[ccp4bb] Beam time available now at MacCHESS

[Doletha Marian Szebenyi]

From: Doletha Marian Szebenyi 
Sent: Wednesday, April 14, 2021 10:12 AM
To: ccp4bb@jiscmail.ac.uk 
Subject: Beam time available now at MacCHESS


Rapid access beam time for macromolecular crystallography is available now at:
[cid:324d0976-5c56-4ddf-884f-4ec63b50ac92]
Features include:

  *   EIGER2 16M detector
  *   Automounter accepting MSC pucks, Unipucks, Rigaku pucks (loaner kit with 
MSC pucks available)
  *   100 µ standard beam or 15 µ minibeam (focused with CRL)
  *   Full 24-hr support for remote or in-person operation
  *   Cryo or room-temperature data collection
  *   High-pressure cryocooling option to improve diffraction quality or trap 
gases
  *   Serial crystallography option (fixed-target)
  *   High-pressure data collection in diamond anvil cell

Visit the CHESS User Portal<https://userdb.chess.cornell.edu> to request beam 
time. For more information, visit our web 
site<https://www.chess.cornell.edu/macchess> or contact me (dm...@cornell.edu).

Marian Szebenyi
Director, MacCHESS



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[ccp4bb] Staff scientist position at CHESS

[Doletha Marian Szebenyi]

We are still accepting applications for the staff scientist position described 
below. Here's a chance to work at a beamline that specializes in non-standard 
experiments, and to contribute to deciding what direction development at 
MacCHESS will take over the next few years.

Staff Scientist position at MacCHESS

The Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron 
Source (MacCHESS) has an opening for a Staff Scientist (Research Associate) to 
run the Flexible Crystallography (FlexX) station. Duties include both support 
of users performing routine macromolecular crystallography (MX) and development 
of novel techniques in X-ray scattering as applied to structural
biology. User support includes continuing developments to maintain a 
state-of-the-art facility. Novel techniques are developed in collaboration with 
scientists who need capabilities beyond the current standard methods. Areas of 
particular interest are crystallography at (1) ambient temperature, including 
serial techniques, and (2) high pressure, in a diamond anvil cell (DAC) or 
using the high pressure cryocooling technique, especially for the trapping of 
intermediate states of reactions in crystallo.

Applicants should have a Ph.D. in a relevant field (biophysics, structural 
biology etc.), and at least 3 years of experience beyond the degree.
Preference will be given to those with experience with methods related to X-ray 
scattering experiments, and to those who have worked at a synchrotron facility. 
Good clear communication skills are a must, including fluency in the English
language.

Appointments are nominally for three years and are renewable, contingent upon 
availability of funds and employee performance.

Located on an Ivy League university campus in picturesque upstate New York, the 
Cornell High-Energy Synchrotron Source (CHESS) serves a world-wide user base of 
structural biologists, chemists, physicists, and engineers. MacCHESS is an 
NIH-supported National Resource providing support for structural biology at 
CHESS.

Applications should be submitted at http://academicjobsonline.org/ (posting 
#20601) and should include a cover letter, a CV, a list of
publications, and a detailed summary of research experience and interests. 
Please arrange to have at least three letters of recommendation sent, as per 
instructions on the academicjobsonline website. The starting date is negotiable.
For more information about the position, see 
https://www.chess.cornell.edu/macchess-staff-scientist.

Cornell University requires all employees to be fully vaccinated against 
COVID-19, or to have obtained a university-approved medical or religious
exemption.

Diversity and Inclusion are a part of Cornell University’s heritage. We’re a 
recognized employer and educator valuing AA/EEO, Protected Veterans, and 
Individuals with Disabilities.



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[ccp4bb] Director of MacCHESS facility

[Doletha Marian Szebenyi]

The Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron 
Source (MacCHESS)is seeking a Director. MacCHESS is a component of CHESS, a 
recently-upgraded synchrotron source serving a wide variety of researchers with 
X-ray science needs, jointly funded by NIH, NSF, and DOD, with assistance from 
New York State. MacCHESS provides a facility where scientists can use both 
established and emerging technologies to pursue the goals of the biomedical 
research community. Work performed at MacCHESS, using tools including, e.g., 
crystallography and small-angle X-ray scattering, yields important insights 
into fundamental biological processes. The MacCHESS Director will play a key 
role, alongside the MacCHESS PI and other members of the CHESS leadership team, 
in the management of the CHESS facility to promote scientific research.

The primary functions of the MacCHESS Director are (1) to ensure smooth 
operation of the facility (personnel management, budgeting, upgrades), (2) to
act as Co-PI on the NIH grant (preparing reports, renewal applications, etc.), 
and (3) to participate in collaborative scientific developments at MacCHESS.

Applicants should have a Ph.D. in a relevant field (biophysics, structural 
biology etc.), and experience managing a group of mixed personnel (scientific,
technical, administrative. Experience with managing grants (writing 
applications, preparing reports, etc.) from federal agencies is highly 
desirable. Experience at a user facility is a plus, as is expertise in methods 
related to X-ray science. Good clear communication skills are a must, including 
fluency in the English language.

Located on an Ivy League university campus in picturesque upstate New York, the 
Cornell High-Energy Synchrotron Source (CHESS) serves a world-wide user base of 
structural biologists, chemists, physicists, and engineers. MacCHESS is an 
NIH-supported National Resource providing support for structural biology at 
CHESS.

Applications should be submitted at http://academicjobsonline.org/ (posting 
#20602) and should include a cover letter, a CV, a list of publications, and a 
detailed summary of research experience and interests. Please arrange to have 
at least three letters of recommendation sent, as per instructions on the 
academicjobsonline website. The starting date is negotiable. For more 
information about the position, see 
https://www.chess.cornell.edu/macchess-program-director-senior-research-associate.

Cornell University requires all employees, to be fully vaccinated against 
COVID-19, or to have obtained a university-approved medical or religious 
exemption.

Diversity and Inclusion are a part of Cornell University’s heritage. We’re a 
recognized employer and educator valuing AA/EEO, Protected Veterans, and 
Individuals with Disabilities.



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[ccp4bb] Beamline Scientist position at MacCHESS

[Doletha Marian Szebenyi]

The Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron 
Source (MacCHESS) has an opening for a Staff Scientist (Research Associate) to 
run the Flexible Crystallography (FlexX) station. Duties include both support 
of users performing routine macromolecular crystallography (MX) and development 
of novel techniques in X-ray scattering as applied to structural biology. User 
support includes continuing developments to maintain a
state-of-the-art facility. Novel techniques are developed in collaboration with 
scientists who need capabilities beyond the current standard methods. Areas of 
particular interest are crystallography at (1) ambient temperature, including 
serial techniques, and (2) high pressure, in a diamond anvil cell (DAC) or
using the high pressure cryocooling technique, especially for the trapping of 
intermediate states of reactions in crystallo.

Applicants should have a Ph.D. in a relevant field (biophysics, structural 
biology etc.), and at least 3 years of experience beyond the degree. Preference 
will be given to those with experience with methods related to X-ray scattering 
experiments, and to those who have worked at a synchrotron facility. Good clear 
communication skills are a must, including fluency in the English language.

Appointments are nominally for three years and are renewable, contingent upon 
availability of funds and employee performance.

Located on an Ivy League university campus in picturesque upstate New York, the 
Cornell High-Energy Synchrotron Source (CHESS) serves a world-wide user base of 
structural biologists, chemists, physicists, and engineers. MacCHESS is an 
NIH-supported National Resource providing support for structural biology at 
CHESS.

Applications should be submitted at http://academicjobsonline.org/ (posting 
#20601) and should include a cover letter, a CV, a list of
publications, and a detailed summary of research experience and interests. 
Please arrange to have at least three letters of recommendation sent, as per
instructions on the academicjobsonline website. The starting date is 
negotiable. For more information about the position, see
https://www.chess.cornell.edu/macchess-staff-scientist.

Cornell University requires all employees, to be fully vaccinated against 
COVID-19, or to have obtained a university-approved medical or religious
exemption.

Diversity and Inclusion are a part of Cornell University’s heritage. We’re a 
recognized employer and educator valuing AA/EEO, Protected Veterans, and
Individuals with Disabilities.



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[ccp4bb] Beam time available now at MacCHESS

[Doletha Marian Szebenyi]

Rapid access beam time for macromolecular crystallography is available now at:
[cid:324d0976-5c56-4ddf-884f-4ec63b50ac92]
Features include:

  *   Recently upgraded 3rd-generation synchrotron source, CHESS-U
  *   EIGER2 16M detector
  *   Automounter accepting MSC pucks, Unipucks, Rigaku pucks (loaner kit with 
MSC pucks available)
  *   100 µ standard beam or 15 µ minibeam (focused with CRL)
  *   Remote operation using NoMachine
  *   24-hr support
  *   Cryo or room-temperature data collection
  *   High-pressure cryocooling option to improve diffraction quality
  *   Serial crystallography option (fixed-target)
  *   High-pressure data collection in diamond anvil cell under development - 
talk to us about it!

Visit the CHESS User Portal<https://userdb.chess.cornell.edu> to request beam 
time. For more information, visit our web 
site<https://www.chess.cornell.edu/macchess> or contact myself 
(dm...@cornell.edu) or Beamline Scientist Aaron Finke (af...@cornell.edu).

Marian Szebenyi
Director, MacCHESS



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[ccp4bb] Postdoc position at CHESS

[Doletha Marian Szebenyi]

The Macromolecular Diffraction and High Pressure Biology resources at the
Cornell High Energy Synchrotron Source (MacCHESS and CHEXS/HP-Bio, respectively)
have an opening for a Postdoctoral Associate to develop applications of high
pressure to answer biological questions concerning enzyme mechanisms, protein
folding, adaptation to extreme environments, and the origin of life. The
primary method to be used is pressurization of macromolecular crystals in a
diamond anvil cell (HP-MX), but other techniques such as high-pressure small
angle X-ray scattering (HP-SAXS) will also be available. A Ph.D. degree in a
relevant field (e.g. structural biology or biophysics) is required.
Experience in crystallography is highly desirable, and experience working with
samples in "non-standard" environments is a plus. The ability to identify
suitable systems for study, through researching previous work and establishing
suitable collaborations, is essential. In addition to pursuing his/her own study
of pressure effects, the successful candidate will be expected to assist
research groups seeking to use high-pressure techniques at CHESS for their work.
Good clear communication skills are a must, including fluency in the English
language. Appointments are for one year at a time and are renewable for
additional years, contingent upon availability of funds and employee
performance.

Located on an Ivy League university campus in picturesque upstate New York,
the Cornell High-Energy Synchrotron Source (CHESS) serves a world-wide user
base of structural biologists, chemists, physicists, and engineers.
MacCHESS is an NIH-supported National Resource providing support for structural
biology at CHESS, and CHEXS is an NSF-supported facility incorporating several
projects, including high-pressure biology.

Applications should be submitted at http://academicjobsonline.org/
(posting #18189) and should include a cover letter, a CV, a list of
publications, and a detailed summary of research experience and interests.
Please arrange to have at least three letters of recommendation sent, as per
instructions on the academicjobsonline website. The starting date is negotiable.
For more information about the position, contact Dr. Marian Szebenyi at
dm...@cornell.edu.

Diversity and Inclusion are a part of Cornell University’s heritage. We’re a
recognized employer and educator valuing AA/EEO, Protected Veterans, and
Individuals with Disabilities.




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[ccp4bb] Beam time available at upgraded MacCHESS

[D. Marian Szebenyi]

Got crystals to check out? The Fall 2019 run at CHESS begins October 16, and 
it's not too late to apply for time. Proposals are accepted any time for beam 
time at the newly upgraded MacCHESS beamlines:


BioSAXS station (formerly G1) - on-site or mail-in BioSAXS, featuring:
* 7-14 KeV, standard beam size 250x200 micron, smaller beam available. In 
commissioning experiment with 50 mA particle beam, 14 KeV X-rays, got 1.4E11 
ph/s through 80x80 micron aperture
* SAXS/WAXS, loading from multiwell trays or effluent from column 
(size-exclusion, ion-exchange, high pressure)

* in-line DLS/MALS
* high-pressure cell
* microfluidic cell for time-resolved experiments
* user-friendly, flexible, experimental control system
* RAW data processing system
* excellent staff support
* coming in November, in-vacuum EIGER 4M detector

FlexX station - on-site or remote macromolecular crystallography, featuring:
* 7-14 KeV, undulator source with multilayer monochromator for high flux. In 
commissioning, with 50 mA particle beam, measured 2E11 ph/s through 100x100 
micron aperture

* single-axis goniostat, PILATUS3 6M detector, BAM2 automounter
* standard crystallography available at start-up, fixed-target serial 
crystallography in early 2020

* high pressure cryocooling available
* data collection at high pressure using a diamond anvil cell under development
* excellent staff support
* we welcome "non-standard" experiments!

Visit http://www.chess.cornell.edu for more information.



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[ccp4bb] Beamtime at upgraded CHESS

[D. Marian Szebenyi]

Having completed a major upgrade, CHESS (Cornell High Energy Synchrotron Source) 
is accepting proposals for beamtime. Of most interest to this community:


BioSAXS station (formerly G1) - on-site or mail-in BioSAXS, featuring:
* 7-14 KeV, standard beam size 250x200 micron, smaller beam available. In 
commissioning experiment with 50 mA particle beam, 14 KeV X-rays, got 1.4E11 
ph/s through 80x80 micron aperture
* SAXS/WAXS, loading from multiwell trays or effluent from column 
(size-exclusion, ion-exchange, high pressure)

* in-line DLS/MALS
* high-pressure cell
* microfluidic cell for time-resolved experiments
* user-friendly, flexible, experimental control system
* RAW data processing system
* excellent staff support
* coming soon, in-vacuum EIGER 4M detector

FlexX station - on-site or remote macromolecular crystallography, featuring:
* 7-14 KeV, undulator source with multilayer monochromator for high flux. In 
commissioning, with 50 mA particle beam, measured 2E11 ph/s through 100x100 
micron aperture

* single-axis goniostat, PILATUS3 6M detector, BAM2 automounter
* standard crystallography available when CHESS comes up in October, 
fixed-target serial crystallography in early 2020

* high pressure cryocooling available
* data collection at high pressure using a diamond anvil cell under development
* excellent staff support
* we welcome "non-standard" experiments!

Visit http://www.chess.cornell.edu for more information.



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[ccp4bb] Proteins under Pressure at CHESS Users' Meeting

[D. Marian Szebenyi]

The annual CHESS Users' Meeting will be held June 4-5, 2019 at Cornell, Ithaca, 
NY. CHESS has just completed a major upgrade to its storage ring and beamlines; 
the meeting will be a great place to find out about the new opportunities for 
science created by CHESS-U, and see the new facilities.


There will be two workshops at the meeting; of particular interest to this 
audience is one on Biomolecules Under Pressure. Speakers will introduce 
high-pressure bioscience as it relates to molecular biophysics, the evolution of 
life, food science and the instrumentation required to perform high-pressure 
biological experiments, primarily using crystallography and SAXS. The workshop 
will include a short overview of data acquisition at the CHESS BioSAXS station.


For more information, and to register, visit 
https://www.chess.cornell.edu/users/2019-chess-users-meeting




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[ccp4bb] Beam time available (soon!) at CHESS

[D. Marian Szebenyi]

Beamtime available at CHESS, Feb. 7 - June 4, 2018


The CHESS/MacCHESS facility, located at Cornell University in Ithaca, NY,
invites macromolecular crystallographers and users of BioSAXS to apply for time
on one or more of our stations:

F1 station, monochromatic wiggler source, suitable for crystallographic data
collection, at an energy appropriate for Se SAD phasing. Equipped with Dectris
Pilatus 6M detector and ALS-type automounter.

G1 station, undulator source with multilayer optics, suitable for BioSAXS
experiments, equipped with dual Pilatus 100-K detectors, automated
sample-handling, in-line SEC-SAXS capability; good data can be obtained over
q-range 0.006 - 0.7 (1/Å).

For 1 week only - G3 station, undulator source with multilayer optics, equipped 
for crystallography, with Pilatus 6M detector (no automounter for this test 
run). The hottest beam at CHESS!


= Special options ==

Pressure cryocooling of (unfrozen) crystals is available by prearrangement.
This method can reduce the damage induced by cryocooling, often with no need
for cryoprotectants (Kim et al., Acta Cryst. D61, 881-890 (2005)). In some
cases, it can reduce initial disorder (high mosaicity, anisotropic diffraction,
some kinds of twinning). Contact Marian Szebenyi (dm...@cornell.edu) for more
information on pressure cryocooling.

High-pressure and time-resolved BioSAXS techniques are under development and
are available on a collaborative basis. Contact Richard Gillilan
(r...@cornell.edu) if you are interested in cutting-edge BioSAXS work.

===  Support ===

CHESS/MacCHESS provides a high level of support for all users. We are
very willing to help with non-standard experimental setups - just ask.
Our staff scientists also invite collaborations for more extended
projects investigating novel techniques.

Remote data collection is available, as well as mail-in service.

 Applying for time 

Apply on-line at http://userdb.chess.cornell.edu. Applications are accepted
at any time, but early submission assures that we will have time to fully 
evaluate your proposal (especially if you have any special needs).


More information is available at the web site http://www.chess.cornell.edu, or
contact administrator Kathy Dedrick, k...@cornell.edu.

[ccp4bb] Beam time available at CHESS

[Doletha Marian Szebenyi]

Beamtime for MX still available at CHESS, Nov. 1 - Dec. 21, 2017


The CHESS/MacCHESS facility, located at Cornell University in Ithaca, NY, 
invites macromolecular crystallographers to apply for time on our F1 station.

This station is well equipped for crystallographic data collection, for MR or 
Se SAD phasing. It features a Dectris Pilatus3 6M detector and an ALS-type 
automounter. We offer remote and mail-in modes of data collection, and our 
expert staff provides exceptional support 24/7. "Non-standard" experiments 
needing some special setup are welcome.

Apply for time on-line at http://userdb.chess.cornell.edu. Applications are 
accepted at any time, and turn-around time can be just a couple of weeks - less 
if you already have a proposal in our system and just need to submit a beamtime 
request.

For more information see the web site http://www.chess.cornell.edu, or contact 
administrator Kathy Dedrick, k...@cornell.edu.

= A special option ==

Pressure cryocooling of (unfrozen) crystals is available by prearrangement. 
This method can reduce the damage induced by cryocooling, often with no need 
for cryoprotectants (Kim et al., Acta Cryst. D61, 881-890 (2005)). In some 
cases, it can reduce initial disorder (high mosaicity, anisotropic diffraction, 
some kinds of twinning). Contact Marian Szebenyi (dm...@cornell.edu) if you 
have questions about pressure cryocooling.

[ccp4bb] Beam time at CHESS

[Marian Szebenyi]

Beamtime available at CHESS, Nov. 1 - Dec. 21, 2017


The CHESS/MacCHESS facility, located at Cornell University in Ithaca, NY,
invites macromolecular crystallographers and users of BioSAXS to apply for time
on one or more of our stations:

F1 station, monochromatic wiggler source, suitable for crystallographic data
collection, at an energy appropriate for Se SAD phasing. Equipped with Dectris
Pilatus 6M detector and ALS-type automounter.

G1 station, undulator source with multilayer optics, suitable for BioSAXS
experiments, equipped with dual Pilatus 100-K detectors, automated
sample-handling, in-line SEC-SAXS capability; good data can be obtained over
q-range 0.006 - 0.7 (1/Å) .

A1 station, monochromatic undulator source, suitable for crystal screening and
native crystallographic data collection, with ADSC Q-210 detector.

= Special options ==

Pressure cryocooling of (unfrozen) crystals is available by prearrangement.
This method can reduce the damage induced by cryocooling, often with no need
for cryoprotectants (Kim et al., Acta Cryst. D61, 881-890 (2005)). In some
cases, it can reduce initial disorder (high mosaicity, anisotropic diffraction,
some kinds of twinning). Contact Marian Szebenyi (dm...@cornell.edu) for more
information on pressure cryocooling.

High-pressure and time-resolved BioSAXS techniques are under development and
are available on a collaborative basis. Contact Richard Gillilan
(r...@cornell.edu) if you are interested in cutting-edge BioSAXS work.

===  Support ===

CHESS/MacCHESS provides a high level of support for all users. We are
very willing to help with non-standard experimental setups - just ask.
Our staff scientists also invite collaborations for more extended
projects investigating novel techniques.

Remote data collection is available, as well as mail-in service.

 Applying for time 

Apply on-line at http://userdb.chess.cornell.edu. Applications are accepted
at any time, but to ensure that there is time for full consideration of your
proposal (especially if you have any special needs), please submit by
September 1 for the upcoming run.

More information is available at the web site http://www.chess.cornell.edu, or
contact administrator Kathy Dedrick, k...@cornell.edu.

[ccp4bb] Post-doc at MacCHESS in BioSAXS

[Marian Szebenyi]

The Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron
Source (MacCHESS) has an opening for a Postdoctoral Associate. Applicants
should have a Ph.D. degree in a relevant field (physics, engineering,
structural biology etc.). Preference will be given to those with experience in
x-ray solution scattering on biological systems (SAXS and WAXS). Activities
will focus on developing cryogenic BioSAXS technology and implementing
time-resolved BioSAXS. Projects may also involve developing novel microfluidic
lab-on-a-chip methods, applying state-of-the art algorithms to data (especially
as relating to mixtures of oligomers and time-resolved data) and automating
data processing at the beamline. Size exclusion chromatography (SEC),
multiangle and dynamic light scattering (MALS/DLS) experience is desirable,
 as is engineering experience developing hardware and software (incluing
nanofabrication). Software development will be done primarily in Python. While
MacCHESS postdocs are not required to do general beamline user support, they
will be expected to help with the annual BioSAXS Essentials training course and
to work closely with beamline users with whom they are collaborating. Good
clear communication skills are a must, including fluency in the English
language. Appointments are for one year at a time and are renewable for
additional years, contingent upon availability of funds and employee
performance.

Located on an Ivy League university campus in picturesque upstate New York,
the Cornell High-Energy Synchrotron Source (CHESS) serves a world-wide user
base of structural biologists, chemists, physicists, and engineers.
MacCHESS is an NIH-supported National Resource providing support for structural
biology at CHESS. MacCHESS is a heavily team-oriented environment.

Applications should be submitted at http://academicjobsonline.org/
(posting #5329) and should include a cover letter, a CV, a list of publications,
and a detailed summary of research experience and interests. Please arrange to
have at least three letters of recommendation sent, as per instructions on the
academicjobsonline website. The starting date is negotiable. For more
information about the position, contact Dr. Marian Szebenyi at
dm...@cornell.edu.

Diversity and Inclusion are a part of Cornell University’s heritage. We’re a
recognized employer and educator valuing AA/EEO, Protected Veterans, and
Individuals with Disabilities.

[ccp4bb] Beam time at CHESS

[Marian Szebenyi]

==
Beamtime available at CHESS, February 19 - April 1, 2014
==

The CHESS/MacCHESS facility, located at Cornell University in Ithaca, NY, 
invites macromolecular crystallographers and users of BioSAXS to apply for time 
on one or more of our stations:


A1 station, monochromatic wiggler source, suitable for Se SAD experiments as 
well as native data collection, with ADSC Q-210 detector and ALS-type automounter.


F1 station, monochromatic wiggler source, suitable for Br SAD or native data, 
with ADSC Q-270 detector and ALS-type automounter.


G1 station, wiggler source with multilayer optics, suitable for BioSAXS 
experiments, equipped with dual Pilatus 100-K detectors, automated 
sample-handling, in-line SEC-SAXS capability; good data can be obtained over 
q-range 0.006 - 0.7 (1/Å) .


F3 station, bending magnet source with multilayer optics, tunable from
5.9 - 15.4 keV, suitable for SAD experiments using Fe, Co, etc., with
ADSC Q-4u detector.

= Special options ==

Pressure-cryocooling of (unfrozen) crystals is available by
prearrangement. This method can reduce the damage induced by
cryocooling, often with no need for cryoprotectants (Kim et al., Acta
Cryst. D61, 881-890 (2005)).

Microbeam (down to about 5 microns) using focusing capillary optics is
available on request at any of the stations.

===  Support ===

CHESS/MacCHESS provides a high level of support for all users. We are
very willing to help with non-standard experimental setups - just ask.
Our staff scientists also invite collaborations for more extended
projects investigating novel techniques.

Mail-in service is available  - we will be pleased to collect (and
process, if you like) data from crystals that you send to us. Remote data 
collection is available for experienced users.


 Applying for time 

Visit http://www.chess.cornell.edu and look at Beam Time under the
Users menu. All applications can be done on line, any time. Processing
of proposals is rapid, with a turn-around time of just a couple of weeks
for the usual Express Mode option.

More information is available on the web site, or contact administrator
Kathy Dedrick, k...@cornell.edu.

[ccp4bb] Post-doc opening at MacCHESS

[Marian Szebenyi]

Postdoctoral Associate: Applications of Pressure to Structural Biology

The Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron 
Source (MacCHESS) has an opening for a post-doctoral associate to continue 
development of the pressure cryocooling method (Kim et al. Acta Cryst. D61, 
881-890 (2005), Kim et al. J. Appl. Crystallog. 46, 234-241 (2013)) and to apply 
pressure cryocooling to areas such as trapping of intermediates in biochemical 
reactions, preparation of samples for diffraction and imaging experiments, and 
elucidation of the effects of pressure on macromolecular structure. Applicants 
should have a Ph.D. degree in structural biology, biophysics, or a related 
field. Experience in hands-on development of sample-handling methods is 
desirable, and experience working at a synchrotron source is a plus. In addition 
to pursuing his/her own study of pressure effects, the successful candidate will 
be expected to collaborate with research groups wishing to apply pressure 
cryocooling to their samples.


The Cornell High-Energy Synchrotron Source (CHESS) serves a world-wide user base 
of structural biologists, chemists, physicists, and engineers. MacCHESS is an 
NIH-supported National Resource providing support for structural biology at 
CHESS. MacCHESS is a heavily team-oriented environment. Good clear communication 
skills are a must, including fluency in the English language. This position is 
renewable for up to 3 years total, contingent upon availability of funds and 
employee performance.


Direct inquiries and applications (include cover letter, CV including 
publications, and detailed summary of research experience and interests, and 
arrange to have at least three letters of reference sent) to:


Dr. Marian Szebenyi
CHESS, 200L Wilson Lab
Cornell University
Ithaca, NY 14853
E-mail: dm...@cornell.edu

Applications must be received by March 31, 2014. Starting date is negotiable.
Cornell is an equal opportunity employer.

[ccp4bb] Beam time at CHESS

[Marian Szebenyi]

==
Beamtime available at CHESS, October 16 - December 13, 2013
==

The CHESS/MacCHESS facility, located at Cornell University in Ithaca,
NY, invites macromolecular crystallographers and users of BioSAXS to
apply for time on one or more of our stations:

A1 station, monochromatic wiggler source, suitable for Se SAD
experiments as well as native data collection, with ADSC Q-210 detector.

F1 station, monochromatic wiggler source, suitable for Br SAD or native
data, with ADSC Q-270 detector and ALS-type automounter.

G1 station, wiggler source with multilayer optics, for BioSAXS experiments;
dual Pilatus 100-K detectors to record SAXS and WAXS data.

= Special options ==

Pressure-cryocooling of (unfrozen) crystals is available by
prearrangement. This method can reduce the damage induced by
cryocooling, often with no need for cryoprotectants (Kim et al., Acta
Cryst. D61, 881-890 (2005)).

Microbeam (down to about 5 microns) using focusing capillary optics is
available on request at any of the stations.

===  Support ===

CHESS/MacCHESS provides a high level of support for all users. We are
very willing to help with non-standard experimental setups - just ask.
Our staff scientists also invite collaborations for more extended
projects investigating novel techniques.

Mail-in service is available  - we will be pleased to collect (and
process, if you like) data from crystals that you send to us.

Remote data collection is available for crystallography experiments by
users familiar with the CHESS facility.

 Applying for time 

Visit http://www.chess.cornell.edu and look at Online Express Mode under the
Users menu. All applications can be done on line, any time. Processing
of proposals is rapid, with a turn-around time of just a couple of weeks.

More information is available on the web site, or contact administrator
Kathy Dedrick, k...@cornell.edu.

 Recent developments 

Crystallography
---

Automounters of the ALS design (BAM-1 on F1, BAM-2 on A1) are available for
both local and remote crystal handling. New mounts facilitate rapid switchover
from standard 100-micron beam to capillary-focused 20-micron beam.

BioSAXS
---

The primary station for BioSAXS has changed from F2 (dual-Si crystal mono)
to G1 (dual multilayer mono). A typical exposure time has been reduced from
10 seconds to 1 second. The accessible q range (combining SAXS and WAXS
data from 2 100-K Pilatus pixel array detectors) is about 0.006 - 0.8
inverse Angstroms. The standard X-ray energy is about 10 KeV.

Samples are handled using a sophisticated flow control system incorporating
a sample-loading robot, new disposable sample cells using a laser-cut
microchannel in place of a capillary, and a thorough cleaning cycle including
a blow-dry step. Control is through the Robocon interface, and preliminary
data reduction is carried out with the RAW software. Both systems are well
tested and maintained and RAW is open-source; all users are encouraged to
download it and install it on their own computers.

An Akta Purifier HPLC system equipped with a size-exclusion column (SEC) is
available for final sample preparation. UV and IR microspectrophotometers are
available for measuring sample concentrations, and new Wyatt instruments
provide DLS, MALS, and dRI capabilities. An in-line configuration of
SEC - DLS/MALS - in-beam flow cell is being assembled in the G1 hutch.

Much information about designing and carrying out a BioSAXS experiment is
available from the web site http://www.macchess.cornell.edu/biosaxs.html.

For more information on SAXS, contact Richard Gillilan,
r...@cornell.edu.

Pressure-cryocooling


Pressure cryocooling has succeeded in improving the observed resolution of
diffraction data from users' crystals in a number of cases. In addition, it
has been able to increase the success rate for cryocooling crystals which had
previously yielded only one good freeze out of dozens or hundreds. In rare
cases, it has even caused twinned crystals to transform to untwinned.

Mounting options for pressure-cooling include (1) oil coated in a loop,
(2) in a liquid-filled capillary, and (3) the capillary shielding method
(Kim et al., J. Appl. Cryst. 46, 234-241 (2013)).

Reminder: pressure-cooling almost never improves crystals that are bad at
room temperature; what it does is reduce damage on cryocooling. Please
verify that your crystals show acceptable diffraction at room
temperature before requesting pressure-cooling.

Note that you will need to provide UNFROZEN crystals for pressure cryocooling;
new designs of crystallization plates (e.g. from MiTeGen) allow safe shipping
of such crystals, so you don't need to travel to CHESS.

For more information on pressure-cryocooling, contact Chae Un Kim,
ck...@cornell.edu.

[ccp4bb] Beamtime available now at CHESS

[Marian Szebenyi]

Beamtime is currently available for the fall 2012 run, now through November 19, 
at the Cornell High Energy Synchrotron Source (CHESS, in Ithaca NY). The 
facility offers:


Monochromatic stations A1 and F1, at 12.7 and 13.5 KeV, with ADSC CCD detectors, 
ALS-style crystal automounters, high-quality goniostat, cryo system, crystal 
centering, etc. Mail-in data collection is supported, as well as remote 
operation at the F1 station for users who are familiar with CHESS.


BioSAXS station F2, with dual Pilatus detectors in SAXS-WAXS configuration, 
automated sample flow system with robotic sample-loading option, adjacent HPLC 
for sample prep, excellent software for immediate data processing.


A high level of support is provided to all users, and we welcome non-standard 
experiments.


For more information, and on-line submission of a beamtime request, visit 
http://www.chess.cornell.edu or contact User Administrator Kathy Dedrick, 
k...@cornell.edu, 607-255-0920.

[ccp4bb] Staff scientist position at MacCHESS

[Marian Szebenyi]

This job was posted earlier, but there is an update to the how-to-apply 
instructions.


The Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron
Source (MacCHESS) has an opening for a Staff Scientist (Research Associate) to
pursue the development of novel techniques in x-ray scattering as applied to
structural biology, and to support users at MacCHESS.  There will also be
opportunities to pursue projects in structural biology, using current
crystallographic and SAXS methods.  Research areas of particular interest
include structure solution from multiple crystals, use of Laue diffraction,
BioSAXS, microfluidics, and user interfaces for beamline operation.  A Ph.D. in
structural biology, biophysics, or a related field, and at least 3 years of
experience beyond the degree in a relevant field is required.  A solid
publication record is essential, and experience working at a synchrotron
facility is highly desirable.  Excellent communication skills are a must,
including fluency in the English language.  Appointments are nominally for three
years with the possibility for renewal, subject to mutual satisfaction and the
availability of funds.

Located on an Ivy League university campus in picturesque upstate New York, the
Cornell High-Energy Synchrotron Source (CHESS) serves a world-wide user base of
structural biologists, chemists, physicists, and engineers.  MacCHESS is an
NIH-supported National Resource providing support for structural biology at
CHESS.  MacCHESS is a heavily team-oriented environment.

Applications should be submitted at http://academicjobsonline.org/ (posting no. 
1422) and should include a cover letter, a CV, a list of publications, and a 
detailed summary of research experience and interests.  Applicants must arrange 
to have at least three letters of recommendation sent, as per instructions on 
the academicjobsonline website. The job is available immediately.


Cornell is an equal opportunity, affirmative action educator and employer.

[ccp4bb] Staff Scientist position at MacCHESS

[Marian Szebenyi]

The Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron 
Source (MacCHESS) has an opening for a Staff Scientist (Research Associate) to 
pursue the development of novel techniques in x-ray scattering as applied to 
structural biology, and to support users at MacCHESS.  There will also be 
opportunities to pursue projects in structural biology, using current 
crystallographic and SAXS methods.  Research areas of particular interest 
include structure solution from multiple crystals, use of Laue diffraction, 
BioSAXS, microfluidics, and user interfaces for beamline operation.  A Ph.D. in 
structural biology, biophysics, or a related field, and at least 3 years of 
experience beyond the degree in a relevant field is required.  A solid 
publication record is essential, and experience working at a synchrotron 
facility is highly desirable.  Excellent communication skills are a must, 
including fluency in the English language.  Appointments are nominally for three 
years with the possibility for renewal, subject to mutual satisfaction and the 
availability of funds.


Located on an Ivy League university campus in picturesque upstate New York, the 
Cornell High-Energy Synchrotron Source (CHESS) serves a world-wide user base of 
structural biologists, chemists, physicists, and engineers.  MacCHESS is an 
NIH-supported National Resource providing support for structural biology at 
CHESS.  MacCHESS is a heavily team-oriented environment.


Please provide an application and have at least three letters of reference sent 
to:

Dr. Marian  Szebenyi, Chair
MacCHESS Staff Scientist Search Committee
c/o Peggy Steenrod
Newman Laboratory
Cornell University
Ithaca, NY  14853  USA

Applications should include a cover letter, curriculum vita, a publication list, 
and a detailed summary of research experience and interests.  Electronic 
submissions and inquiries may be addressed to search-cla...@cornell.edu.  Salary 
and starting date are negotiable.


Cornell is an equal opportunity, affirmative action educator and employer.

[ccp4bb] Staff scientist opening at MacCHESS

[Marian Szebenyi]

The Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron 
Source (MacCHESS) has an opening for a Staff Scientist (Research Associate) to 
pursue the development of novel techniques in x-ray scattering as applied to 
structural biology, and to support users at MacCHESS.  There will also be 
opportunities to pursue projects in structural biology, using current 
crystallographic and SAXS methods.  Research areas of particular interest 
include structure solution from multiple crystals, developing a pipeline 
approach for microcrystals, phasing methods, and use of Laue diffraction.  A 
Ph.D. in structural biology, biophysics, or a related field, and at least 5 
years of experience beyond the degree in a relevant field is required.  A solid 
publication record is essential, and experience as a staff member at a 
synchrotron facility is highly desirable.  Excellent communication skills are a 
must, including fluency in the English language.  Appointments are nominally for 
three years with the possibility for renewal, subject to mutual satisfaction and 
the availability of funds.


Located on an Ivy League university campus in picturesque upstate New York, the 
Cornell High-Energy Synchrotron Source (CHESS) serves a world-wide user base of 
structural biologists, chemists, physicists, and engineers.  MacCHESS is an 
NIH-supported National Resource providing support for structural biology at 
CHESS.  MacCHESS is a heavily team-oriented environment.


Please provide an application and have at least three letters of reference sent 
to:

Dr. Marian  Szebenyi, Chair
MacCHESS Staff Scientist Search Committee
c/o Peggy Steenrod
Newman Laboratory
Cornell University
Ithaca, NY  14853  USA

Applications should include a cover letter, curriculum vita, a publication list, 
and a detailed summary of research experience and interests.  Electronic 
submissions and inquiries may be addressed to search-cla...@cornell.edu. 
Complete applications will be considered immediately.  The starting date is 
negotiable.


Cornell is an equal opportunity, affirmative action educator and employer.

[ccp4bb] Biomolecular Structure from Nanocrystals and Diffuse Scattering Workshop

[Marian Szebenyi]

Announcing a workshop on:

Biomolecular Structure from Nanocrystals and Diffuse Scattering

June 13-14, 2011 at Cornell University, Ithaca NY

Organized by Ed Lattman (Hauptmann-Woodward Medical Research Inst.),
Mavis Agbandje-McKenna (University of Florida), Keith Moffat (University of 
Chicago),  Sol Gruner (Cornell University)


FMI: http://erl.chess.cornell.edu/gatherings/2011_Workshops/details2.htm

This workshop is #2 of 6 in the series Science at the Hard X-ray Diffraction 
Limit, devoted to science with diffraction-limited, high repetition rate, hard 
X-ray sources, e.g., Energy Recovery Linac and Ultimate Storage Ring. Find a 
summary of all the workshops at:


http://erl.chess.cornell.edu/gatherings/2011_Workshops/index.htm

Re: [ccp4bb] Processing Laue data

[Marian Szebenyi]

A version of the Daresbury Laue programs that can process ADSC CCD data (Q-210, 
Q-315, etc.), and also has some improvements to the indexing routine for the 
case of sparse diffraction patterns, is available from CHESS, 
ftp://waterline.chess.cornell.edu/pub


Some documentation (as text files) and sample data files are included.

Marian Szebenyi
MacCHESS

REX PALMER wrote:

What programs are available for processing Laue data to produce an
intensity data set?
Are explanatory notes or publications available?
Rex Palmer
Birkbeck College

Re: [ccp4bb] Problem with finding of spots

[Marian Szebenyi]

Petr,

Looks to me as if the problem is that your spots are very fuzzy, so even though 
you can see them the spot-picking algorithms prefer to pick the sharp little 
spots which are really noise. What I would do is set your peak-picking 
parameters to pick very few spots, e.g. use Fewer peaks many times. Then 
manually pick the spots you want to use. This is a pain, but you should only 
need to do it on one image, and, at least in mosflm, you can save the spots file 
and add to it if the first try doesn't produce an indexing.


Marian Szebenyi
MacCHESS

Petr Kolenko wrote:

Dear colleagues,

I am working on one dataset that is hard to process. The data are about
3A of resolution. As we are not able to reproduce the experiment again,
I have to use this one, collected in a dirty way.
The problem starts immediately with finding of spots. I have tried
HKL2000, XDS, D*trek, ipmosflm, imosflm, but none of them gave a good
read-out of the images. All the programs find some spots in wrong
positions and the real spots are not covered. Here is an example:

http://kolda.webz.cz/image-predictions.jpg

The data were collected in-house, Saturn 944++ CCD, and all the
necessary information should be in the header properly. I checked the
distance, other parameters, but the problem is with finding of correct
or real spots on the image. This should be even header-independent,
should not? All the programs fail (or even crash) in this routine. Does
anyone have any suggestion, please?

Btw, we have several structures in the PDB from this experimental setup.
This is the first problem I have met.

Many thanks for any response.

Petr

--
Petr Kolenko
petr.kole...@biochemtech.uni-halle.de
mailto:petr.kole...@biochemtech.uni-halle.de
http://kolda.webz.cz

[ccp4bb] Beam time at CHESS

[Marian Szebenyi]

==
Beamtime available at CHESS, October 13 - December 7, 2010
==

The CHESS/MacCHESS facility, located at Cornell University in Ithaca, NY, 
invites macromolecular crystallographers and users of BioSAXS to apply for time 
on one or more of our stations:


A1 station, monochromatic wiggler source, suitable for Se SAD experiments as 
well as native data collection, with ADSC Q-210 detector.


F1 station, monochromatic wiggler source, suitable for Br SAD or native data, 
with ADSC Q-270 detector and ALS-type automounter.


F2 station, wiggler source tunable from 7 - 14 keV, can be configured either for 
MAD/SAD experiments, with ADSC Q-210 detector, or for BioSAXS experiments, with 
ADSC Q-1 detector.


G1 station, wiggler source with multilayer optics, general purpose station which 
will be available for SAXS experiments during part of the run; good data can be 
obtained for d-spacings up to 2500 Angstroms.


= Special options ==

Pressure-cryocooling of (unfrozen) crystals is available by prearrangement. This 
method can reduce the damage induced by cryocooling, often with no need for 
cryoprotectants (Kim et al., Acta Cryst. D61, 881-890 (2005)).


Microbeam (down to about 5 microns) using focusing capillary optics is available 
on request at any of the stations.


===  Support ===

CHESS/MacCHESS provides a high level of support for all users. We are very 
willing to help with non-standard experimental setups - just ask. Our staff 
scientists also invite collaborations for more extended projects investigating 
novel techniques.


Mail-in service is available  - we will be pleased to collect (and process, if 
you like) data from crystals that you send to us.


 Applying for time 

Visit http://www.chess.cornell.edu and look at Beam Time under the Users 
menu. All applications can be done on line, any time. Processing of proposals is 
rapid, with a turn-around time of just a couple of weeks for the usual Express 
Mode option.


More information is available on the web site, or contact administrator
Kathy Dedrick, k...@cornell.edu.

= More about pressure-cryocooling =

In 2009, pressure-cooling succeeded in increasing the success rate for 
cryocooling users' crystals which had previously yielded only one good freeze 
out of dozens or hundreds.


The option of pressure-cooling in capillaries is available for crystals which 
are not compatible with oil coating, or are subject to mechanical damage during 
loop mounting.


Reminder: pressure-cooling will not improve crystals that are bad at room 
temperature; what it does is reduce damage on cryocooling. Please verify that 
your crystals show acceptable diffraction at room temperature before requesting 
pressure-cooling.


For more information on pressure-cryocooling, contact Chae Un Kim, 
ck...@cornell.edu.

[ccp4bb] Beam time at CHESS

[Marian Szebenyi]

==
Beamtime available at CHESS, June 2 - July 20, 2010
==

The CHESS/MacCHESS facility, located at Cornell University in Ithaca, 
NY, invites macromolecular crystallographers and users of BioSAXS to 
apply for time on one or more of our stations:


A1 station, monochromatic wiggler source, suitable for Se SAD 
experiments as well as native data collection, with ADSC Q-210 detector.


F1 station, monochromatic wiggler source, suitable for Br SAD or native 
data, with ADSC Q-270 detector and ALS-type automounter.


F2 station, wiggler source tunable from 7 - 14 keV, can be configured 
either for MAD/SAD experiments, with ADSC Q-210 detector, or for BioSAXS 
experiments, with ADSC Q-1 detector.


F3 station, bending magnet source with multilayer optics, tunable from 
5.9 - 15.4 keV, suitable for SAD experiments using Fe, Co, etc., with 
ADSC Q-4u detector.


G1 station, wiggler source with multilayer optics, general purpose 
station one of whose standard configurations is for SAXS experiments; 
good data can be obtained for d-spacings up to 2500 Angstroms.


= Special options ==

Pressure-cryocooling of (unfrozen) crystals is available by 
prearrangement. This method can reduce the damage induced by 
cryocooling, often with no need for cryoprotectants (Kim et al., Acta 
Cryst. D61, 881-890 (2005)).


Microbeam (down to about 5 microns) using focusing capillary optics is 
available on request at any of the stations.


===  Support ===

CHESS/MacCHESS provides a high level of support for all users. We are 
very willing to help with non-standard experimental setups - just ask. 
Our staff scientists also invite collaborations for more extended 
projects investigating novel techniques. Mail-in service is available  - 
we will be pleased to collect (and process, if you like) data from 
crystals that you send to us.


 Applying for time 

Visit http://www.chess.cornell.edu and look at Beam Time under the 
Users menu. All applications can be done on line, any time. Processing 
of proposals is rapid, with a turn-around time of just a couple of weeks 
for the usual Express Mode option.


More information is available on the web site, or contact administrator 
Kathy Dedrick, k...@cornell.edu.


 Recent developments 

SAXS


F2 station continues to improve as a SAXS beamline. In this 
configuration, the large Q210 detector has been replaced with a freshly 
re-calibrated Q1 detector. This move was motivated by pedestal mismatch 
and ghosting problems that made the Q210 a less-than-optimal detector 
for SAXS. The Q1 was used very successfully for SAXS in G1 for a number 
of years and should improve wide-angle data quality significantly at F2.


Søren Nielson has recently joined MacCHESS as a postdoc. He specialized 
in BioSAXS and microfluidics (lab on a chip) at the Technical 
University of Denmark and is the author of the BioXTAS RAW data 
processing program (J.App. Cryst. 42 pp 959-964 (2009)). During the 
coming run, we expect to have fully customized and tested this software 
for automated data processing on our SAXS beamlines. This 
freely-available open-source code should also be valuable for those 
processing SAXS data at home.


MacCHESS has purchased a pipetting robot for automated sample loading, 
including preparation of dilution series. The robot will be tested on F2 
and G1 during this run and may be available to selected users once 
testing is complete. We also hope to test a basic SAXS flow cell. If 
sufficient sample is available (30-50 ul), the use of a flow cell can 
eliminate the effects of radiation damage and allow for dramatically 
better signal-to-noise in data collection.


For more information on SAXS, contact Richard Gillilan, r...@cornell.edu.

Pressure-cryocooling


In 2009, pressure-cooling succeeded in increasing the success rate for 
cryocooling users' crystals which had previously yielded only one good 
freeze out of dozens or hundreds.


The option of pressure-cooling in capillaries is available for crystals 
which are not compatible with oil coating, or are subject to mechanical 
damage during loop mounting.


Reminder: pressure-cooling will not improve crystals that are bad at 
room temperature; what it does is reduce damage on cryocooling. Please 
verify that your crystals show acceptable diffraction at room 
temperature before requesting pressure-cooling.


For more information on pressure-cryocooling, contact Chae Un Kim, 
ck...@cornell.edu.

Re: [ccp4bb] short step

[Marian Szebenyi]

Ed,

Did you tell scalepack not to add partials? It certainly shouldn't be 
doing this when your oscillation ranges overlap - perhaps it is smart 
enough to realize this is the situation, perhaps not.


Marian Szebenyi
MacCHESS

Ed Pozharski wrote:

Ed,

thanks - this is a great suggestion.  Unfortunately, it's not the
problem - I had the oscillation start 0.0 range 0.5 step 0.001
statement in the denzo input file.  Denzo runs fine and there is no
slippage issue. I tried turning off postrefinement and both batch and
crystal rotx refinement (batch is what I do generally), to no avail.

Ed.

On Mon, 2010-02-22 at 19:11 -0500, Edward A. Berry wrote:

Try grepping crystal your .x files (or whatever you called the
denzo output files). Also grep for start.

By default denzo updates start-phi to the end
of the previous oscillation.  Since 0,5 degree is within radius of
convergence, it re-refines crystal rotx to be compatible with this
assumption and the oscillation photograph, which means crystal rotx
will be moving backwards 0.5 degrees for each frame. Scalepack
in postrefinement sees this as a serious case of slippage and is
unable to postrefine a value of crystal rotx that is compatible with
all the frames.

It may be possible to turn of post-refinement with POSTREFINE 0
or some such.

Ed

Ed Pozharski wrote:

I want to process bunch of frames with extremely short step - i.e. these
are 0.5degree oscillations but crystal only rotates by 1 degree over
1000 frames (I would have kept it at the same orientation if Rigaku
control software would allow zero step).  Denzo can process the frames
all right, but scalepack chokes on it saying Floating Exception.  I
don't have much experience with mosflm, and it failed also.

What I wonder is if this happens because both programs have some bug in
these unusual conditions or there is something fundamental that prevents
scaling such data?

Cheers,

Ed.

Re: [ccp4bb] Integration

[Marian Szebenyi]

Vin,

This effect is what you see when the goniometer's rotation axis is not 
exactly perpendicular to the beam. HKL2000 is compensating for rotations 
that are actually due to goniometer misalignment by changing the crystal 
orientation angles. It does not cause any harm to your data, unless 
things are so far off that refinement gets lost, which does not seem to 
have been the case for your data.


Marian Szebenyi
MacCHESS

Vin Purp wrote:
Hi, sorry for the non-ccp4 related question. 


I have one data set that yields peculiar results when I use HKL2000 (or
3000) to integrate it. 


Background: I have crystals that index to the I222 sg. I have shot and
collected datasets, integrated, molreped and refined  many hundreds of these
same crystals and know them very well. However, I recently collected data
that has the following 'problem' when I integrate: I collected 450 frames at
0.3 width (135 deg) .The Rot. Change vs. Frame window in the HKL program
(Integration tab) shows that in the first 150 frames, the x and z  deviates
+30 and frames 150-450 x and z cross to a negative change and finish at
-120. The Y-axis doesn't deviate from 0 the entire time. 


All other statistics look 'normal' for the integration; mosaicity is a bit
high (0.75-1), the Chi sq. hovers near 1 for all frames, and the 'Cell' and
'Distance' vs. frame do not deviate from 0 much at all over all frames. I
have played with integration box size, spot size, elongation and background
with the same results.

Other stats: data set is ~1.60 Ang. resolution; unit cell = 128x140x168
Ang.; Roverall = 4.2% 


 I was curious as to what this phenomena is due to. Any ideas are appreciated.

Re: [ccp4bb] data reduction

[Doletha Marian Szebenyi]

Alex,

With regard to scalepack, be sure you use NO MERGE ORIGINAL INDEX, not
just NO MERGE.

Marian Szebenyi
MacCHESS

 Dear all:

 I am trying to solve a structure from apparently a hexagonal crystal.
 I indexed and scaled data  in P6 in Scalepack (with merging) then used
 Scalepack2mtz (with ensure unique reflections and add Rfree as well as
 the truncate procedure), and then attempted to run molecular
 replacement with Phaser. Now the problem appeared - Phaser immediately
 quits with the following error message FATAL RUNTIME ERROR:
 Reflections are not a unique set by symmetry. I do not understand
 this at all.

 I also tried running scalepack using the NO MERGE macro as people have
 indicated earlier on this bb (thank you again!, I also checked the
 scl.in that is written out and it had the NO MERGE statement), and
 then tried to run pointless to verify the spacegroup but the program
 complained the reflections are merged (that is impossible, I checked
 the number of reflections in the unmerged and merged files and they
 were different as one would expect). I repeated the procedures several
 times and I always get the same errors. I can't make any sense of this
 and I can't move forward. Any ideas?

 Many thanks,
 Alex






 On Jul 30, 2009, at 7:03 PM, CCP4BB automatic digest system wrote:

 There are 13 messages totalling 1026 lines in this issue.

 Topics of the day:

  1. refmac failed message (2)
  2. question of extra high B factor (6)
  3. Coot:findwaters in REFMAC (2)
  4. Postdoctoral position in protein crystallography at Karolinska
 Institutet
  5. OpenGL Stereo 3D on 120 Hz LCDs, at last!
  6. Foils for energy calibration

 --

 Date:Thu, 30 Jul 2009 10:50:13 GMT
 From:Elad Binshtien ela...@bgu.ac.il
 Subject: refmac failed message

 This is a multi-part message in MIME format.


 8d5c55134e491a1d1bdd
 Content-Type: text/plain; charset=utf-8
 Content-Disposition: inline
 Content-Transfer-Encoding: quoted-printable

 Dear all=2C


 I am refining a structure in Refmac at 2=2E2 A in win OS=2E=C2=A0
 Howeve=
 r=2C
 Refmac failed and send this message=3A =C2=A0 =C2=A0 =C2=A0=C2=A0
 forrtl=
 =3A error (72)=3A floating overflow=C2=A0 =


 Thank you in advance for your any helpful suggestions=2E=C2=A0 =



 Best=2C
 Elad


 Elad Binshtein
 Ph=2ED student =

 Department of Life Science =

 Ben Gurion University of the Negev
 Ph=3A 972-8-6461325=E2=80=8E

 8d5c55134e491a1d1bdd
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 Content-Transfer-Encoding: quoted-printable

 Dear all=2C=3Cbr=3E=3Cbr=3E=3Cbr=3EI am refining a structure in
 Refmac a=
 t 2=2E2 A in win OS=2E=26nbsp=3B However=2C
 Refmac failed and send this message=3A =26nbsp=3B =26nbsp=3B
 =26nbsp=3B=26=
 nbsp=3B forrtl=3A error (72)=3A floating overflow=26nbsp=3B
 =3Cbr=3E=3Cb=
 r=3E Thank you in advance for your any helpful
 suggestions=2E=26nbsp=3B =
 =
 3Cbr
 =3E=3Cbr=3E=3Cbr=3EBest=2C=3Cbr=3EElad=3Cbr=3E=3CBR=3E=3CBR=3EElad =
 Binshtein=3Cbr=3EPh=2ED student =3Cbr=3EDepartment of Life Science
 =3Cbr=
 =3EBen Gurion University of the Negev=3Cbr=3EPh=3A 972-8-6461325=3C/
 BR=3E=
 =3C/BR=3E=E2=80=8E

 8d5c55134e491a1d1bdd--

 --

 Date:Thu, 30 Jul 2009 13:25:43 +0100
 From:Stein, ND (Norman) norman.st...@stfc.ac.uk
 Subject: Re: refmac failed message

 This is a multi-part message in MIME format.

 --_=_NextPart_001_01CA1110.DB7CC0CB
 Content-Type: text/plain;
  charset=windows-1255
 Content-Transfer-Encoding: quoted-printable

 Hi Elad
 =20
 You don't say which version of Refmac you are using but I think the =
 first thing to do would be to try the latest version (5.5.0102). You
 can =
 pick this up from
 =20
 ftp://ftp.ccp4.ac.uk/nds/windows/refmac_5.5.0102/refmac5.exe
 =20
 Copy this exe file to the bin subdirectory of your CCP4
 installation. =
 (Probably wise to make a backup copy of the existing refmac5.exe
 first).
 =20
 Best wishes
 =20
 Norman Stein
 CCP4

 

 From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf
 Of =
 Elad Binshtien
 Sent: 30 July 2009 11:50
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] refmac failed message


 Dear all,


 I am refining a structure in Refmac at 2.2 A in win OS.  However,
 Refmac =
 failed and send this message:forrtl: error (72): floating =
 overflow =20

 Thank you in advance for your any helpful suggestions. =20


 Best,
 Elad


 Elad Binshtein
 Ph.D student=20
 Department of Life Science=20
 Ben Gurion University of the Negev
 Ph: 972-8-6461325

 =FD=20

 -- =0AScanned by iCritical.=0A

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 !DOCTYPE HTML PUBLIC -//W3C//DTD HTML 4.0 Transitional//EN
 HTMLHEAD
 META http-equiv=3DContent-Type content=3Dtext/html; =
 charset=3Dwindows-1255
 META content

[ccp4bb] Postdoctoral position, MacCHESS, Ithaca NY

[Marian Szebenyi]

MacCHESS (Macromolecular diffraction at Cornell High Energy Synchrotron 
Source) has an opening for a post-doctoral associate to work on 
developing novel methods of 3D visualization of protein crystals mounted 
on a synchrotron beamline, for the purpose of crystal centering and 
motion planning during data collection. Confocal microscopy will be the 
initial method investigated. The position is suitable for persons with a 
Ph.D. in biophysics, physics, optical engineering, image processing, 
spectroscopy, or similar fields and a strong interest in hands-on 
development of equipment and techniques. Experience in Python or Java 
GUI programming is a plus.


Located on an ivy-league university campus in picturesque upstate New
York, the Cornell High-Energy Synchrotron Source (CHESS) serves a
world-wide user base of structural biologists, chemists, physicists, and
engineers. MacCHESS is an NIH-supported National Resource providing
support for structural biology at CHESS. MacCHESS is a heavily team-
oriented environment. Good clear communication skills are a must, 
including fluency in the English language.


This is an entry-level post-doctoral position for one year, renewable 
for an additional year subject to mutual agreement and continued 
availability of funds.


Please provide an application and arrange to have at least three letters 
of reference sent to:


Dr. Marian  Szebenyi, Chair
Postdoctoral Associate Search Committee
Newman Lab
Cornell University
Ithaca, NY  14853  USA

Applications should include a cover letter, curriculum vita, a 
publication list, and a detailed summary of research experience and 
interests.  Electronic submissions and inquiries may be addressed to 
search-l...@cornell.edu.


Deadline for application is November 15, 2009. Starting date is
negotiable. Cornell is an equal opportunity employer.

[ccp4bb] Beamtime at Cornell High Energy Synchrotron Source

[Marian Szebenyi]

==
Beamtime available at CHESS, September 16-November 10, 2009
==

The CHESS/MacCHESS facility, located at Cornell University in Ithaca, 
NY, invites macromolecular crystallographers and users of BioSAXS to 
apply for time on one or more of our stations:


A1 station, monochromatic wiggler source, suitable for Se SAD 
experiments as well as native data collection, with ADSC Q-210 detector.


F1 station, monochromatic wiggler source, suitable for Br SAD or native 
data, with ADSC Q-270 detector and ALS-type automounter.


F2 station, wiggler source tunable from 7 - 14 keV, suitable for MAD/SAD 
experiments, with ADSC Q-210 detector. Also can be equipped for BioSAXS 
experiments.


F3 station, bending magnet source with multilayer optics, tunable from 
5.9 - 15.4 keV, suitable for SAD experiments using Fe, Co, etc., with 
ADSC Q-4u detector.


G1 station, wiggler source with multilayer optics, general purpose 
station one of whose standard configurations is for SAXS experiments; 
good data can be obtained for d-spacings up to 2500 Angstroms.


= Special options ==

Pressure-cryocooling of (unfrozen) crystals is available by 
prearrangement. This method can reduce the damage induced by 
cryocooling, often with no need for cryoprotectants (Kim et al., Acta 
Cryst. D61, 881-890 (2005)).


Microbeam (down to about 5 microns) using focusing capillary optics is 
available on request at any of the stations.


===  Support ===

CHESS/MacCHESS provides a high level of support for all users. We are 
very willing to help with non-standard experimental setups - just ask. 
Our staff scientists also invite collaborations for more extended 
projects investigating novel techniques.


Mail-in service is available  - we will be pleased to collect (and 
process, if you like) data from crystals that you send to us.


 Applying for time 

Visit http://www.chess.cornell.edu and look at Beam Time under the 
Users menu. All applications can be done on line, any time. Processing 
of proposals is rapid, with a turn-around time of just a couple of weeks 
for the usual Express Mode option.


More information is available on the web site, or contact administrator 
Kathy Dedrick, k...@cornell.edu.

Re: [ccp4bb] Tough ligand to bind?

[Marian Szebenyi]

Nian,

Have you considered pressure-freezing, the method developed by Sol 
Gruner's group at Cornell? If cryoprotectants are causing the problem, 
freezing under pressure reduces the need for them. It's also possible 
that your ligand is present but disordered in the crystal, and 
pressure-freezing can also act to stabilize a single conformation. See 
Kim et al., Acta Cryst. D61, 881 (2005), also Albright et al., Cell 126, 
 1147 (2006) - a case where pressure caused a ligand to become visible.


Marian Szebenyi
MacCHESS

Nian Huang wrote:

Dear All,

I have been trying to get a protein-ligand complex crystal for a long
time. Here, ligand is either substrate or product for this kinase. I
have tried many methods: soaking with apo-crystal, co-crystal with
different concentration of ligand and screen for new conditions. I got
a couple of co-crystals with the new conditions, but still no ligand
was found in the active site.

Anybody has some new ideas that I can try? I have been using glycerol
as my cryoprotectant. Could cryoprotectant have some negative effect
on co-crystal? I will try to collect some data at room temperature in
the future.

Thank you in advance for your suggestion.

Nian

Dept of Biochemistry
UT Southwestern Medical Center