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2dx Overview Contents Protocols Computing... crash total computer: ssh from another machine sudo init 3 sudo kill 9 whatever Xorg sudo init ...
NYSBC CEMfac all hours access Contents How to acquire authorization for independent use of microscopes at any hour of the day The electron microscopes are in principle ...
Name: Ann McDermott Email: aem5@columbia.edu Company Name: Columbia University Company URL: http://www.cise.columbia.edu/nsec/team/mcdermott.html ...
Biomek NXP robot Contents Before each use Empty the "Waste" bottle if it is almost full Check the level of water in the "Source" bottle. It should be well ...
Contents CEM Data Transfer Data generated on the Technai is copied to the DL380 nightly to the /home//temdata directory. The data can be downloaded using the NYSBC ...
Contents IF CCD blank enable window is closed, then CCD blanking box won't work Occasionally, box won't work even though CCD blank Enable is open and checked ...
Contents Tecnai F20 Procedure Go to low dose Exposure mode Set beam intensity to 1 second exposure time In SerialEM, set Record time to 1 second, ...
Contents CCPN WORKSHOP AT NYSBC, 8 Sep 2008 , A 11 REGISTRATION STEPS 1 If you want to use the software, you need to register with CCPN http://www.ccpn.ac ...
Procedure for using the CEM facility at the NYSBC The NYSBC The New York Structural Biology Center is a 501 (c)(3) corporation incorporated in the State of New York ...
Image processing ZeissDensitometer Z/I Imaging (Zeiss) Photoscan Scanner Data processing computer cluster Users have access to a number ...
Contents Ed's Overview of EM (cartoon version) Choice of an appropriate structural biological technique Before beginning a project one must match the biological ...
Contents General guidelines home directory has 20 GB space allocated to all of CEM computing /usr/data has 100 GB of space allocated to all of CEM computing ...
Contents Administration logs Jan 2011 Set up and installed new computer, cem15 CentOS 5.5, RAID5, 5.2 TB disk All standard EM software installed ...
Contents Workstations Workstation Name IP OS data drive cores RAM CPU type Minotaur 192.168.5.184 !CentOS 5 theseus 641 GB 4 cores 8 GB ...
Visit the !CryoEM web site at http://cryoem.nysbc.org Cryoelectron Microscopy of Macromolecular Assemblies Graduate Course offered for the 10th year at NYSBC Fall ...
Visit the !CryoEM web site at http://cryoem.nysbc.org Cryoelectron Microscopy of Macromolecular Assemblies Graduate Course offered for the 7th year at NYSBC Fall ...
Visit the !CryoEM web site at http://cryoem.nysbc.org Cryoelectron Microscopy of Macromolecular Assemblies Graduate Course offered for the 8th year at NYSBC Fall ...
Visit the !CryoEM web site at http://cryoem.nysbc.org Cryoelectron Microscopy of Macromolecular Assemblies Graduate Course offered for the 9th year at NYSBC Fall ...
Visit the !CryoEM web site at http://cryoem.nysbc.org Cryoelectron Microscopy of Macromolecular Assemblies Graduate Course offered for the 10th year at NYSBC Fall ...
Visit Cryo EM website at http://www.nysbc.org/facilities/CEM Course Materials for Graduate Course "CryoElectron Microscopy of Macromolecular Complexes" Dec. 5 ...
Contents Player required for arf video files nbr2player.msi: MS windows player for arf files Lectures Structure Validation and Fitting Dec. 9 Lecture ...
Cryoelectron Microscopy of Macromolecular Assemblies 2010 NYU course # G16.4408 4 credits credit also available at other institutions Instructors DavidStokes ...
Contents Practical Sessions Homework : preparation for practical session II Download and install IMOD on your mac/pc/linux system Get the latest stable ...
Contents Instructors DavidStokes: stokes@saturn.med.nyu.edu BillRice: rice@nysbc.org IbanUbarretxena: iu@sci.ccny.cuny.edu HernandoJoseSosa: hsosa ...
Contents Fib/SEM CemFibSEMProcessing tif2mrc Image .tif rawstack.mrc xfalign matt 0.1 reduce 1 bilinear params 2 sobel rawstack.mrc rawstack.xf xftoxg n 0 rawstack ...
Capabilities of NYSBC's CEM Lab Printable Brochure General Information The goal of the NYSBC cryoelectron microscopy facility is to help researchers elucidate ...
Capabilities of NYSBC's CEM Lab General Information The goal of the NYSBC cryoelectron microscopy facility is to help researchers elucidate the intermolecular interactions ...
Notes on Compiling and Using Helical Reconstruction Programs from Toyoshima Lab Migration to Unwin software hfts was modified to add zorg to parameter list for ...
IT resources This page is now broken into two parts: CemITSystem for system admin related issues CemITApplications for issues related to EM software Set ALLOWTOPICVIEW ...
IT resources at the CEMfac List of supported SoftWare EmIP GUI for image processing Tomography MontageNavigator hints on using the Navigator in SerialEM ...
IT resources at the CEMfac TemimpsTwikiToWebList add TWiki pages to TEMIMPS web site CemTwikiToWebList add TWiki pages to public web site CemTwikiToWebListTest ...
Capabilities of NYSBC's CEM Lab Printable Brochure Introduction The goal of the NYSBC cryoelectron microscopy facility is to help researchers elucidate the intermolecular ...
Visit Cryo EM website at http://www.nysbc.org/facilities/CEM !CryoEM facility at NY Structural Biology Center CapabilitiesCEM.doc: MS Word version CapabilitiesCEM ...
Dear Committee members, Further to my last message, I am attaching the documents recently sent to our two potential vendors requesting their Best and Final Offers ...
Contents Calendar Standard Institutional Abbreviations: AECO CUNY COLU NYU NYSB MSSM MSKC RU WADS WEIL 30 May 2016 Memorial ...
Contents General Questions Question: I have a protein and want to do EM, what do I do? If you have a protein or a protein complex that has a MW ~300kDa ...
Capabilities of NYSBC's CEM Lab General Information The goal of the NYSBC cryoelectron microscopy facility is to help researchers elucidate the intermolecular interactions ...
Contents CEM Practical Signup and Information place and time Practicals will be from 10 am to 1 pm, Oct 29 Nov. 2 (single particle reconstruction and tomography ...
Principles Protocols Single Particle For single particle projects, we are using two packages: SPIDER and EMAN In general, EMAN is easier to use and get ...
Contents NYSBC Policy and Protocol for Remote Access to CEM Computers. CemRemoteoperationRequest NYSBC is offering capability to remotely access CEM Computers ...
Contents Robot Instructions These instructions are not meant to replace proper training Preparation Start usage log Switch toggle to robot . ...
Reading and setting robot coordinates in robot controllers Manual robot control and hand controller operation using iRobot to manually control robot movement ...
Contents Leginon/Robot Technical Guide Minghui robot tech guide.doc: Robot Technical Guide (MS Word format) Leginon Update As of Feb 2010, Leginon is under major ...
Contents User Guide for Robot/Leginon on JEOL 1230 Minghui Hu Friday, February 26, 2010 Minghui Leginon setup guide.doc: MS Word version PC access abc123 Checklists ...
Contents Camera Webpages http://192.168.5.160 http://192.168.5.166 Automated Control and Robotics on 1230 Options for Automated Control ...
Contents Please Use the New Scheduler email emg@nysbc.org if you do not yet have an account Equipment FSU freeze subsititution unit PF Gatan ...
Contents Signup for sample prep equipment Rules signup on a first come first served basis signup with your !TwikiName list the time period you want ...
Courses and Seminars related to !CryoEM At the NYSBC CEM User meeting and Annual BBQ Event: CEM user meeting Location: NYSBC, Room A 11 Time: Friday, August 22, ...
(Archive)Courses and Seminars related to !CryoEM 2013 At the NYSBC Semester long Course : "Cryoelectron Microscopy of Macromolecular Assemblies" This comprehensive ...
Contents Ongoing issues Tecnai New apertures installed March 6 2015 Objective: 100 um, 50 um, 50 um, 40 um condenser: 150 um, 100 um, 70 um, 50 um BUT third ...
Procedure for using the CEM facility at the NYSBC The NYSBC The New York Structural Biology Center is a 501 (c)(3) corporation incorporated in the State of New York ...
Procedure for using the CEM facility at the NYSBC The NYSBC The New York Structural Biology Center is a 501 (c)(3) corporation incorporated in the State of New York ...
Contents CEM Signup Rules 1 Bill Rice is the administrator for the booking software (rice@nysbc.org). 1 Signups open at noon on Monday for the following week ...
Contents Notes on using the ingle particle helical suite of software Source http://emlab.rose2.brandeis.edu/helical publication: sample data: http ...
Overview Interested in Cryoem? (How to begin a project) CemInterested Cryoem at NYSBC CemIntroduction General info on cryoem at NYSBC CemGeneralInfo ...
Contents Listing of twiki pages to be automatically copied to nysbc web pages Instructions List any pages here that you want to be mirrored on our public site ...
twikipage TemimpsJobs InstallwxPython PlungeFreezing CemProtocPlungefreezing PPPioloformGrids PPFiducialsTomography PPCarbonSandwich ...
CEMUserhandbook ver1.pdf: CEM User Handbook version 1.00 EM User Handbook Note: Policies may have been updated since this handbook has been completed so please contact ...
Contents Cluster Usage Instructions The Computing Cluster at NYSBC is now fully operational. Requests for processing time can be made to infotech@nysbc.org. Technical ...
Contents Audio solution for conference room What we want We would like to set up a course to be broadcast over the internet to users in Albany. In order to do this ...
Contents March 2010 We will be given 1 month notice before final trench is dug. Anticipated date is not included in current construction schedules. Cryo EM As ...
Contents Cyana documentation at NYSBC Reference papers /guntert03.pdf Suggested local procedure Preparing files 1 Login to the appropriate server, currently ...
Contents Recent changes and critical comments on CYANA Releases CYANA 2.0, a major new version of the Cyana software package for NMR structure calculation and automated ...
Contents Mixing 8 and 16/24/32 bit displays in Linux (Redhat) Problem Older display software, such as WEB, does not support displays higher than 8 bit ...
Contents Drift Test Align microscope 200kx recommended magnification Insert quantifoil grid Insert holder Cool down holder if testing cryo ...
Statement: A dual beam scanning electron microscope is requested for creating large scale reconstructions of tissue. This instrument will be situated at the New York ...
Return to the Cryo EM Website at http://www.nysbc.org/facilities/CEM Dual Tilt axis tomography on the JEOL 3200FSC New How to use the dual tilt holders of the ...
EM Imaging Processing GUI EMIP EMIP is a Graphical User Interface written in wxPython that collects information from the user and runs existing programs from ...
Contents Spider tail command in FC8 and above, starting spider gives an error : sort open failed: 2n: no such file or directory basename: missing operand ...
Return to the Cryo EM Website at http://www.nysbc.org/facilities/CEM Tecnai Tomography Contents This Software Is NO LONGER IN USE at NYSBC: Use SerialEM Microscope ...
Contents Processing of Tomograms using the FSU package fiducial free system new scripts automate much hand editing of files list of scripts setup ...
Contents Automated Control and Robotics on 1230 Options for Automated Control SerialEM already installed, but does not fully work because of emulator ...
How to retrieve your EM data Contents How to download your data from NYSBC You should already be set up with an sftp account to sftp.nysbc.org sftp ...
CONFERENCE CALLING and REMOTE PC VIEW CONFERENCING We now have available the gotomeeting protocol (see http://www.gotomeeting.com ). 1. limited to 15 people total ...
Tuesday Group Meeting Reports 03/05/2013 UMA, MCMJR1 (Iban) 5 mutations done bt Bryan (as in the published paper). Expression ok. Will be scaled up at MSSM ...
Return to Cryo EM web page at http://www.nysbc.org/facilities/CEM Principles Protocols Helical Reconstruction using EMIP This protocol uses software that originated ...
Contents Prerequisites 1 python 1 gtk and glib. If the FSU software has been installed already then the required libraries should already be present 1 wxGTK ...
Contents JEOL 2100 Controls, Comparison with Tecnai Hardware Controls JEOL Tecnai BEAM Gun Valve Open (software switch on Tecnai) OL ...
Room 118 LogBook; experiments, debugging and updating... Manual use of 1230 1. Check the robot is not running (Leginon would appear and run on the main screen ...
Contents User Instructions for 2100F Assumed that the microscope has already been aligned and software set up for imaging All users REQUIRE training with ...
Contents User Instructions for 3200FSC These are for users who come to use the microscope Assumed that the microscope has already been aligned and software ...
Contents JEOL 3200 training 3200 training notes.doc: DLS notes on 3200 training Cryogen fill Chuck dewar Fill in morning and last thing at night ...
Name: Joachim Frank Email: tb2319@columbia.edu Company Name: Columbia Office Company URL: Location: ColumbiaMedCenterOffice Country: USA ...
Booting into Linux using Knoppix Live CD Download the above file and burn it as a CD image. Reboot your computer, choosing this CD as the boot device. This will ...
Contents Configuration of the Memory Hole on 64 bit AMD Systems The Problem From the official Tyan FAQ: Why does my OS see less than the total memory installed ...
META GROUP MEETINGS #8211; NYSBC Held in A 11 Park Building NEXT MEETING ... We would like to provide each participating group the opportunity to conduct ...
2007 Calendar Year DATE EVENT 25 Jan 2007 THURSDAY NOON VISITOR SEMINAR, Dr. Chiara Pastore, NIMR London, 'Insights into Iron Sulphur cluster ...
META GROUP MEETINGS – NYSBC Held in A 11 Park Building at 1:30 pm unless noted otherwise MEETINGS IN NEXT SIX WEEKS Other questions? See MetaGroupFaq 2008 ...
Contents Making Movies from Image Stills under Linux Required Software 1 ImageMagick for easy format conversion, cropping, etc. 1 mjpegtools for encoding ...
Contents NMR Data Transfer Direct transfer of files directly to a Spectrometer by any user is not permitted for security reasons. Data can be transferred to the ...
Contents New User Setup Tecnai F20 Create new accounts on both computers and Greymatter Set passwords to never expire Windows 2000 or XP ...
Contents Nikon Ti U Inverted Light Microscope (basic instructions) Note: If there is a user after you, leave the Hg lamp on. Every time you turn on the Hg bulb ...
Contents Processing Bruker digitally filtered data Sep 2005 There is 1 message totalling 121 lines in this issue. Topics of the day: 1. Processing Bruker digitally ...
Contents Internal features Fitting a single Kd to multiple shift titration data NmrTitration 1 Demo script LIBRARY:matlab/lib1/titrationscript.html or NmrTitration ...
Contents Operation of the NYSBC NMR Instruments. Important new information on temperature calibration June 2007 Nmr Password Synchronization Quick ...
Contents Nmr Proteomics List NESG This is the html version of the file http://www.nesg.org/docs/NESG2.1.doc. Northeast Structural Genomics Consortium ...
Contents NYSBC Policy and Protocol for Remote NMR Spectrometer Operations. NmrRemoteoperationRequest General considerations for remote use NMR Specific ...
Requests for DNP spectrometer time can submitted at DnpNmrSchedule The availability of 750 and 900 MHz Solid state probes can be found at SolidsProbestatus ...
Requests for DNP spectrometer time can submitted at DnpNmrSchedule The availability of 750 and 900 MHz Solid state probes can be found at SolidsProbestatus ...
Contents NMR Short Course, TBD Solution NMR WHO ...
Contents NMR Software See also NmrIT Target for support in Protein Nmr Course NmrPipe NmrView XplorNih Other systems of interest CyanA ...
Contents NMR Solid State Short Course Solid State NMR WHO The short course for NMR is a training period for spectrometer ...
Contents Moving Blog Library access including on line jounrals WITH ID CARD Faculty staff located on the Resnick campus must register in person at ...
Contents Protein NMR Course NEXT OFFERED Jan 2009 CURRENTLY IN PROGRESS NmrCourse Compact summary of course, see below for full notes Course materials ...
Contents Protein NMR Course Spring 2015 Compact summary of course, see below for full notes Information about grades for the University admin folks ...
Q A When will the course next be offered? Tentatively, in January 2XXX Do you know when the list of presentation topics will be provided? The presentation ...
Contents RCS system type "man rcsintro" on any linux system ... RCSINTRO(1) RCSINTRO(1) NAME rcsintro introduction ...
Contents NYSBC Policy and Protocol for Remote Access to Computers. This is a general policy outline. Specific details for operations are available at CemRemoteoperations ...
Contents Structure Calculation in NMR Notes for Round Table Discussion Jan 18 MetaGroup The purpose of this round table is to increase the understanding of the ...
Return to the Cryo EM Website at http://www.nysbc.org/facilities/CEM SerialEM Use Serial EM provided by David Mastronarde and colleagues from Univ. of Colorado, ...
New York Structural Biology Center, Information Technology Department New York Structural Biology Center Using the NYSBC SFTP ...
SPARTA: Shifts Predicted from Analogy in Residue type and Torsion Angle – NYSBC notes As described in the paper: Protein backbone chemical shifts predicted from ...
How to use Shutter box Control Application from TVIPS Background Tietz shutterbox has separate beam blank and camera shutter controls This allows beam to ...
PROTOCOLS from Stokes Lab Members Cell Culture yeast growth protocol vink.doc: Yeast Culture (Martin Vink) 12/2007 Yeast cultures.doc: Yeast culture protocol ...
TLC of lipids and detergents – Martin's procedure Materials TLC Silica gel 60 W F254 These instructions are relevant for these plates only. They can be ordered ...
Contents Sample Insertion InsertRoomTemperatureSample InsertCryoSample Tecnai F20 Problems Instructions to Retrieve CCDBlankEnable Film Jam Access ...
FEI TF20 Microscope Parameters wavelengths 200kV: 0.02508 A objective lenses f Cs 2.1 mm Chromatic aberration Aperture Sizes Condensor ...
Visit the Cryo EM Website at http://www.nysbc.org/facilities/CEM Tecnai F20 (basic operations) TEM data computer controls Fast Scan CCD holds data and provides ...
Contents blank minutes page.doc: template for minutes TEMIMPS PImtg Oct 10 2012.txt TEMIMPS PImtg Sep 4 2012.txt PI Meeting in Washington DC 7/2012 TEMIMPS ...
Annual Report 5/1/2012 Quarterly Report 4/1/2012 Quarterly Report 1/1/2012 Quarterly Report 10/1/2011 Quarterly Report 7/1/2011 Annual Report: May 1, 2011 Quarterly ...
Workshop in Electron Crystallography The Transcontinental EM Initiative for Membrane Protein Structure (TEMIMPS) is hosting a workshop in the theory and practice of ...
TEMIMPS Workshop in Electron Crystallography Lecture Materials August 15 19, 2011 University of Washington School of Medicine, Seattle, Washington Lectures Lecture ...
Contents TEMIMPS Workshop Schedule 2011 Monday Aug. 15 Tuesday Aug. 16 Wednesday Aug. 17 Thursday Aug 18 Friday Aug. 19 0830 Lecture: WelcomeLogistics and Introduction ...
Workshop in Dual Beam Scanning Electron Microscopy at the New York Structural Biology Center This workshop will introduce the new Helios 650 Nanolab microscope at ...
Visit the Cryo EM Website at http://www.nysbc.org/facilities/CEM Tomography using TVIPS EM Menu 3.0 Contents This Software Is No Longer In Use at NYSBC : Use SerialEM ...
The Office of Research Computing (ORC) aims to provide a state of the art Information Technology platform for all scientific information technology including the acquisition ...
Return to the Cryo EM Website at http://www.nysbc.org/facilities/CEM Tietz Tomography through EM Menu FEI Tomography software SerialEM tomography software Dual ...
Calibration and Parameter setting of 2DX Robot Vacuum set points vacuum set points for insertion and extraction are contained in the file ~/robot software/robot ...
NYSBC INFOTECH – WIFI AVAILABILITY To control possible misuse from logins outside the NYSBC building, a password requirement is being installed. Anyone ...
Return to Cryo EM web page at http://www.nysbc.org/facilities/CEM Principles Protocols Protocols Wohlwend Jump to Principles Start up Preparation ...
Contents XPLOR NIH supported version Source http://nmr.cit.nih.gov/xplor nih/download.cgi Local sources xplor nih 2.16.0 db.tar.gz: V 16 required databases ...
Screening and Scanning EM Film Procedure with screen shots available on web site http://www.nysbc.org/facilities/CEM/Zeiss PhotoScan Usage.html Download MSWord ...
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