Cambridge, UK  
(full-time, permanent)



Vernalis Research (based at Granta Park in Cambridge, UK) has a new full-time 
position for a Scientist to join our Biophysics group. Working in collaboration 
with an integrated team of protein scientists, NMR spectroscopists and 
Crystallographers, your primary role will be the discovery and optimisation of 
protein crystals for X-ray data collection and analysis, supporting multiple 
projects ranging from target validation to lead optimisation.



This post would suit someone with a practical understanding of protein 
biochemistry and laboratory-based research experience, preferably gained within 
a drug discovery environment. Applications will be considered from graduates 
with a BSc/MSc in Biochemistry, Biophysics, Chemistry, Molecular Biology or 
other related discipline, as well as candidates with an equivalent level of 
work experience.



Further details about the position can be found on our website:



Scientist, Crystallisation | Vernalis 
Research<https://www.vernalis.com/jobs/scientist-crystallisation/>



And on LinkedIn:



https://www.linkedin.com/​jobs/view/2586994587/<https://www.linkedin.com/jobs/view/2586994587/>



To apply, send your CV and a covering email to 
h...@vernalis.com<mailto:h...@vernalis.com>



We are looking forward to hearing from you.



With best wishes,



Lisa Baker BSc (Hons), PhD.

Vernalis (R) Limited

Granta Park

Great Abington

Cambridge

CB21 6GB

United Kingdom





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for the named addressee(s) only and access to it by anyone else is 
unauthorised. If you are not an addressee, any disclosure or copying of the 
contents of this email or any action taken (or not taken) in reliance on it is 
unauthorised and may be unlawful. If you have received this email in error, 
please notify the sender or postmas...@vernalis.com. Email is not a secure 
method of communication and the Company cannot accept responsibility for the 
accuracy or completeness of this message or any attachment(s). Please check 
this email for virus infection for which the Company accepts no responsibility. 
If verification of this email is sought then please request a hard copy. Unless 
otherwise stated, any views or opinions presented are solely those of the 
author and do not represent those of the Company.

Vernalis (R) Limited (no. 1985479)
Granta Park, Great Abington
Cambridge, CB21 6GB, United Kingdom
Tel: +44 (0)1223 895 555




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[ccp4bb] Stanford-SLAC CryoEM Center (S2C2) Workshop on Specimen Preparation and Data Collection March 3-4, 2021

[Dunn, Lisa B.]

S2C2  -  CryoEM Specimen Preparation and Data Collection Workshop March 3-4, 
2021

Stanford-SLAC CryoEM Center (S2C2) will offer a specimen preparation and data 
collection workshop via Zoom webinar between March 3-4, 2021 from 8:00 AM to 
approximately 1:00 PM (PST) daily.  This workshop will give participants an 
introduction to cryo-specimen preparation approaches.  Our guest lecturers 
include:


* Prof. Peter J. Peters, Maastricht Multimodal Molecular Imaging 
Institute (M4i), Maastricht University and CryoSol-World, Netherlands

* Dr. Benjamin Bammes, Direct Electron, LP

* Dr. Jeff Lengyel, Thermo Fisher

* Dr. Christopher Russo, LMB, MRC, Cambridge, UK

* Dr. Sahil Gulati, Ametek

* Dr. Yee L. Ting, SLAC National Accelerator Lab

* Dr. Patrick Mitchell, SLAC National Accelerator Lab

There is no cost for this workshop.  Please visit our workshop 
website
 for the application form and information on participation requirements.   
Applications must be submitted by February 17, 2021.

Organizer:  Wah Chiu, Stanford University

The 
S2C2
 is supported by the National Institutes of Health Common Fund Transformative 
High Resolution Cryo-Electron Microscopy 
program.





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[ccp4bb] Call for Stanford-SLAC Cryo-EM Center Proposal Applications

[Dunn, Lisa B.]

Dear Colleagues,



I am pleased to announce that our Stanford-SLAC Cryo-EM Center (S2C2) is now 
equipped with three fully operational Titan Krios electron microscopes, two 
with K3 detectors and one with a Falcon 4 detector. Our microscopes are capable 
of resolving atomic resolution structures of biological macromolecules (DOI: 
10.1038/s41422-020-00432-2).  We welcome project applications from the 
scientific community for collecting high resolution electron microscopic images 
with the assistance of our cryoEM scientific staff 
(https://cryoem.slac.stanford.edu/s2c2/project-requests).



We also host regular training sessions on the various steps of cryoEM for 
beginners. During this pandemic time, our user facility and training activities 
are done entirely remotely.  We look forward to seeing you and your colleagues 
in our Center.


Wishing you a happy and safe holiday!

Wah Chiu

Wallenberg-Bienenstock Professor

Stanford University

w...@stanford.edu




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[ccp4bb] S2C2 CryoEM CCP-EM Modeling Workshop, November 10-13, 2020

[Dunn, Lisa B.]

S2C2 Workshop - CryoEM CCP-EM Modeling
Stanford-SLAC Cryo-EM Center (S2C2) will offer a modeling workshop held via 
Zoom Webinar between November 10-13, 2020 from 8:00 AM - 2:00 PM (PDT) daily.  
This workshop will give participants an introduction to atomic model building 
into cryo-EM maps using the tools available in the CCP-EM software suite.  
There is no cost for this workshop.  Please visit the workshop 
website
 to apply by 5:00 PM (PDT) on November 2, 2020.
Our guest trainers for this event are:

-  Dr. Colin Palmer, CCP-EM, STFC Rutherford Appleton Laboratory

-  Dr. Tom Burnley, CCP-EM, STFC Rutherford Appleton Laboratory

-  Dr. Kevin Cowtan, Dept. of Chemistry, University of York

-  Prof. Paul Emsley, MRC-LMB, Cambridge

-  Asst. Prof. Arjen Jakobi, Dept. of Bionanoscience, TU Delft

-  Dr. Agnel Praveen Joseph, CCP-EM

-  Dr. Robert Nicholls, MRC-LMB, Cambridge

-  Prof. Maya Topf, CCP-EM, ISMB Birkbeck, University of London

-  Dr. Martin Winn, CCP-EM.
Organizers:  Prof. Wah Chiu, Dr. Michael Schmid, Stanford University, and Dr. 
Colin Palmer, CCP-EM, STFC Rutherford Appleton Laboratory

The 
S2C2
 is supported by the National Institutes of Health Common Fund Transformative 
High Resolution Cryo-Electron Microscopy 
program.





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[ccp4bb] EVENT DATE CORRECTION: Stanford-SLAC CryoEM Center (S2C2) Workshop on CryoEM of COVID-related Macromolecules, September 28, 2020

[Dunn, Lisa B.]

S2C2 Workshop - CryoEM of COVID-related Macromolecules, September 28, 2020   
8:00 AM- 1:00 PM (PDT)

Held as part of a suite of workshops during the SSRL/LCLS Annual Users' 
Meeting, this session highlights the recent use of cryoEM structure 
determination of SARS-COVID-2 related macromolecules. Speakers will cover 
structures of different molecular components of the virus and the cellular 
interacting partners. Some of talks will describe the impact of the structural 
results on vaccine and drug developments.   There is no cost for this workshop 
but you must register by 5 PM Pacific, September 25.   Register:  
https://events.bizzabo.com/SLAC-UsersMeeting-2020

Agenda:
-  David Veesler, University of Washington, Seattle:  Structural 
studies of the SARS-CoV Spike Glycoprotein
-  David Stuart, Oxford University and Diamond Light Source:  The use 
of cryoEM structural information to advance SARS2-CoV-2 biology and therapy
-  Goran Kokic, Max Planck Institute for Biophysical Chemistry, 
Göttingen:  Structure of replicating SARS-COV-2 polymerase
-  Erica Ollmann Saphire, La Jolla Institute for Immunology:  
Antibodies against Emerging Viral Disease
-  Rhiju Das, Stanford University:  CryoEM of previously unsolvable RNA 
structures including coronavirus genome element
-  Stephan Wilkens, SUNY Upstate Medical University, Syracuse:  
Targeting Vacuolar H+-ATPase for Antiviral Therapy

Organizer:  Wah Chiu, Stanford University

The S2C2 is supported by the National Institutes of Health Common Fund 
Transformative High Resolution Cryo-Electron 
Microscopy program.





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[ccp4bb] Stanford-SLAC CryoEM Center (S2C2) Workshop on CryoEM of COVID-related Macromolecules, October 28, 2020

[Dunn, Lisa B.]

S2C2 Workshop - CryoEM of COVID-related Macromolecules, October 28, 2020   8:00 
AM- 1:00 PM (PDT)

Held as part of a suite of workshops during the SSRL/LCLS Annual Users' 
Meeting, this session highlights the recent use of cryoEM structure 
determination of SARS-COVID-2 related macromolecules. Speakers will cover 
structures of different molecular components of the virus and the cellular 
interacting partners. Some of talks will describe the impact of the structural 
results on vaccine and drug developments.   There is no cost for this workshop 
but you must register by 5 PM Pacific, September 25.   Register:  
https://events.bizzabo.com/SLAC-UsersMeeting-2020

Agenda:
-  David Veesler, University of Washington, Seattle:  Structural 
studies of the SARS-CoV Spike Glycoprotein
-  David Stuart, Oxford University and Diamond Light Source:  The use 
of cryoEM structural information to advance SARS2-CoV-2 biology and therapy
-  Goran Kokic, Max Planck Institute for Biophysical Chemistry, 
Göttingen:  Structure of replicating SARS-COV-2 polymerase
-  Erica Ollmann Saphire, La Jolla Institute for Immunology:  
Antibodies against Emerging Viral Disease
-  Rhiju Das, Stanford University:  CryoEM of previously unsolvable RNA 
structures including coronavirus genome element
-  Stephan Wilkens, SUNY Upstate Medical University, Syracuse:  
Targeting Vacuolar H+-ATPase for Antiviral Therapy

Organizer:  Wah Chiu, Stanford University

The S2C2 is supported by the National Institutes of Health Common Fund 
Transformative High Resolution Cryo-Electron 
Microscopy program.





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[ccp4bb] Call for Stanford-SLAC CryoEM Center (S2C2) Applications

[Dunn, Lisa B.]

We would like to announce the full operation of two new Titan-Krios electron 
microscopes with high-throughput detectors (K3 and Falcon 4) dedicated to high 
resolution biological single particle data collection at the Stanford-SLAC 
CryoEM Center (S2C2) located in the new Arrillaga Science Center at SLAC, 
Stanford University. This increased capacity will allow more users, longer data 
collection sessions, and more sessions per project. We also offer cryoEM 
instruments for in-residence training in cryoEM using our other Titan-Krios or 
Talos-Arctica electron microscopes. We welcome anyone with an interest to apply 
for time at our facility for data collection and/or for in-depth training in 
high resolution cryoEM. A rapid turnaround on project application evaluation by 
our expert panel is in place. More information on the user and trainee project 
application can be found at  
https://cryoem.slac.stanford.edu/s2c2/project-requests and 
https://cryoem.slac.stanford.edu/s2c2/training/residence-training-program


Stay well and safe !

Wah Chiu, Director of Stanford-SLAC CryoEM Center




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[ccp4bb] Duax High School Program | Hauptman-Woodward Medical Research Institute

[Lisa J. Keefe]

Colleagues,

This workshop is virtual this summer, and therefore available to students 
worldwide.  Please share with your student science enthusiasts.

-Lisa

Lisa J Keefe, PhD

IMCA-CAT <http://www.imca-cat.org/>  Industrial Macromolecular 
Crystallography Association - Collaborative Access Team
630.252.0544  •  Sector 17 @ Advanced Photon Source, Argonne National 
Laboratory

Vice President for Advancing Therapeutics
Hauptman-Woodward Medical Research Institute <http://hwi.buffalo.edu/>

CEO (interim)
American Crystallographic Association <http://www.amercrystalassn.org/>

Chair-Elect
Council of Scientific Society Presidents 
<https://www.sciencepresidents.org/>
.
> 
> https://hwi.buffalo.edu/duax-high-school-program/ 
> <https://hwi.buffalo.edu/duax-high-school-program/>
> 
> Duax High School Program
> 
> The Eleventh Annual Summer Workshop in Molecular Bioinformatics 2020
> 
> The 2020 HWI Duax Summer Workshop will be held online from July 6 to July 24 
> from 9 AM to 1 PM five days a week. We can accommodate 60 students. Students 
> who commit to attend the entire three weeks will be given preference.
> 
> Sessions will begin with the entire group at 9 AM for presentations and at 10 
> AM break into study groups lead by HWI team leaders.  The web accounts will 
> be provided by HWI.  The program will culminate with students doing online 
> presentations for the full cohort as well as interested members of the 
> community.
> 
> First-time students must complete an application form with essay questions 
> concerning their goals and motivations.  COMPLETE THE APPLICATION HERE 
> <https://hwi.buffalo.edu/summer-workshop-in-molecular-bioinformatics-application/%20>.
>  We have been accepting students from 7th to 12th grades and have not 
> rejected anyone who completed the application. There are no other 
> prerequisites. Students will be accepted into the program in the order their 
> completed application is received. If more than 60 applications are received, 
> it may not be possible to accommodate the overflow.
> 
> Description of Program
> 
> Training is computer intensive. The students learn to use state of the art 
> computer programs for amino and nucleic acid sequence analysis of the genomes 
> of all bacteria and eukaryotes. The training includes the use of the most 
> heavily used programs for biological analysis on the World Wide Web and a 
> suite of unique programs developed in our laboratory for proteomic and 
> genomic analysis. The students mine the data in the gene and protein banks of 
> the world.
> 
> The four major goals of the research are to determine (1) the origin and 
> evolution of the genetic code, (2) the order of evolution of all bacterial 
> species, (3) the nature of evolution of the sequence and function of families 
> of proteins present in all species, and (4) the amino acid residues 
> responsible for substrate specificity in families of enzymes.
> 
> The students are not replicating previous experiments for which the results 
> are already known. They are conducting experiments that have never been done 
> before, that challenge basic tenets of structural biology. In this way 
> students learn that genuine research demands flexibility, adaptability, 
> creativity and patience.
> 
> The students are given opportunities to present their research goals and 
> results and their interpretation of their data to coworkers, classmates, 
> laymen, and scientists.
> 
> The Roy Carver Foundation and donations from various supporters make the HWI 
> Duax High School Program possible.  We thank them for their philanthropy.
> 
> There is an attendance fee of $100 for the 2020 school and should be paid at 
> the time of application.  Fee waivers for students with demonstrated need are 
> available.










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[ccp4bb] Call for Microscope Time Proposals at the Stanford-SLAC Cryo-EM Center (S2C2)

[Dunn, Lisa B.]

June 1, 2020 is the next deadline for submitting proposals for microscope time 
at the Stanford-SLAC Cryo-EM Center (S2C2).

Additional electron cryo-microscope capacity is in place at our facility.  We 
hope to resume regular user operations in June in a phased approach beginning 
with remote data collection.   Information about the project application 
process is available at:  
https://cryoem.slac.stanford.edu/s2c2/project-requests .  Register in the user 
portal at https://userportal.slac.stanford.edu/ to submit your proposal.

If you have any questions about your application, including our preliminary 
data and biosafety requirements, please feel free to send a message to 
s...@slac.stanford.edu.

The missions of the Stanford-SLAC Cryo-EM Center (S2C2) are:

  1.  to provide access to state-of-the-art cryo-EM instruments for data 
collection towards atomic resolution structure determination of biochemically 
purified single particles
  2.  to enable scientists across the nation to become independent cryo-EM 
investigators


The S2C2 is supported by the National Institutes of Health Common Fund 
Transformative High Resolution Cryo-Electron 
Microscopy program.




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[ccp4bb] Stanford-SLAC Cryo-EM Center (S2C2) Workshop on CryoEM Image Processing - June 10-12, 2020

[Dunn, Lisa B.]

S2C2 Workshop - CryoEM Image Processing - June 10-12, 2020 (Zoom webinar)

Stanford-SLAC Cryo-EM Center (S2C2) will offer a training workshop June 10-12, 
2020. This workshop will include all steps of image reconstruction and the 
practical use of software for single particle image reconstruction available 
under CryoSPARC. This workshop will consist of three days of lectures and 
hands-on training.  Zoom teleconferencing will be available for the lectures, 
demonstration of the practical material and the practical participation.

There is no fee for this workshop.  The practical sessions are limited to 60 
participants.  If you are interested, apply by May 25 for participation in the 
practical sessions or by June 1 for the lecture sessions only.

* 
Agenda

* 
Application

We look forward to providing this training!
The S2C2 is supported by the National Institutes of Health Common Fund 
Transformative High Resolution Cryo-Electron 
Microscopy program.




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[ccp4bb] Open for COVID-19 Research for Structural Biology Data Collection

[Dunn, Lisa B.]

The SSRL Structural Biology beamlines 12-2, 9-2 and 4-2 and the Stanford-SLAC 
CryoEM facilities are open to user projects that are related to COVID-19 
research. CryoEM Proposals may be submitted as service projects through our 
Stanford-SLAC Cryo-EM Center<https://cryoem.slac.stanford.edu/s2c2/> (S2C2) 
program or as collaborative projects through our National Center for 
Macromolecular Imaging<https://cryoem.slac.stanford.edu/ncmi/> (NCMI) program. 
Registration and proposal submittal are facilitated through our user 
portal<https://userportal.slac.stanford.edu/>, as are similar applications for 
COVID-19 related research on structural molecular biology beamlines at the 
Stanford Synchrotron Radiation Lightsource<https://www-ssrl.slac.stanford.edu/> 
(SSRL).



For questions regarding the application process, please contact Lisa Dunn 
(l...@slac.stanford.edu<mailto:l...@slac.stanford.edu>).



Feel share this information with others who may have COVID-19 related research 
projects.



Links

SSRL:  https://www-ssrl.slac.stanford.edu/

S2C2:  https://cryoem.slac.stanford.edu/s2c2/

NCMI: https://cryoem.slac.stanford.edu/ncmi/

User Portal:  https://userportal.slac.stanford.edu/

SSRL Rapid Access:  
https://www-ssrl.slac.stanford.edu/content/user-resources/rapid-access-ssrl-resources-covid-19-research











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[ccp4bb] Call for Stanford-SLAC Cryo-EM Center (S2C2) Applications: March 1, 2020

[Dunn, Lisa B.]

March 1 is the next deadline for submitting data collection and training 
proposals to the Stanford-SLAC Cryo-EM Center (S2C2).

The missions of the Stanford-SLAC Cryo-EM Center (S2C2) are:

  1.  to provide access to state-of-the-art cryo-EM instruments for data 
collection towards atomic resolution structure determination of biochemically 
purified single particles
  2.  to enable scientists across the nation to become independent cryo-EM 
investigators

Additional electron cryo-microscope capacity is in place at our facility.   
Information about the project application process is available at:  
https://cryoem.slac.stanford.edu/s2c2/project-requests .Register in the 
user portal at https://userportal.slac.stanford.edu/ to submit your proposal.

If you have any questions about your application, including our preliminary 
data and biosafety requirements, please feel free to send a message to 
s...@slac.stanford.edu<mailto:s...@slac.stanford.edu>.

Best regards,

Lisa Dunn
Stanford-SLAC Cryo-EM Center (S2C2)
SLAC National Accelerator Laboratory
2575 Sand Hill Rd.
Menlo Park, CA 94025
l...@slac.stanford.edu<mailto:l...@slac.stanford.edu>





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[ccp4bb] Stanford-SLAC Cryo-EM Center (S2C2) Workshop – Specimen Preparation and Data Collection

[Dunn, Lisa B.]

S2C2 Workshop – Cryo-EM Specimen Preparation and Data Collection, March 23-25, 
2020

Stanford-SLAC Cryo-EM Center (S2C2) will offer a beginning cryo-EM training 
workshop held at SLAC National Accelerator Laboratory between March 23 and 25, 
2020.  Onsite attendance for the lecture sessions is limited to ~40 
participants with additional access provided via Zoom teleconferencing.  The 
hands-on sessions are limited to 12 participants.  There is no fee for this 
workshop.  If you are interested, you may apply by March 15, 2020 at:   
https://cryoem.slac.stanford.edu/s2c2/training/s2c2-workshops/next-workshop

Day 1: March 23, 2020
Wah Chiu : TEM basics and radiation damage
Robert M. Glaeser : Challenges in cryo-specimen preparation, and principles 
of image phase contrast and phase plate
Christopher Booth : Principles and operation of direct detector and energy 
filter
Yee Ting Li : CryoEM elogbook; data management and image quality assessment 
during data collection
Yifan Cheng : Best practices in cryoEM: what to do and not to do in 
tackling a new specimen

Day 2: March 24, 2020
Brenda Gonzalez and Ziwei Huang : Using virtual reality for training in 
cryo-specimen preparation for cryoEM
Practical sessions in small groups for cryo-specimen preparation and cryoEM 
operation

Day 3: March 25, 2020
Practical sessions in small groups for cryo-specimen preparation and cryoEM 
operation

We look forward to providing this training in March!

The Organizers

Corey Hecksel
heck...@stanford.edu

Michael Schmid
mfsch...@stanford.edu

The S2C2 is supported by the National Institutes of Health Common Fund 
Transformative High Resolution Cryo-Electron 
Microscopy program.




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[ccp4bb] S2C2 Modeling Workshop, 15–17 January 2020

[Dunn, Lisa B.]

S2C2 Modeling Workshop,  15–17 January 2020



Stanford-SLAC CryoEM Center (S²C²) will offer a training workshop held at SLAC 
National Accelerator Laboratory between January 15 and 17, 2020.  This workshop 
covers the basic principles and practical protocols to obtain atomic models 
based on cryo-EM density maps at near atomic resolution. This workshop will 
consist of three days of lectures and hands-on training sessions.

Speakers

· Paul Adams, LBNL

· Tom Goddard, UCSF

· Greg Pintilie, Consultant, Stanford University

· Cathy Lawson, Rutgers

There is no fee for this workshop.  If you are interested in attending in 
person please apply by December 20, 2019. 
https://cryoem.slac.stanford.edu/s2c2/training/s2c2-workshops/next-workshop


The missions of the Stanford-SLAC Cryo-EM Center (S2C2) are:

1. to provide access to state-of-the-art cryo-EM instruments for data 
collection towards atomic resolution structure determination of biochemically 
purified single particles.

2. to enable scientists across the nation to become independent cryo-EM 
investigators capable to carry out the entire workflow from specimen 
preparation to structure validation.

The S2C2 is supported by the National Institutes of Health Common Fund 
Transformative High Resolution Cryo-Electron Microscopy 
program.

See also:

Future S²C² Training 
Workshops

In-Residence Training 
Program

Project Application

Onsite Stanford Guest 
House  and  
Stanford Lodging Guide




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[ccp4bb] November 1, 2019 Deadline for S2C2 Proposals

[Dunn, Lisa B.]

 November 1 is the next deadline for submitting proposals to the Stanford-SLAC 
Cryo-EM Center (S2C2).

 The missions of the Stanford-SLAC Cryo-EM Center (S2C2) are:

  1.  to provide access to state-of-the-art cryo-EM instruments for data 
collection towards atomic resolution structure determination of biochemically 
purified single particles
  2.  to enable scientists across the nation to become independent cryo-EM 
investigators
More information about the S2C2 program and the project application process is 
available at:  https://cryoem.slac.stanford.edu/s2c2/.Register in the user 
portal at https://userportal.slac.stanford.edu/ to submit your proposal.

Best regards,

Lisa Dunn
Stanford-SLAC Cryo-EM Center (S2C2)
SLAC National Accelerator Laboratory
2575 Sand Hill Rd.
Menlo Park, CA 94025
l...@slac.stanford.edu<mailto:l...@slac.stanford.edu>




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[ccp4bb] Call for Stanford-SLAC Cryo-EM Center (S2C2) Applications: Deadline November 1, 2019

[Dunn, Lisa B.]

Dear All,

The next deadline for submitting proposals to the Stanford-SLAC Cryo-EM Center 
(S2C2) is November 1, 2019.

 The missions of the Stanford-SLAC Cryo-EM Center (S2C2) are:

  1.  to provide access to state-of-the-art cryo-EM instruments for data 
collection towards atomic resolution structure determination of biochemically 
purified single particles
  2.  to enable scientists across the nation to become independent cryo-EM 
investigators
More information about the S2C2 program and the project application process is 
available at:  https://cryoem.slac.stanford.edu/s2c2/.Register in the user 
portal at https://userportal.slac.stanford.edu/ to submit your proposal.

Best regards,

Lisa Dunn
Stanford-SLAC Cryo-EM Center (S2C2)
SLAC National Accelerator Laboratory
2575 Sand Hill Rd.
Menlo Park, CA 94025
l...@slac.stanford.edu<mailto:l...@slac.stanford.edu>




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[ccp4bb] Stanford-SLAC Cryo-EM Center (S2C2) Image Processing Workshop - Nov. 18-20, 2019

[Dunn, Lisa B.]

S2C2 Workshop - Image Processing, November 18-20, 2019
Stanford-SLAC Cryo-EM Center (S2C2) will offer a training workshop held at SLAC 
National Accelerator Laboratory between November 18 and 20, 2019. This workshop 
will include all steps of image reconstruction and the practical use of 
software for single particle image reconstruction available under Scipion. This 
workshop will consist of three days of lectures and hands-on training sessions 
led by Profs. David DeRosier, Jose Maria Carazo, Georgios Skiniotis and 
colleagues. The practical sessions will be conducted via cloud computing 
accounts and is only available on-site to a limited number of participants. 
Zoom teleconferencing will be available for the lectures and demonstration of 
the practical material  but will not have a practical participation option. If 
you are interested, you may apply before October 31, 2019.

There is no fee for this workshop.  If you are interested, please apply by 
October 31, 2019.   https://cryoem.slac.stanford.edu/s2c2/training/workshops


The Organizers (Wah Chiu, Georgios Skiniotis, Britt Hedman, Michael Schmid)



The S2C2  https://cryoem.slac.stanford.edu/s2c2/ is supported by the National 
Institutes of Health Common Fund Transformative High Resolution Cryo-Electron 
Microscopy program.




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[ccp4bb] Stanford-SLAC Cryo-EM Center (S2C2) Workshop for Beginners - Sep. 11-13, 2019

[Dunn, Lisa B.]

S2C2 Workshop - Cryo-EM for Beginners September 11-13, 2019


Location: SLAC National Accelerator Laboratory, Menlo Park, CA USA


Stanford-SLAC Cryo-EM Center (S2C2) is offering a training workshop on 
experimental aspects of cryo-EM tailored to beginners.  This workshop will be 
held at SLAC National Accelerator Laboratory between September 11 and 13, 2019. 
Preference of trainees is given to individuals who have research projects ready 
for cryo-EM investigations and have a background in structural biology. This 
workshop will consist of three days of morning lectures and afternoon hands-on 
training sessions.  Onsite attendance for the lecture sessions is limited to 
~40 participants with additional access provided via Zoom teleconferencing.  
The hands-on sessions are limited to 8 participants. If you are interested, you 
may apply before August 31, 2019.


There is no fee for this workshop.  The workshop agenda and application form 
can be found at: https://cryoem.slac.stanford.edu/s2c2/training/workshops


We look forward to providing this training in September!



The Organizers (Wah Chiu, Georgios Skiniotis, Britt Hedman, Michael Schmid)


The S2C2 is supported by the National Institutes of Health Common Fund 
Transformative High Resolution Cryo-Electron 
Microscopy program.



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[ccp4bb] Position Opening: Synchrotron Macromolecular Crystallographer @ IMCA-CAT

[Lisa J. Keefe]

Dear Colleagues,


POSITION:  Synchrotron Macromolecular Crystallographer
LOCATION:  IMCA-CAT at the Advanced Photon Source (near Chicago, IL)


The Industrial Macromolecular Crystallography Association - Collaborative 
Access Team (IMCA-CAT) and the Hauptman-Woodward Medical Research Institute 
(HWI) seek an inventive macromolecular crystallographer to join the IMCA-CAT 
team in accelerating pharmaceutical drug discovery through synchrotron-based 
structural biology research. As an employee of HWI, you will be based at the 
center of the team’s operations at the Advanced Photon Source (APS), Argonne 
National Laboratory, near Chicago, IL. This is an ideal position for a 
motivated scientist who is passionate about delivering strategic value, 
developing new technologies, and working in a high- powered, collaborative 
environment.


DESCRIPTION:
This is an exciting time to join IMCA-CAT. Underway this summer is the first of 
a two-phase upgrade that will significantly increase throughput and establish a 
strong foundation upon which to build capacity. The second phase upgrade, 
currently in design, will profoundly increase capacity and dramatically expand 
capability for challenging research projects.

The successful candidate will be an integral part of these upgrade activities 
while maintaining flow of diffraction data for pharmaceutical research 
projects. The candidate will work closely with IMCA-CAT colleagues in an 
inclusive and respectful environment, and is expected to take initiative and 
contribute to the team effort.

On any given day, you will do one or all of these things:
• Contribute to drug discovery research efforts using a growing 
portfolio of synchrotron sources.
• Enhance the structural biology programs for pharmaceutical 
structure-based drug design.
• Provide experiment support for scientists from the structural biology 
community who conduct research using the IMCA-CAT synchrotron beamlines.
• Ensure beamline instrumentation is operational and produces data of 
the highest quality.
• Expand the experiment envelope of the beamline.
• Establish efficient protocols for accelerating data acquisition while 
enhancing data security.
• Develop automated methods for acquiring quality data from challenging 
samples.
• Participate in highly collaborative working groups.
• Engage in the technical development of new strategies for ultra-high 
throughput.
• Collaborate with staff on strategically-aligned research and 
development projects.
• Communicate with researchers and present at meetings.
• Conduct independent and/or collaborative research.


DESIRED SKILLS and EXPERIENCE:
• PhD in a relevant field.
• Expertise in macromolecular crystallography.
• Outstanding experimental skills.
• Considerable mechanical skills.
• Highly collaborative and team-oriented approach to conducting work 
and solving problems.
• Excellent written and oral communication skills.
• Deeply proactive approach to meeting and exceeding goals.
• Ability to meet requirements for site access to Argonne National 
Laboratory.


TO APPLY:
Send an introductory email, cv, and contact information for three references to 
Lisa Keefe, IMCA-CAT Director and HWI Vice President of Advancing Therapeutics, 
at ke...@imca-cat.org <mailto:ke...@imca-cat.org>.


LEARN MORE:
Visit our websites to learn more about IMCA-CAT (www.imca-cat.org 
<http://www.imca-cat.org/>) and HWI (www.hwi.buffalo.edu 
<http://www.hwi.buffalo.edu/>). 


HWI is an equal opportunity employer.


Lisa J Keefe, PhD

Director
IMCA-CAT <http://www.imca-cat.org/>  Industrial Macromolecular 
Crystallography Association - Collaborative Access Team
630.252.0544  •  Sector 17 @ Advanced Photon Source, Argonne National 
Laboratory

Vice President for Advancing Therapeutics
Hauptman-Woodward Medical Research Institute <http://hwi.buffalo.edu/>

Past-President
American Crystallographic Association <http://www.amercrystalassn.org/>
.







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[ccp4bb] Stanford-SLAC Cryo-EM Center (S2C2) Modeling Workshop

[Dunn, Lisa B.]

S2C2 Modeling Workshop - July 10-12, 2019

Location: SLAC National Accelerator Laboratory, Menlo Park, CA USA

Dear Colleagues

The missions of the Stanford-SLAC Cryo-EM Center (S2C2) are:


1.   to provide access to state-of-the-art cryo-EM instruments for data 
collection towards atomic resolution structure determination of biochemically 
purified single particles.

2.   to enable scientists across the nation to become independent cryo-EM 
investigators capable to carry out the entire workflow from specimen 
preparation to structure validation.
We are pleased to announce that S2C2 will host a three-day Cryo-EM Modeling 
workshop on July 10-12, 2019.  This workshop, the third in a series, will cover 
the basic principles and practical protocols to obtain atomic models based on 
cryo-EM density maps at near atomic resolution.

The workshop will be conducted by experts in the field of map visualization, 
density segmentation and annotation, model building, model optimization, and 
ligand fitting. Special attention will be devoted to validation tools that 
ensure model reliability and acceptability for deposition to map and model 
databases.

The workshop agenda can be found at:   
https://cryoem.slac.stanford.edu/s2c2/training/workshops

There is no registration fee for this workshop, but in-person attendance is 
limited to 40 participants.   
https://cryoem.slac.stanford.edu/s2c2/content/s%C2%B2c%C2%B2-event-application

We look forward to providing this training in July!

The Organizers (Wah Chiu, Georgios Skiniotis, Britt Hedman, Michael Schmid)




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[ccp4bb] Call for Stanford-SLAC Cryo-EM Center (S2C2) Proposals

[Dunn, Lisa B.]

Dear All,

June 1 is the next deadline for submitting project proposals to the 
Stanford-SLAC Cryo-EM Center (S2C2).  Please apply at  
https://userportal.slac.stanford.edu/

More information about the S2C2 program and the project application process is 
available at:  https://cryoem.slac.stanford.edu/s2c2/

Best regards,

Lisa Dunn
Stanford-SLAC Cryo-EM Center (S2C2)
SLAC National Accelerator Laboratory
2575 Sand Hill Rd.
Menlo Park, CA 94025
l...@slac.stanford.edu<mailto:l...@slac.stanford.edu>




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[ccp4bb] Call for Stanford-SLAC Cryo-EM Center (S2C2) Applications: Deadline June 1, 2019

[Dunn, Lisa B.]

Dear All,

The second deadline for submitting proposals to the Stanford-SLAC Cryo-EM 
Center (S2C2) is coming up soon.Please apply at  
https://userportal.slac.stanford.edu/  by June 1.

The missions of the Stanford-SLAC Cryo-EM Center (S2C2) are:

  1.  to provide access to state-of-the-art cryo-EM instruments for data 
collection towards atomic resolution structure determination of biochemically 
purified single particles
  2.  to enable scientists across the nation to become independent cryo-EM 
investigators
More information about the S2C2 program and the project application process is 
available at:  https://cryoem.slac.stanford.edu/s2c2/.

Best regards,

Lisa Dunn
Stanford-SLAC Cryo-EM Center (S2C2)
SLAC National Accelerator Laboratory
2575 Sand Hill Rd.
Menlo Park, CA 94025
l...@slac.stanford.edu<mailto:l...@slac.stanford.edu>




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[ccp4bb] crystallography software on mac

[LISA]

Hi all,

Since I updated to Yosemite on my Mac,* pymol* and *phenix *does not work
any more. Pymol can not be re-installed after updated to yosemite.
The previous version of mac is 10.6 and the fink on my mac is also 10.6. Do
I need to update the fink to 10.10? How to make the pymol work?  Thank you.

Best Regards,

Lisa

[ccp4bb] protein polymerization

[LISA]

Dear All,

My proein is polymerzated and elutate in the void volum when runnning gel
filtration Superdex 200. I can get a small crystal after a  lot of
optimization. But the resolution is still very low (about 8A ). I try to
find the sites involved in polymerization. Is there some software to
predicat the amino acids which are involved in protein polymerization?
And All  suggestion to the crystal optimization are welcome.  Thank you.

Best Regards,

Lisa

[ccp4bb] ccp4 version in sharp

[LISA]

Hi all,
I tried to run autosharp and get the following error message about ccp4 version.


 *WARNING* : Your CCP4 [1
http://127.0.0.1:8080/users/wangyl/logfiles/SAD-cas-ta-ha.0/CHECKS/LISTautoSHARP.html#CCP4]
version (6.4.0) is newer than the
   supported ones (and therefore untested) - this might not work. Please
   use a supported CCP4 version (4.2.2 up to 6.3.0 with the latest
   patches applied from the official CCP4 problems page)


My computer installed both ccp4 6.3.0 and 6.4.0
*. *
How to change the ccp4 version for sharp without reinstall sharp? Thank you.

Best Regards,

lisa

Re: [ccp4bb] Can Mathew's coefficient tell about a complex

[LISA]

If you want to know what in your crystal, run SDS-PAGE of your crystal.


On Thu, Dec 5, 2013 at 6:39 AM, Kris Tesh kris.t...@att.net wrote:

 If either of the two protein structures has been determined/deposited, I
 would check if your unit cell matched one of them.

 Kris F. Tesh, Ph. D.
 Department of Biology and Biochemistry
 University of Houston

   --
  *From:* Tanner, John J. tanne...@missouri.edu
 *To:* CCP4BB@JISCMAIL.AC.UK
 *Sent:* Wednesday, December 4, 2013 4:29 PM
 *Subject:* Re: [ccp4bb] Can Mathew's coefficient tell about a complex

  First of all, there are two Ts and no apostrophe in Matthews.  The
 method is based on the following paper, which is worth reading.  It is one
 of the first examples, possibly the first, of structural bioinformatics.

  J Mol Biol. 1968 Apr 28;33(2):491-7.
 Solvent content of protein crystals.
 Matthews BW.
 http://www.ncbi.nlm.nih.gov/pubmed/5700707

  Secondly, you might run a gel on your crystals.


   John J. Tanner
 Professor of Biochemistry and Chemistry
 University of Missouri-Columbia
 125 Chemistry Building
 Columbia, MO 65211
 Phone: 573-884-1280
 Fax: 573-882-2754
 Email: tanne...@missouri.edu
 http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html

  On Dec 4, 2013, at 4:06 PM, abbas maqbool abbas_maqb...@yahoo.com
  wrote:

   Dear All,
  I crystallized a complex of two proteins and got x-ray data. However I
 dont know if I have got complex or just one of the protein has
 crystallized. Can I check it by mathew's coefficient? If yes how? One of my
 protein is 30 kDa nad other one is 12 kDa.
  Actually I calculated Mathew's coeffient (based on Mol. wt of complex
 42000 Da), and results were like that


  Cell Volume = 993567
  Nmol/asymMathews coeff%solvent
  13.94   68
  21.9737
  3 1.36


  Can any one please explain what does it suggest?

  Thanks
  Abbas

[ccp4bb] rotation peak number in new version phaser

[LISA]

hi all,

I try to solve the crystal structures of a mult-domain protein with phaser.
I cannot solve the structure by automatic search using domain structure as
the models. I tried to do the rotation search using the fast or brute
rotation function. I defined the rotation search peaks number is 1000. But
I only get no more than 100 peaks. I tried the phaser in ccp4-6.3.0 and
ccp4-6.4.0. But I can only get much less peaks than I required in the
rotation. But the old version phaser can give about 1000 peaks if I use
brute rotation function ask for 1000 peaks. How can I more rotation peaks
in the new version phaser
?
 Thank you.

Lisa

Re: [ccp4bb] the f' and f'' of heavy cluster

[LISA]

Dear Dr. Matthias Zebisch,

how to do the specific cluster search in phaser sad pipline? Thank you.

Lisa


On Thu, Nov 21, 2013 at 3:37 PM, Matthias Zebisch 
matthias.zebi...@bbz.uni-leipzig.de wrote:

 Dear Lisa,

 if you have proper anomalous data I rather recommend using the Phaser SAD
 pipeline and specify cluster search.
 Worked instantly for me.

 Good luck!

 -
 Dr. Matthias Zebisch
 Division of Structural Biology,
 Wellcome Trust Centre for Human Genetics,
 University of Oxford,
 Roosevelt Drive,
 Oxford OX3 7BN, UK

 Phone (+44) 1865 287549;
 Fax (+44) 1865 287547
 Email matth...@strubi.ox.ac.uk
 Website http://www.strubi.ox.ac.uk
 -


 On 11/21/2013 6:29 AM, LISA wrote:

 Dear All,
 I am running autosharp with a single wavelength data soked with Ta6Br12.
 This data collected at the wavelength of 1.254A. I told the autosharp the
 f' -20 and f''10.5. The autosharp result said these values are not correct?
 How can we get the f' and f'' of this cluster? Thank you.
 Lisa

[ccp4bb] the f' and f'' of heavy cluster

[LISA]

Dear All,

I am running autosharp with a single wavelength data soked with Ta6Br12.
This data collected at the wavelength of 1.254A. I told the autosharp the
f' -20 and f''10.5. The autosharp result said these values are not correct?
How can we get the f' and f'' of this cluster? Thank you.

Lisa

[ccp4bb] how to improve experimental phase by combining partial homology models

[LISA]

Dear all,

I am now working on a very  low resolution phase determination (around 4.5A
with hg anomalous signal around 5.5 A). I can find the Hg sites and get the
phase, but the density map is not so good.
Two components of my protein complex (about 1/3) has a homologue model
which is also can not  be found using Phaser. My native data is 3.5 A.

Can I combine the experimental phase and homology model to improve electron
density?  Is there anybody can help find which program can work on this?
Thank you.

Lisa

[ccp4bb] how to solve crystal structure using published EM structure

[LISA]

Hi All,

The EM  structure of a complex was published at 8A. If we can collect
crystal data of this complex. How to get the phase of this crystal with the
EM structure? Thank you.

Sincerely,

Lisa

[ccp4bb] software molecular replacement

[LISA]

Hi all,
There are so many software for MR, such as phaser, balbe,molrep, and amore.
What is difference between them? Which one is powerful?
Please give some comments for these software?Thank you.

Sincerely,
lisa

[ccp4bb] how to make protein topology figure based on its structure

[LISA]

Hi all,
I want to make a topological figure of my protein  with a b-sheet and helix
based on its crystal structure. Please recommend some online sever of
software?
Thank you.

lisa

[ccp4bb] how to update phenix

[LISA]

Hi all,
 My mac has the old version of phenix. How can i update to the new verison?
Should I delete the old version and download the new version to install as
the fist time ? Thanks

lisa

[ccp4bb] install crystallography software on mac

[LISA]

Hi all,
I am trying to install ccp4, phenix, coot and other crystallography
software on my mac. I am not familiar with mac, neither Linux system.
Please give me some protocols to install these software and how to update
them. I appreciate it.

Lisa

[ccp4bb] edit chi angles of DNA in coot

[LISA]

Hi all,
I am refining a protein-DNA complex. But when I adjust the position of DNA
by edit chi angels, the phosphate does not move. Only the sugar and base
move
Here is partial DNA pdb. Is there any format problem of my pdb or I miss
some library?
ATOM  10825  PAd D  11  17.140  11.607  42.723  1.00
29.20   P
ATOM  10826  O1P  Ad D  11  16.898  12.582  41.641  1.00
29.72   O
ATOM  10827  O2P  Ad D  11  18.154  11.916  43.743  1.00
33.07   O
ATOM  10828  O5*  Ad D  11  17.537  10.169  42.137  1.00
31.19   O
ATOM  10829  C5*  Ad D  11  17.790   9.108  43.047  1.00
25.02   C
ATOM  10830  C4*  Ad D  11  17.956   7.803  42.314  1.00
30.93   C
ATOM  10831  O4*  Ad D  11  16.670   7.304  41.858  1.00
29.79   O
ATOM  10832  C1*  Ad D  11  16.870   6.713  40.601  1.00
36.62   C
ATOM  10833  N9   Ad D  11  15.636   6.710  39.824  1.00
33.20   N
ATOM  10834  C8   Ad D  11  14.968   7.801  39.371  1.00
22.90   C
ATOM  10835  N7   Ad D  11  13.896   7.505  38.680  1.00
26.56   N
ATOM  10836  C5   Ad D  11  13.870   6.121  38.654  1.00
31.80   C
ATOM  10837  C4   Ad D  11  14.942   5.617  39.358  1.00
32.61   C
ATOM  10838  N3   Ad D  11  15.238   4.325  39.551  1.00
27.80   N
ATOM  10839  C2   Ad D  11  14.334   3.546  38.961  1.00
27.51   C
ATOM  10840  N1   Ad D  11  13.252   3.882  38.250  1.00
21.29   N
ATOM  10841  C6   Ad D  11  12.980   5.187  38.073  1.00
31.66   C
ATOM  10842  N6   Ad D  11  11.890   5.516  37.368  1.00
29.64   N
ATOM  10843  C2*  Ad D  11  17.929   7.576  39.923  1.00
36.75   C
ATOM  10844  C3*  Ad D  11  18.836   7.949  41.084  1.00
36.29   C
ATOM  10845  O3*  Ad D  11  19.919   7.056  41.170  1.00
37.96   O
ATOM  10846  PCd D  12  21.191   7.246  40.214  1.00
55.12   P
ATOM  10847  O1P  Cd D  12  22.397   7.328  41.071  1.00
49.33   O
ATOM  10848  O2P  Cd D  12  20.886   8.343  39.272  1.00
47.47   O
ATOM  10849  O5*  Cd D  12  21.226   5.885  39.374  1.00
51.47   O
ATOM  10850  C5*  Cd D  12  21.346   4.667  40.093  1.00
49.75   C
ATOM  10851  C4*  Cd D  12  20.769   3.488  39.334  1.00
39.32   C
ATOM  10852  O4*  Cd D  12  19.343   3.656  39.226  1.00
32.96   O
ATOM  10853  C1*  Cd D  12  18.882   2.909  38.120  1.00
30.55   C
ATOM  10854  N1   Cd D  12  17.966   3.801  37.377  1.00
31.81   N
ATOM  10855  C2   Cd D  12  16.867   3.239  36.734  1.00
24.72   C
ATOM  10856  O2   Cd D  12  16.717   2.019  36.807  1.00
32.01   O
ATOM  10857  N3   Cd D  12  16.011   4.047  36.070  1.00
23.04   N
ATOM  10858  C4   Cd D  12  16.243   5.365  36.022  1.00
28.69   C
ATOM  10859  N4   Cd D  12  15.377   6.135  35.351  1.00
18.23   N
ATOM  10860  C5   Cd D  12  17.370   5.958  36.668  1.00
27.01   C
ATOM  10861  C6   Cd D  12  18.198   5.145  37.329  1.00
28.78   C
ATOM  10862  C2*  Cd D  12  20.104   2.429  37.341  1.00
34.57   C
ATOM  10863  C3*  Cd D  12  21.222   3.310  37.890  1.00
31.03   C
ATOM  10864  O3*  Cd D  12  22.469   2.619  37.840  1.00
34.98   O

[ccp4bb] gedit on mac terminal

[LISA]

Hi all,
I installed gedit on my mac applications. But i can not use it by terminal.
Please help me figure it out. Thanks.

lisa

[ccp4bb] protein degradation in crystal

[LISA]

Hi All,
I have an 36KD protein which can be crystallize in two days. Most of the
crystals are very big. But all cystals have poor resolution,lower than 3.8
A. I picked some crystals, washed them in the mother solution and then run
SDS-PAGE. It is surprised to find that different cystals have different
components. Some crystals have several samll bands below the band of the
protein. And in some crysals the bigger size band (as the construct should
be) almost disappared and have smear. Does the protein was degradated in
the crystals? Did someone met the similar problem as I? Thanks

All the best
lisa

[ccp4bb] domain predication

[LISA]

Dear All,
I have a big protein having more than 2000 amino acids. which sever is good
to predicate the domains or motifs it has. Thank you.
lisa

[ccp4bb] Macromolecular Crystallography Beamline Scientist Position at NSLS-II

[Miller, Lisa M]

Beamline Scientist Position for Macromolecular Crystallography Beamlines at 
NSLS-II

The Photon Sciences Directorate at Brookhaven National Laboratory is seeking an 
experienced scientist to support the development of a Microfocusing 
Macromolecular Crystallography Beamline (FMX) and a Highly Automated 
Macromolecular Crystallography Beamline (AMX) at the National Synchrotron Light 
Source II (NSLS-II), which is a new 3rd-generation synchrotron facility being 
constructed on Long Island, New York, with extremely high brightness and 
exceptional beam stability over a wide spectral range.

As a scientific staff member reporting to the Group Leader for the FMX/ AMX 
beamlines in the Photon Division, the selected candidate will be part of a 
group of scientific and engineering staff to design and build a pair of 
state-of-the-art macromolecular crystallography beamlines and its associated 
scientific programs at NSLS-II. Responsibilities include interacting with the 
scientific user community to define the mission and technical scope of the 
beamlines, and supporting all aspects of the beamline design, construction, 
commissioning, and operations.

Qualifications Required:
*   Ph.D. in structural biology, physics, biophysics, or a related field
*   At least two (2) years of post-doctoral experience in macromolecular 
crystallography at a synchrotron beamline
*   Experience in synchrotron-based research is required in one of three 
scientific areas: (1) high throughput macromolecular crystallography, (2) 
design and development of crystallography instrumentation and methods, or (3) 
operation of a macromolecular crystallography user program at a synchrotron
*   Excellent written and oral communications skills
*   The ability to interact effectively in a team environment with a 
diverse group of scientists, engineers, technical staff, and users.

Qualifications Preferred:
*   Experience with experimental investigations at the micro- or nano scale
*   Experience in process automation and remote control
*   Experience with crystallographic data analysis and structure solving
*   Experience in the design and analysis of optical components
*   Prior experience in project planning, execution, and reporting.

The selected candidate will be placed at the appropriate scientific level 
dependent upon depth and breadth of relevant knowledge and skills he or she 
brings to the position, as well as the amount of relevant experience.

For more information, go to http://www.bnl.gov/HR/careers/ and see Job ID# 
16236 or contact Dieter Schneider at schnei...@bnl.govmailto:schnei...@bnl.gov

Deadline for applications is November 27, 2012.

[ccp4bb] Associate Division Director for Structural Biology at NSLS-II

[Miller, Lisa M]

Associate Division Director for Structural Biology
National Synchrotron Light Source II
Brookhaven National Laboratory

The Photon Sciences Directorate at Brookhaven National Laboratory is seeking an 
experienced and internationally recognized scientist to fill a new leadership 
position as Associate Division Director (ADD) for Structural Biology in the 
Photon Division. Reporting to the Division Director, the ADD for Structural 
Biology will work closely with the Chief Life Scientist to lead the Photon 
Sciences effort to plan, develop, and conduct a highly productive and 
high-impact structural biology program at NSLS-II structural biology beamlines 
covering a suite of techniques from macromolecular crystallography to X-ray 
scattering. NSLS-II is a new third generation synchrotron facility being 
constructed on Long Island, New York with extremely high brightness and 
exceptional beam stability that are expected to benefit the structural biology 
program.

Specific roles and responsibilities include:
*   Leading the effort in planning and implementing structural biology 
beamlines and supporting facilities and associated scientific programs, 
including interacting with various stakeholders such as the scientific user 
community and funding agencies
*   Coordinating and overseeing  structural  beamline development, upgrade, 
and operation activities with scientists and user communities, including 
oversight of partner user programs and staff beam time usages
*   Managing all aspects of staffing and budgetary resources of the 
Structural Biology Program including workforce planning, developing, 
recommending, and implementing approved staffing and budgetary plans as required
*   Conducting a research program in structural biology, methodology, or 
synchrotron instrumentation
*   Ensuring a safe, positive, and productive working environment

Qualifications Required:
*   Ph.D. in biochemistry, biophysics, or a related field
*   Minimum of 10 years of working experience associated with managing or 
developing synchrotron-based structural biology programs or facilities
*   Experience in synchrotron-based research in structural biology
*   Excellent written and oral communication skills
*   The ability to interact effectively in a team environment with a 
diverse group of scientists, engineers, technical staff, users, and other 
stakeholders

Qualifications Preferred:
*   Active research program in structural biology or in methodology or 
synchrotron instrumentation
*   Experience with grant writing and demonstrated success in securing 
research funding
*   Prior experience in managing construction and/or operation of a 
synchrotron beamline or instrumentation, including project planning, execution, 
reporting, and budget and resource management

At Brookhaven National Laboratory we believe that a comprehensive employee 
benefits program is an important and meaningful part of the compensation 
employees receive. Our benefits program includes but is not limited to: Medical 
Plans, Vacation, Holidays, Dental Plans, Life Insurance, 401(k) Plan, 
Retirement Plan, On-site Child Development Center, swimming pool, weight room, 
tennis courts and many other employee perks and benefits. BNL is an Affirmative 
Action/Equal Opportunity Employer committed to the development of a diverse 
workforce.

Please visit http://www.bnl.gov/HR/careers/ and apply to Job ID# 16185
For questions, please contact Dr. Qun Shen at 
qs...@bnl.govmailto:qs...@bnl.gov or Mr. Peter Esposito at 
petere...@bnl.govmailto:petere...@bnl.gov

[ccp4bb] llg is negative in phaser

[LISA]

Hi all,

does anyone solve their structure by molecular replacement  with phaser
with LLG  0?
Thanks

lisa

[ccp4bb] how to get phase of huge complex

[LISA]

Hi all,

My work is to solve huge complex containing 4 different proteins and total
molecular weight is about 300 KD. I can purify the complex by co-expression
them in E.coli.  This complex contains 8 protein A, 2 protein B and 1
protein C and D. protein B and protein C  have homology structures
deposited in PDB database. No homology structure available for protein A
and D, which contribute 60% of the whole molecular weight for the complex.

  Now I am trying to find a way to solve the phase of this complex. I
am thinking of use sad or mad with se-Met.   There total 111 Met
residues in this complex. Is it possible to solve this complex by se-Met?
Does someone have experience to solve huge complex structure with se-met?
It is also very welcome for all the suggestion. Thank you.

All the best,

Lisa

[ccp4bb] alternative conformation refinement by phenix

[LISA]

Hi all,

I am refining a DNA-protein complex structure by phenix.  My protein is a
nuclease and the DNA bound to protein is a mixture of the substrate and
product. Partial  DNA was cleavaged by the protein and others is keep a
un-cleavaged strand. I am trying to rerine this mixture with phenix.  My
DNA sequence is *AG*NN. Half of DNA was cleavaged between AG and
half DNA keep a uncleavaged strand as my sequence.  Nucleic acid AG have
two conformations in this structure and a water molecule located close to
the phosphate group when it uncleavaged. I defined AADE and BADE, AGUA and
BGUA with 0.5 occupancy. I also give the water mentioned above 0.5
occupancy. I try to refine this structure by phenix but failed. Please give
me some suggestion about this DNA alternative confromation refinement? How
should I define the occ.params file? Thank you in advance.

Lisa

[ccp4bb] phaser: high z score but no sol

[LISA]

Hi all,

I am trying to solve one structure by molecular replacement with phaser in
CCP4. This  a complex of a multi-domain domains with small ligand. I have
structues of this protein in apo state and with other similar ligand.  The
space group of this crystal is P21. This crystal should have 4 molecules in
ASU.  I used the full protein as model but did get any sol and LLG is below
zero. Then each domain were used as the search models in phaser with
rotation and tranlsation. I can the get high z score (20), and LLG is
raising. It looks like I get the right sol, but it  have more 50 clashes.
Why phaser give wrong sol with so high z socre? Can anyone give me some
suggestion to solve my strucutes? Thank you.
Best

Lisa

[ccp4bb] DNA in coot

[LISA]

Hi all,

I am refining a structue  of protein-DNA complex with coot. I add DNA by
adding ideal DNA/RNA in the other model. But I cannot edit chi angle of
these nucletide, neither the mutate.  When I press the mutate  and my DNA,
coot give amino acid not nucletide. Why?

Thanks

Lisa

[ccp4bb] DNA length for crystallization

[LISA]

Hi all,

I have a DNA binding protein. I can get crystals when I mix 8-28 nt dsDNA
with my protein. But neither of them has good diffraction. Some biochemical
data said the longer of DNA, the tigher of the binding betwwen DNA and my
protein. The binding is not sequence-specfic. Does anyone have suggestion
of the optimization? What is the good length of DNA for crystallization?
Thank you.

Lisa

[ccp4bb] low resolution of DNA binding protein

[LISA]

Hi all,

I have a DNA binding protein. I get crystals of this protein by
co-crystallization with different dsDNAs. But all the crystals have very
poor resolution, about 10-20A. I tried to purify protein-DNA complex before
setting trays, but it didn't work. Please give me some suggestion. Thanks.

lisa

[ccp4bb] how to improve resolution

[LISA]

Hi all,

I have a DNA binding protein. I get crystals of this protein by
co-crystallization with different dsDNAs. But all the crystals have very
poor resolution, about 10-20A. I tried to purify protein-DNA complex before
setting trays, but it didn't work.The shape of my crystal is not bad.
Please give me some suggestion. Thanks.

lisa

[ccp4bb] Beamline Scientist position available for macromolecular crystallography beamlines at NSLS-II

[Lisa Miller]

The Photon Sciences Directorate at Brookhaven National Laboratory is seeking an 
experienced scientist to lead the effort in the development of a pair of canted 
macromolecular crystallography beamlines at NSLS-II, which is a new 
third-generation synchrotron facility being constructed on Long Island, New 
York, with extremely high brightness and exceptional beam stability over a wide 
spectral range.  As the Group Leader, the selected candidate will lead a group 
of scientific and engineering staff to design, build, and commission a pair of 
state-of-the-art macromolecular crystallography beamlines, known as (1) the 
Frontier Macromolecular Crystallography (FMX) beamline and (2) the Highly 
Automated Beamline for Macromolecular Crystallography (AMX) beamline.  Please 
see http://www.bnl.gov/nsls2/beamlines/2010BeamlineProposal-Approved.asp for 
more information.  Responsibilities include interacting with the scientific 
user community to define the mission and technical scope of the beamline and 
managing all aspects of the beamline design, construction, and commissioning, 
including aspects associated with work planning and execution and cost and 
schedule performance reporting. 

For more information and to apply, go to: http://www.bnl.gov/HR/careers/

[ccp4bb] Beamline Scientist position available for small- and wide- angle x-ray scattering beamline at NSLS-II

[Lisa Miller]

The Photon Sciences Directorate at Brookhaven National Laboratory is seeking an 
experienced scientist to lead the effort in the development of a small- and 
wide-angle x-ray scattering (SAXS/WAXS) beamline at NSLS-II, which is a new 
third-generation synchrotron facility being constructed on Long Island, New 
York, with extremely high brightness and exceptional beam stability over a wide 
spectral range.  As the Group Leader, the selected candidate will lead a group 
of scientific and engineering staff to design, build, and commission a state of 
the art SAXS/WAXS beam line, known as High Brilliance X-ray Scattering for Life 
Sciences (LIX), and it’s associated scientific programs at NSLS-II; please see 
http://www.bnl.gov/nsls2/beamlines/2010BeamlineProposal-Approved.asp for more 
information.  Responsibilities include interacting with the scientific user 
community to define the mission and technical scope of the beamline and 
managing all aspects of the beamline design, construction, and commissioning, 
including aspects associated with work planning and execution and cost and 
schedule performance reporting. 

For more information and to apply, go to: http://www.bnl.gov/HR/careers/

[ccp4bb] gst-tag protein purify problem

[LISA]

hi guys,
I have a DNA binding protein and expressed the DNA binding domain (150
aa) with his-sumo tag or gst tag at the n-terminal. I tried to purified it
with Ni column or Gst column separately. But purity is lower than 50% after
Ni or GST column. This protein only stable with 1M Nacl or higher. I worked
on it almost half year. But I still can not get the pure protein.
please give me some suggestions. Thank you.

Lisa

[ccp4bb] how to install cns1.3 to mac (10.6) by fink

[LISA]

Hi all,
I installed fink 64 bit on my mac osx 10.6. I want to install cns by fink. I
found only cns 1.3 is suitable for osx 10.6. Can someone help me to install
this program? Thanks.
Lisa

[ccp4bb] coot command cannot be located in phenix

[LISA]

Hi all,
I installed phenix1.7 on my mac osx 10.6. But I cannot open coot in this
phenix.When I press coot, it said coot command cannot be located. How to
fix this problem? Thank.
Lisa

[ccp4bb] how to use mac to solve structures

[LISA]

Hi all,
 I just start to install crystallography software on my new mac. My os X
version is 10.6. Can some one show me how to install phenix, cns , ccp4 and
so on? Thank you.

Lisa

Re: [ccp4bb] how to use mac to solve structures

[LISA]

Thank you for responds. Dr. Scott asked to install xcode before install
fink. Does my new mac pro has xcode already? How to check it? I find xcode
3.25 is 3G on apple site. It is very big.

On Sat, Feb 5, 2011 at 1:37 PM, Jürgen Bosch jubo...@jhsph.edu wrote:

 Just google for crystallography on os x and you will find Bill Scott's
 excellent guide through the galaxy.
 Jürgen

 ..
 Jürgen Bosch
 Johns Hopkins Bloomberg School of Public Health
 Department of Biochemistry  Molecular Biology
 Johns Hopkins Malaria Research Institute
 615 North Wolfe Street, W8708
 Baltimore, MD 21205
 Phone: +1-410-614-4742
 Lab:  +1-410-614-4894
 Fax:  +1-410-955-3655
 http://web.mac.com/bosch_lab/

 On Feb 5, 2011, at 0:33, LISA science...@gmail.com wrote:

  Hi all,
   I just start to install crystallography software on my new mac. My os X
 version is 10.6. Can some one show me how to install phenix, cns , ccp4 and
 so on? Thank you.
 
  Lisa
 

[ccp4bb] how to refine RNA with two phosphate at 5' by phenix

[Lisa Wang]

hi all,
I have one structure contains dsRNA with two phosphate group at 5'.. I named
the first residue GDP and got a cif file by running phenix.elbow. Then I
refine my structure by running phenix.refine my.pdb my.cif. But the fist and
the second residue do not link with each other, that is no bond between O3*
of the fist residue and P of the second residue.
Please give me some idea. Thanks

[ccp4bb] molecular replacement in phaser

[Lisa Wang]

Hi all,
I got one data about 3.0 A, belong to C2 space group. There are two protein
molecules and one 18-nt dsRNA per ASU. The structure of  last 100aa
(C-terminal) has been reported, and 400 aa at N-terminalhe has homology
structure with sequence identiy 30%. I try to solve it by MR with phaser.
I did rotation and tranlation with 18-nt ideal dsRNA first, then search with
C-terminal model. I got about 20 sol after seaching dsRNA with TFZ 8-10.0. I
use all of them to serch the first c-terminal, and second C-terminal. Ding
this process,  LLG keep on increasing, and TFZ is higher than 10. But all
have serious clash. It looks like all the sol are wrong.

Please give me a hand.

Re: [ccp4bb] DNA binding protein

[Lisa Mathiasen]

You can run a few µl of your sample on a native gel or agarose gel and 
visualise co-purified DNA by ethidium bromide/gel red staining.

If your protein is stable at high salt concentrations (and a lot of DNA-binding 
proteins are) you can use a high salt concentration (like 1 M) in the lysis 
buffer.

Ion exchange is also a good way to get rid of DNA, in my experience.

Lisa 

[ccp4bb] Postdoctoral Research Scientist, Cambridge, UK.

[Lisa Baker]

Job Title
Postdoctoral Research Scientist
Description
Vernalis is a specialist bio-pharmaceutical company with a marketed
product, frovatriptan, several product candidates in clinical trials and
a research capability based on structure-based drug discovery
technologies.
We are seeking a macromolecular crystallographer with a keen interest in
fragment-based drug design and high-throughput crystallography. You'll
be part of a multi-disciplinary team that includes macro-molecular
biologists, NMR spectroscopists, medicinal chemists and computational
chemists. Your knowledge of crystallization, data collection, data
analysis, structure solution and structure validation will play a
pivotal role in the success of our drug-design efforts.
Find out more about us by visiting www.vernalis.com
http://www.vernalis.com/ . 
Duties
*   Participation in all in-house research programmes, including
presentation and publication of the results; 
*   Rapid data collection and structure solution of protein-ligand
complex structures; 
*   Assist in crystallisation trials;
*   Assist in the development of new technologies within the
company.
Education / Work Experience
*   PhD in relevant discipline; 
*   Demonstratable experience or knowledge of macromolecular
crystallography;
*   Experience with Windows/Linux/Unix and appropriate
crystallographic software suites;
*   Experience of data collection at synchrotrons;
*   Experience or knowledge in molecular biology and protein
crystallization; 
*   Experimental research experience; 
*   Must be available to travel occasionally within the UK and
abroad, including overnight stay.
Personal Qualities
*   Good problem solving; 
*   Good interpersonal, communication and presentational skills; 
*   Good organisational and planning skills;
*   Ability to interact effectively with staff at all levels; 
*   Ability to work as part of a multi-disciplinary team; 
*   Self motivation.
Post details
Full time, initial one year fixed term contract (maternity cover).
Start date
August 2009
Salary information
Negotiable, depending upon skills, qualifications and previous
experience. 
Location
Granta Park, Cambridge, UK.
Application deadline
Friday 8th May 2009
Application details
Applications should include a covering letter describing relevant
research experience to date, a CV, and the names and addresses of two
referees. These should be sent by email to h...@vernalis.com. Any informal
enquiries can be sent via email to l.ba...@vernalis.com. 
 
 

__
PLEASE READ: This email is confidential and may be privileged. It is intended 
for the named addressee(s) only and access to it by anyone else is 
unauthorised. If you are not an addressee, any disclosure or copying of the 
contents of this email or any action taken (or not taken) in reliance on it is 
unauthorised and may be unlawful. If you have received this email in error, 
please notify the sender or postmas...@vernalis.com. Email is not a secure 
method of communication and the Company cannot accept responsibility for the 
accuracy or completeness of this message or any attachment(s). Please check 
this email for virus infection for which the Company accepts no responsibility. 
If verification of this email is sought then please request a hard copy. Unless 
otherwise stated, any views or opinions presented are solely those of the 
author and do not represent those of the Company.

The Vernalis Group of Companies
Oakdene Court
613 Reading Road
Winnersh, Berkshire
RG41 5UA.
Tel: +44 118 977 3133

To access trading company registration and address details, please go to the 
Vernalis website at www.vernalis.com and click on the Company address and 
registration details link at the bottom of the page..
__

[ccp4bb] reifine metal with phenix

[Lisa Wang]

Hi all,
 The resolution of my structure is 3.1A. There are three Mg binds in this
structure. I try to refine it with phenix. There are cleare extrea density
before I add Mg atoms. But when I put Mg in the central of density with good
coordination and try to refine it by phenix, those Mg move away.Does phenix
need addiational paramters file to refine Mg and keedp it 2.1A   2.1A from
it coordinated atom?
 Thanks.
Lisa

[ccp4bb] Rwork and Rfree in Sfcheck

[Lisa Wang]

Hello all,
I have a complex structure  with resolution 2.7A The total molecular weight
is 80KD, and about 10% is disordered. I refined this structure to R and
Rfree 25.5% and 29.7% with CNS. I also tried refmac5, but the R and Rfree
have no difference with CNS. I use sfcheck of ccp4 to check this structure.
But sfcheck give the R-factor for all relections 29%. and Rfree 33%. Why
sfcheck and CNS give different  R and Rfree?
Which R and Rfree is true?
Best
Lisa

Re: [ccp4bb] problem on protein precipitation

[Lisa A Nagy]

Hi Lei,

 

Try this:

50-100 mM Arginine in your buffers. Or Glutamic Acid.  Or both.

 

--

Lisa A. Nagy, Ph.D.

University of Alabama-Birmingham

[EMAIL PROTECTED]

 

 

 

From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Zheng, Lei
Sent: Wednesday, January 23, 2008 10:51 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] problem on protein precipitation

 

Hi ccp4ers,

 

Sorry for this out-topic question:

Recently we have a membrane protein expressed, after solubilized with
detergent and purified from IMAC, the protein looks beautiful in SEC.
However, it completely precipitates after the 2-3 days storage in 4
degree. We supplement 2 mM DTT in the new elute from IMAC, the protein
looks happy during weeks at 4 degree. However, it starts to form an
invisible aggregate (verified from SEC) during the protein concentration
by Centricon. I know this is not uncommon problem for both soluble and
membrane proteins and wonder if anyone has any tip and experience to
overcome this problem.

The protein pI is 8.6, buffer used is pH 7.6. Glycerol is always present
during the purification. We do have high salt (500mM) in the buffer.

 

Thank you for you input in advance,

Lei

 

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot

[Lisa A Nagy]

Al's Oil on the plates:
What a nightmare!!!
The oil creeps up the plate and over the sides. It dissolves adhesives. 
It makes me say bad words in multiple languages. 
Bigger drops + no oil = fewer bad words.

Lisa
--
Lisa A. Nagy, Ph.D.
University of Alabama-Birmingham
[EMAIL PROTECTED]

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Patrick Shaw Stewart
Sent: Friday, January 18, 2008 2:20 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Fwd: [ccp4bb] crystallisation robot

One thing that people often overlook is that quite a lot of protein
can be lost by denaturation on the surface of the drop.  This is more
significant for smaller drops.  Two suggestions: (1) increase the
proportion of protein in the - technical term - teeny drop to say two
thirds and (2) cover the drops with oil eg Al's oils
(silicone/paraffin).  You still get vapor diffusion though the oil ,
and you'd like to slow up equilibration.  of course (2) slows up the
robotics a little, but both should be trivial to set up..

Re: [ccp4bb] crystallisation robot

[Lisa A Nagy]

You optimize that variable as well in scale-up.
That is the problem with nano-drop screening- sometimes it is near
impossible to scale up the drops. You have to re-screen around the
conditions (response surface methods can conserve experiments) because
the kinetics change so much between nano and big drops.

The smaller they are, the harder it is to scale up, so we compromise
between protein consumption and scalability. I think with most of these
machines, you _can_ tweak it to dispense in the 20-50nl range
accurately. To do that, you have to avoid using an air gap- either by
drawing (and diluting) your protein against a column of water, or by
using some other liquid (oil) between your protein and the dispensing
fluid. Many times these tiny drops yield crystals much faster because
they have more surface area to volume. But once you have them- well-
that's where I've pulled out my hair. Scale-up is hard, and for delicate
proteins (1% crystalline hits), near impossible from the 20 nl drops.
That's the main reason we use bigger drops. 

In the early stages of a project, there is often a great deal of batch
to batch variability in the protein samples. Minimizing this, and
getting consistent polydispersity measurements can go a long way toward
making scale-ups easier.
All this screening is for naught if you need to optimize using a second
batch of protein which behaves differently from the first, or if your
first/only batch is degraded by the time you have hits to optimize. If
you are fortunate to be producing your own protein, you can personally
make sure you are producing consistent batches. The worst thing you can
do is screen on the hearts, then optimize/scaleup with the tails (of the
protein peak in the purification). 

Personally, I think having a liquid handling robot is almost as
important as a crystallization robot.

Lisa

P.S. Confidential to various sales people:
1. If you had visited us, you would have known we were going to buy
another robot. 
2. If you had visited us, you would have known I was in the group.
3. If a member of our group didn't contact you and request information
for purchasing your fabulous robot based on your website/mailings/ads,
then your marketing people (not us) have the problem.
4. Sole source justification. Features and Price. 20K is a significant
difference, and we didn't need the extra features on your machine. Or we
needed features yours didn't have. 
5. Sending snarky email messages about me to my coworkers makes all of
us less inclined to view your company favorably for future purchases. 

--
Lisa A. Nagy, Ph.D.
University of Alabama-Birmingham
[EMAIL PROTECTED]



-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Oganesyan, Vaheh
Sent: Wednesday, January 16, 2008 9:06 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] crystallisation robot
...
Once in a while I get large crystal that can be used for data
collection, but in most of the cases optimization in hanging 1+1 uL
drops is required.
What I found quite difficult to do is to choose the appropriate protein
concentration when moving from 200+200nL to 1+1 uL. Sometimes protein
should be diluted 3-4 times, sometimes it shouldn't. How others are
approaching this issue?

Vaheh

Re: [ccp4bb] crystallization robot

[Lisa A Nagy]

I was wrong on the price- yes $300/per, but still, it was a lot of money
when we had catastrophic crash several years ago (due to something going
haywire- not a script or operator error). I know the nitonol tips are
not fool-proof- they just seem a bit more forgiving than the ceramic
tips. 

 

As far as the length of time plates are on the deck, we have always used
humidity chambers. We build them out of lexan. Also, though 100 nl can
be dispensed accurately, we prefer to spend the protein and go for
larger drops, since it is really nice to be able to harvest from the
drop. Our home-built robot can dispense 20nl accurately (although it
uses a lot of recoverable protein to do it)- and while pretty crystals
form, you can't do much with them. We typically dispense larger drops on
that machine as well. 

 

--
Lisa Nagy
University of Alabama-Birmingham
[EMAIL PROTECTED]

Re: [ccp4bb] crystallization robot

[Lisa A Nagy]

We chose the Phoenix crystallization robot because:

It has no expensive consumables (tips) intrinsic to the machine. This
was also a big item for us because we worry about being able to run the
machine for more than 3 years. Would the tips for our 2008 machine be
available in 2014? 

It is easy to program (BIG ITEM) for different tray configurations, and
various dispensing methods- even on the same tray. Right now you may not
think you'll have to vary drop sizes or add additional components
(ligand? detergent?) to your drops, but you probably will.

It can draw from 2ml block plates. Reformatting from block plates to
your trays is a pain.

The nitinol tips won't break (Compared to ~$700 apiece for the
incredibly breakable ceramic tips on some other machines).

It has cooling blocks for your samples. This is more important than you
think.

It's fast.

It is easily integrated into a fully automated lab system. Right now,
though, our humans (including me) are cheaper than rails and robots.

It's incredibly accurate, even with 30% PEG 4000 (we tested this
ourselves). 

You can use it for other low volume dispensing applications.


--
Lisa Nagy
University of Alabama-Birmingham
[EMAIL PROTECTED]  

Re: [ccp4bb] crystallization robot

[Lisa A Nagy]

The phoenix can dispense multiple drops per well. You can easily
program dispensing on the deck wherever, whatever and whenever, as long
as it fits in the plate holder . It can handle at least the 1536 pitch
(4 x 384), so if you specify the quadrant of the 384 well cell it will
dispense there. Your drops may merge, though. It has a separate
dispensing head for proteins or additives. You can dispense from up to
16 protein tubes (chilled) and 2 ambient tubes, plus whatever is on
the deck, in whatever order you want. Since the setup programming is an
easy gui, it's not a big deal.

 

I am certain that the mosquito sheets would work on any robot. 

 

From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Van Den Berg, Bert
Sent: Wednesday, January 09, 2008 11:00 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] crystallization robot

 

The mosquito has special (albeit fairly pricey at $13 each) plastic
sheets that allow setup of hanging drops in a 96-well format. It can
also do multiple drops per well. As far as I know this is a capability
unique to the Mosquito but I may be wrong.

 

Bert van den Berg
University of Massachusetts Medical School
Program in Molecular Medicine
Biotech II, 373 Plantation Street, Suite 115
Worcester MA 01605
Phone: 508 856 1201 (office); 508 856 1211 (lab)
e-mail: [EMAIL PROTECTED]
http://www.umassmed.edu/pmm/faculty/vandenberg.cfm

 



From: CCP4 bulletin board on behalf of Lisa A Nagy
Sent: Wed 1/9/2008 11:53 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] crystallization robot

Looking at the mosquito, it doesn't have any cover-slip handling
robotics, either. So it's the same thing- rearrange the dispense
location and flip the cover- which is either a glass plate or mylar or
a tape seal.

--
Lisa Nagy
University of Alabama-Birmingham
[EMAIL PROTECTED] 

Re: [ccp4bb] crystal with precipitation

[Lisa A Nagy]

Oh, there is do much you can do!
Lots of alternatives:
1. Decrease or increase the protein concentration (with a corresponding
increase or decrease of precipitant.
2. Use a temperature gradient.
3. Set up in a capillary with liquid-liquid diffusion 
4. SEED!

#3 or #4 are your best bets, probably. 

For the capillaries, using Hamilton syringes:
Pipet 20 ul protein in a 50 ul capillary. Ease it away from the end.
When you are done, make sure you can reach the liquid with the syringe
from the other side. 
Hold your finger on one end. Seal the other end with sticky wax
Layer 5 ul water on top.
Carefully layer the precipitant (10-30 ul) on top of the water.
You might want to use a 4mM glass capillary mounted on a syringe,
instead of Hamiltons.
Seal the other end. 
Wait 3 days. 
Then look.

Naturally, you can scale this down using 20 ul capillaries, or even
smaller X ray capillaries. 
But then you can't use syringes to load them, use smaller capillaries. 
On the upside, you could shoot directly from the experiment.

This has worked well for me.

Lisa

-Original Message-
From: CCP4 bulletin board on behalf of shivesh kumar
Sent: Wed 8/22/2007 3:22 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] crystal with precipitation
 
Dear all
I am trying to crystallize a 7kDa protein using MPD as a precipitant at
16C.I have got small florets at 55-65% of MPD in 3-4 days.The problem is
that the drop is precipitating in one day only and the crystals are
coming
with precipitation.I have added 5% glycerol and 100mM of Nacl as an
additive
with the mother liquor to avoid precipitation.But,the precipitation is
still
there.The volume of the mother liquor is 500 microlt.The drop size is
2+2.I
welcome all the suggestions regarding avoiding the precipitation.Thanx
is
advance.
Shivesh kumar

Re: [ccp4bb] The importance of USING our validation tools

[Lisa A Nagy]

Dear all,
I agree with MM about the ligand and complex structures. Even in the
most honest circumstances, it is easy to get carried away with hopes and
excitement. My personal embarassing experience was some years ago. It
involved a protein that I had crystallized in a different space group in
the presence of inhibitor- 2.5A data. The MR model had some gaps a
moderate distance from the binding pocket. Lo and behold, some new, very
rough  density appeared very very close to a binding site- close enough
to get my hopes up. I communicated my elation to the PI, handed over
pictures of the rough blobs of density, and started trying to build the
ligand in. 

I should have moderated my emotions in light of the early state of the
refinement. After finding a somewhat plausible fit in the density, I ran
several rounds of the Wonderful Amazing Revealer of Proteindensity
program. By the end I was almost in tears. The difference density began
to take on a helical shape, and then the connections started growing,
leading all the way up to one of the gaps. Side chains too, so I had no
trouble with the register. The R-factors didn't change too much, but the
geometries and maps in the area started looking really nice. Or should I
say, proper.

Very nice silver platter (that my head was on when it was handed it back
to me).

Lisa