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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 ...
Contents How to get a new affiliate endorsed and started (IF you are a Member of any NYSBC Scientific Committee please follow the EndorserEdit link to complete ...
Contents Loading MRC files: Need to select RAW data need to tell it image size (from header) Use "float", data type 1 header is 1024 bytes Loading ...
Contents Making Movies in Amira Instructions for version 3.0 (and above?) from David Stokes (created by Wanzhong He) 1 "install" the following scripts ...
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 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, ...
Policy on Time Allocation for NYSBC Electron Microscopy Facilities For each month, each Member Institution is entitled to a share of the resources proportional ...
Contents Processing FIB SEM data Make a stack of images 1 Copy data over from microscope 1 Select useful images 1 Make an mrc stack from several tif images ...
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 EMAN Refinement Files needed threed.0a.mrc the strating model, perhaps produced by common lines start.hed, start.img the particle stack ...
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 ...
Contents Slice and View Images Images collected using slice and view are saved as a series of 8 bit tiffs Since contrast on SEM is inverted from usual TEM ...
IT resources at the CEMfac List of supported SoftWare EmIP GUI for image processing Tomography MontageNavigator hints on using the Navigator in SerialEM ...
Contents Networking nfs mounts made directories /cem02bigdata/, cem03bigdata/, /cem12data/, ... change group of each one from "staff" to "wheel" under ...
Rules for Requests 1 Priority for each microscope is given according to preallocated schedule CemMicroscopeSchedule confirmed bookings are also shown on ...
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 Reconstruction by Random Conical Tilt Principals For a very good description, see Frank (2006) Three Dimensional Electron Microscopy of Macromolecular ...
Please Use the New Scheduler This page kept for historical reasons If you do not yet have an account, please email emg@nysbc.org Rules for Requests ...
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 Camera Webpages http://192.168.5.160 http://192.168.5.166 Automated Control and Robotics on 1230 Options for Automated Control ...
Single Particle Projects Random Conical Tilt (RCT) procedure methods used Oct 2012 Collect Data Prepare grids typically negative stain Use SerialEM to ...
Contents Install download and install EMAN2 daily release in EMAN2/eman2.cshrc, Pythonpath needs to be corrected from default: setenv PYTHONPATH $ ...
Contents Initial Setup need following packages: Apache, subversion, mod dav svn (install with yum) configuration edit /etc/httpd/conf.d/subversion.conf ...
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 Cyana documentation at NYSBC Reference papers /guntert03.pdf Suggested local procedure Preparing files 1 Login to the appropriate server, currently ...
DSA for DC: Matlab program (Drop Shape Measurement for Detergent Concentration quantification) Contents Program Installation DSA for DC is a matlab program developed ...
Conversion of a set of Digital Micrograph files to Tiff format: Had a cd of dm3 files, with various filenames, spread across many directories em2em did ...
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 ...
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 Installation and Updating of EMAN2 Download and untar the latest release from http://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstall go to installation ...
Contents General issues of scheduling at NYSBC Types of scheduling 1 "Type I" Scheduling of Phase I NMR instruments and any other resource predominanly funded ...
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 ...
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 ...
NEW YORK STRUCTURAL BIOLOGY CENTER POLICIES Printable version of this file. (pdf format) COMPUTER ELECTRONIC COMMUNICATIONS POLICY The Center’s policy on the ...
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 ...
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 Papers with high citation statistics associated with NYSBC investigators NMR/ Structural Biology Based on an ISI search using the terms "NMR AND (protein ...
Contents 2DX Installation 2DX v2 Nov 14 2007 installed version 2.1 rpm does not work on any of our linux boxes gives floating point exception ...
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 Nota: next updates of Leginon should be done on jeol1230 and on cem12. April Mai 2011 Modification of pyscope/jeol1230.py see jeol1230.py Autofocus ...
Automation of jeol1230 with iRobot, Leginon and Animated TEM Contents Startup User manual to use Leginon combined with the Matlab nodes associated to the Animated ...
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 2015 ...
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 ...
The following changes in booking NMR time are being introduced. During 2Q/2009, on line booking will start for the period beginning 3Q/2009. It is planned to modify ...
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 Password Synchronization on Spectrometers Passwords are synchronized between the Spectrometers and the SFTP server every 10 minutes. Initial Password The ...
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 ...
NMR SCHEDULE FOR NYSBC . This is the ALPHA release of the cycle 24 schedule. You are advised when using this for planning to always reload your ...
Created 7 Jul 2009 NOW LOCKED FOR ACCOUNTING. MAKE NEW SCHEDULE REQUESTS ON NmrSchedule33 ALL ADDITIONAL CREDITS / ADJUSTMENT TO BE MADE IN NmrSchedule33 Cycle ...
This is a test page to illustrate how an allocation alogorithm might work for the next quarter. THIS IS NOT AN ACTUAL SCHEDULE The current actual schedule is at ...
NMR Trade This page is for authorized persons to request a trade of a previuusly allocated or requested weeks on NmrSchedule for something else, usually a later ...
Contents Visitors !! We welcome everyone at the public seminars and meetings at NYSBC. Those formally affiliated with the Center are welcome during all ...
Return to Cryo EM web page at http://www.nysbc.org/facilities/CEM Principles Protocols Protocols Using the PDS 1010GM Microdensitometer Download MSWord file ...
Contents RCS system type "man rcsintro" on any linux system ... RCSINTRO(1) RCSINTRO(1) NAME rcsintro introduction ...
Contents One Line scripts for sed HANDY ONE LINERS FOR SED (Unix stream editor) Apr. 26, 2004 compiled by Eric Pement pemente at northpark dot edu ...
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 ...
Contents Instructions for processing Single particle crystals 1 Setup directories: mkdir doc mkdir patch mkdir coran mkdir classavg 2 Convert from mrc ...
Contents List of Supported Software EM Image Processing Program Version Location Installed on cluster? Spider 15.10, 17.12 /cryoem/spider ...
How to tunnel port through SSH (e.g. for using VNC remotely) Why? If you are at another institution or at home and wish to use/monitor NYSBC computer like the cluster ...
xtracedrop program for characterizing drop shape and quantifying detergent concentrations Contents Program Installation xtracedrop is a python program (xtracedrop ...
Thermoshake Program tcontrol.zip Other info (from inheco contact) Attached is the DLL Command Set. you will find the description of the error 16 (No or false Modbus ...
(15.4; 688.1; 0.1) Robot Manuals (leave this at the top) Controller manual RCX142 e.pdf: rcx142 manual (this is most useful) RCX143 144 e 0322 v1.02.pdf ...
Contents XEASY manual: 3. The XEASY Model previous: 2. Using XEASY / contents 3. The XEASY Model To enable computer supported spectra interpretation, an operational ...
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For copyright reasons, you will not be able to access articles on computers outside the networks of the Member Institutions NYSBC affiliates are welcome to make ...
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