t 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...@sl
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
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
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
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
**
Elec
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
s/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 Pa
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
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
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
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.
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.
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
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 - Collabo
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
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
t;, 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...@sl
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.sta
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
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
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.
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.
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
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
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.buffal
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
://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>
To unsubscrib
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.
you.
Best Regards,
Lisa
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
.
Best Regards,
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.
in the new version phaser
?
Thank you.
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
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
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
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
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
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
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
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
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
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
the best
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
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
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
Hi all,
does anyone solve their structure by molecular replacement with phaser
with LLG 0?
Thanks
lisa
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
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
.
Why phaser give wrong sol with so high z socre? Can anyone give me some
suggestion to solve my strucutes? Thank you.
Best
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
suggestion
of the optimization? What is the good length of DNA for crystallization?
Thank you.
Lisa
.
lisa
give me some suggestion. Thanks.
lisa
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
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
. I worked
on it almost half year. But I still can not get the pure protein.
please give me some suggestions. Thank you.
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
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
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
, 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
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
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.
buffer.
Ion exchange is also a good way to get rid of DNA, in my experience.
Lisa
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
away.Does phenix
need addiational paramters file to refine Mg and keedp it 2.1A 2.1A from
it coordinated atom?
Thanks.
Lisa
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
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
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
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
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]
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
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
.
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
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
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