EMAN Wiki

align2d

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T18:57:10+00:00

align2d This program will align a set of images to a reference Usage align2d [fixn=] [noflip] [precen] [seqali] [eulali] [pgm] [log] [edgenorm] [keepeulers] Parameters Reference image Images to be aligned

align3d

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T18:57:32+00:00

align3d Rotational and translational alignment of 3d models Usage align3d [checkflip] [trans] [refine] [slow] [noshrink] [p3d] [saveref] [precen] Parameters The reference to align to Volume to be aligned

align3dsym

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T18:57:51+00:00

align3dsym This will rotate a 3D model so its symmetric axes are aligned on the predefined axes Usage align3dsym sym= [mask=] [imask=] [refine] Parameters Source file Destination file

cibrclusters

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T21:32:28+00:00

CIBR Cluster Co-op WARNING: The existing CIBR clusters are now >10 years old, and we no longer know how long the room housing them will remain operational due to BCM cuts. If you have material on the CIBR Clusters we strongly suggest moving it to local storage at your earliest convenience. Note also that

cibrclusters_sphere

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T21:20:15+00:00

Return to the CIBR Cluster Home Page Sphere Overview Sphere is a medium-scale high performance linux cluster purchased by a collaborative arrangement between CIBR, and the Ludtke, Barth, Waterland and Guan labs. Each group that contributed financially to the purchase of the cluster is entitled to a proportional amount of the overall compute capacity of the cluster. In theory, the cluster can provide up to 6M CPU-hr of computation annually, however, it is impossible to keep such a cluster ful…

compileemanonubuntu10.04

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:07:16+00:00

This page wasn't converted from the old Wiki

eman1

Anonymous (anonymous@undisclosed.example.com) — 2025-06-19T03:43:04+00:00

EMAN 1.9 released 02/2009 IMPORTANT NOTICE - EMAN1 is now quite out of date, and is no longer being updated in any way. Modern standards require “gold standard” resolution assessment and many reviewers will also require things like tilt validation. All of these things are fully supported in EMAN2. EMAN2.1 has eliminated all of the issues users found frustrating about EMAN2.0, and we strongly encourage people to upgrade.

eman1_faq

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T14:46:26+00:00

FAQ This is the new EMAN Frequently Asked Questions page : * YOU MUST CREATE AN ACCOUNT FOR YOURSELF TO EDIT THIS PAGE. Click on the Login button above, then follow the UserPreferences link. * Create a new link below by copying an existing one, and put a summary of your question as the description

eman1_faq_asymmetric

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T15:48:57+00:00

Q: I have an asymmetric particle, how do I get a good starting model and refine it ? A: Note: The EMAN2 workflow includes a method for automating the process of generating many initial models, automatically refining each with downsampled data, and assessing the results. This may be a much easier solution than the EMAN1 methods below. You can use EMAN1 class-averages with the e2initialmodel.py program in EMAN2, then take the resulting model back into EMAN1 (if you really want to move back to EMA…

eman1_faq_filter_when_i_lowpass_filter_a_map_the_resolution_looks_too_high_and_when_i_combine_multiple_filters_the_results_aren_t_what_i_expected

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T17:49:32+00:00

Q: EMAN1/FAQ/Filter When I lowpass filter a map the resolution looks too high, and when I combine multiple filters, the results aren't what I expected. A: The behavior you're seeing is exactly correct. While there was a time at which in icosahedral reconstructions, people tended to use a 'hard' cutoff filter, eventually they realized how nasty the ringing artifacts this produced were, and switched to smoother filters. In most cryoEM work, people use Gaussian filters nowadays, though in some ins…

eman1_faq_gui1

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T14:40:22+00:00

The reason for this error is that you are running a very old Linux system. The X window libraries are not compatible with the one I used to compile EMAN1.8. If you don't want to upgrade your Linux, you can download the daily release of EMAN. It is built on an old Linux system. This daily release copy will not run on most current Linux system. That's the reason we build the EMAN 1.8 binary on a newer system to cover current Linux release and some older system (but not too old).

eman1_install

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:01:25+00:00

EMAN1 Installation and Tips EMAN1 is now 15-20 years old. Please do not assume you will be able to easily get it to compile or install on a modern Linux distro. It isn't impossible, but it isn't likely to be easy. Binary Packages We provide EMAN1 binary packages on several platforms: Linux(x86), Linux(x86_64), SGI(Irix6.5), Win32, Mac

eman1_library

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:24:10+00:00

EMAN1 Programmer Docs Under Construction (LOL)

eman1_programs

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:17:23+00:00

EMAN1 Individual Programs There are over 200 command-line programs in EMAN, this list contains more detailed documentation for the most commonly used programs. See the fixed documentation for a full list. GUI Programs eman Image browser and tutorial interface boxer Manual particle picking ctfit CTF parameter determination and simulation

eman1_programs_applyctf

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:00:02+00:00

applyctf Applies/corrects CTF to sets of particle images Usage applyctf [setparm] [fixnoise] [parmimg=] [memfile=] [parmmem=] [parm=] [sffile=] [applyctf] [flipphase] [invert] [applyB[=]] [addnoise[=]] [wiener] [mrc] [inplace]

eman1_programs_batchboxer

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T18:59:08+00:00
batchboxer This program is used for offline boxing of micrographs (MRC format ONLY!) Usage batchboxer [input=] [dbbox=] [imgbox=] [refimg=] [auto[=,,]] [mindist=] [xform=,,] [scale=] [newsize=] [output=] [ctfout=] [dbout=] [invert] [adjust=] [insideonly]

eman1_programs_boxer

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:20:00+00:00
A graphical program for locating particles within micrographs. Usage boxer [] [area=,,] Description Boxer is a graphical program for selecting particles from micrographs (or CCD frames). Particle selection can be performed manually or semi-automatically. Run the program with the name of the image containing particles to be selected.

eman1_programs_ctfit

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:20:41+00:00
ctfit A graphical utility for determining CTF parameters directly from data collected on transmission electron microscopes. Usage . ctfit Overview Data collected on a transmission electron microscope contains an artifact due to physics of electron optics. This artifact is known as the contrast transfer function, or CTF, of the microscope. In addition, incoherent background noise from multiple sources is present in the images. 'ctfit' allows the user to determine the paramters of the CTF in…

eman1_programs_eman

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:18:51+00:00
The main graphical user interface for the EMAN package. Usage eman Description This is the main graphical user interface program for EMAN. It has 2 purposes. First, It will take you step by step through the process of performing a single particle reconstruction. Second, it has a file/history browser which allows you to analyze the results of your reconstruction, view image files, create figures for presentations, etc.

eman1_programs_fitctf

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T18:59:33+00:00
fitctf This program estimates CTF parameters in batch. The results should be checked in CTFIT Usage fitctf [sf=] [apix=] [V=] [Cs=] [over=] [acmax=] [acfix=] [Bhint=] [Bexp] [debug]

eman1_programs_foldhunter

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:09:39+00:00
foldhunter.py Python script for quickly running foldhunterP in chimera Usage foldhunter.py Parameters: Input mrc file Input pdb/mrc file resolution a/pix Description Runs foldhunter

eman1_programs_helixboxer

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:23:12+00:00
helixhunter.py Python script for quickly running helixhunter in chimera Usage helixhunter.py Parameters || ||Input mrc file|| || ||anstroms/pixel|| Description Generates pdb helices from target mrc using helixhunter

eman1_programs_helixhunter

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:11:54+00:00
helixhunter.py Python script for quickly running helixhunter in chimera Usage helixhunter.py Parameters Input mrc file anstroms/pixel Description Generates pdb helices from target mrc using helixhunter ----------

eman1_programs_iminfo

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T18:50:00+00:00
iminfo This program provides basic information about image files Usage iminfo [all] [stat] [first=] [last=] Parameters File to examine[all]Give detailed information about each image in a stack file[stat]Statistical information about the image(s)

eman1_programs_multirefine

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T18:47:29+00:00
multirefine . This performs refinement on a set of 3D models simultaneously Usage . multirefine <# models> [sym=,,...] [] Parameters As in refine <# models>The number of 3D models being refined[sym=,,

eman1_programs_proc2d

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T18:47:58+00:00
proc2d This program performs various processing operations on images and sets of images proc2d [first=] [last=] [list=] [exclude=] [nobad] [inplace] [edgenorm] [norm[=,]] [invert] [flip] [rot=] [trans=,] [center] [acfcenter] [scale=] [clip=] [shrink=] [meanshrink=] [apix=] [lp=] [hp=] [tlp=] [rfilt=[,[,[,]]]] [blfilt=

eman1_programs_proc3d

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T18:48:29+00:00
proc3d Misc. 3d image processing proc3d proc3d [shrink=
] [scale=] [clip=] [fftclip=] [rot=] [rotspin=] [trans=] [posttrans=] [center] [acfcen] [apix=] [origin=] [lp=] [hp=] [tlp=] [unhp=] [filefilt=] [rfilt=[,[,[,]]]] [blfilt=] [normfilt=] [axialf…

eman1_programs_procpdb

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T18:49:14+00:00
procpdb.py This program is for performing simple operations on PDB files Usage procpdb.py [] [rot=] [trans=] [posttrans=] [centeratoms] [centerelec] [centermass] [animorph=,,] [apix=] [split] [include=[helix,sheet,other] [chains=]

eman1_programs_qindex

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:21:55+00:00
qindex qindex is an experimental program to do initial screening of 2-D crystals, and perform single-particle style averaging on data from poorly ordered crystals. It was developed in collaboration with Gina Sosinsky (as an end-user). This is not exhaustive documentation, but should be enough to get you started with it:

eman1_programs_qsegment

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:21:29+00:00
qsegment . A graphical program for segmentation and simple exploration of 3D models Usage . qsegment Description This program is used to interactively segment (split into pieces) a 3D volume dataset. It can also be used to examine 3D data slice by slice from any angle. This is the initial release of this program, and the documentation is not complete yet. email sludtke@bcm.tmc.edu if you need assistance.

eman1_programs_refine

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T18:46:11+00:00
refine This is the main refinement loop in EMAN. It has a tremendous number of options. Usage refine mask= [proc=] [hard=] [simple] [ctfc=] [ctfcw=] [phaseopt] [setsf=[,[,]] [median] [nweight] [sym=] [ang=] [anglist=] [maxshift=] [pad=] [classkeep=] [classiter=] [refmaskali] [filt3d=] [sep=] [xfiles=,,] [3dit=

eman1_programs_refine2d

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T18:45:41+00:00
refine2d.py This program performs 2-D refinement of particle sets. No 3-D references or models are used. Usage refine2d.py [--iter=] [--ninitcls=<# initial classes>] [--finalsep=<# split each class>] [--minptcl=] [--proc=<# processors>] [

eman1_programs_sfmerge

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:00:24+00:00
sfmerge.py Combines a structure factor from CTFIT with a simulated curve for use in CTF correction Usage sfmerge.py Parameters File produced by CTFIT 2 column text file containing high resolution structure factor

eman1_programs_speedtest

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T18:52:44+00:00
speedtest This program runs a set of speed tests on the current machine. Usage speedtest Description This program runs a set of speed tests in the current computer. It should have at least 1 unloaded processor, and minimal i/o occuring when this is run. It will give a single value which should be generally proportional to how fast refine will run on a given computer. It is a 'real world' test, in that it simulates a variety of actual operations performed by a refinement procedure. Don't …

eman1_programs_v4

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:21:06+00:00
V4 . An interactive program for viewing projections generated from 3d models Usage . v4 <3d model 1> <3d model 2> ...<
> <3d model> is a list of files containing valid 3d models<
> Typical usage: v4 threed.1a.mrc threed.2a.mrc Description

eman1_projects

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:12:42+00:00
Q: I was in Houston for your last workshop on EMAn and i would like to know when we can obtain the videos from the course. They are being converted, but it is a slow process. They should be available on the workshop page when done. (and now 18 months later, I have no idea what happened :^( )

eman1_spaoverview

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:16:42+00:00
under construction For the moment, please continue to use the tutorial interface in the 'eman' program. Just run 'eman' and hit 'step 1'.

eman2

Anonymous (anonymous@undisclosed.example.com) — 2026-02-10T12:24:05+00:00
EMAN2.99.47 UPDATE 7/7/25 The EMAN2 wiki was undergoing a massive hacker attack, and we were forced to update to a newer Wiki system. The transition should now be complete, but the URLs for links are using a new style so old bookmarks won't work, so you will need to navigate to the pages again and re-bookmark.

eman_compile_macos_x

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:08:10+00:00
PREFACE This page contains instructions on compiling EMAN for OS X for use on a single machine. Instructions for a distributable build, that includes all dependencies inside a single package, are here: EMAN_COMPILE_MacOS_X_for_Distribution Building on 10.5 is highly recommended over 10.4 because of compilation problems, old version of built-in python, and less included dependencies. These instructions will only cover 10.5. Building on x86 and ppc should both be supported. For 64 bit support, e…

eman_compile_macos_x_for_distribution

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:13:58+00:00
PREFACE This page contains instructions on compiling EMAN for OS X in a format suitable for distribution for the 4 main OS X supported architectures: 32 and 64 bit PowerPC and Intel x86. This requires significantly more work than setting up a simple environment to use on just one machine. Instructions for a non-distributable build are here: $BROOT and $

eman_compile_static

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:05:05+00:00
The idea to semi-static build EMAN is to link EMAN’s dependency libraries statically into EMAN’s shared libraries: libEM.so, libpyEM.so, libqEM.so, libqsci.so. By this way, the compiled EMAN can be run on another system even though it does not have those dependent libraries. You can specify each dependent library in ccmake to link to static library, for example libgsl.a instead of libgsl.so. And make sure there is no shared library in the same directory, otherwise, linker will prefer the shared …

eman_compile_ubuntu7.04

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:06:15+00:00
This page wasn't transferred to the new wiki

eman_compile_unix

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:02:39+00:00
EMAN depends on some third party libraries: Some dependency libraries are mandatory, like fftw2, gsl, and cmake for eman compilation. Some others are optional, like boost.python, Python if you need run Pyhton program in EMAN or want to program in Python with EMAN, you can turn this option off by switching ENABLE_PYTHON to off. And ${EMANDIR}/bin:$${EMANDIR}/lib:$${EMANDIR}/lib:$

eman_compile_windows

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:04:35+00:00
First of all, install a windows version of CMAKE. Then open Cmake, specify visual studio 2003 .NET as your compiler (or other compiler available on your windows system). Then specify EMAN source directory and build directory. Then configure and build to get a project file for VC++ 2003 .NET. Start your visual C++ 2003 .NET, open the project file for EMAN, then build all. There are several things need your attention to build EMAN successfully: 1. Add a blank config.h file to your /eman directory;

emen

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:20:05+00:00
[EMEN2|width="250"] EMEN2 An extesible, object-oriented electronic lab notebook Structural and computational biologists frequently work with complex data sets assembled from diverse experimental sources, public resources, and analysis methods. Archiving and mining these data sets with their complicated interrelationships remains a persistent challenge, particularly with “open science” initiatives to make entire workflows, including all raw and intermediate data, available with publications.…

emen2

Anonymous (anonymous@undisclosed.example.com) — 2025-06-19T03:41:52+00:00
[EMEN2|width="250"] EMEN2 An extesible, object-oriented electronic lab notebook Structural and computational biologists frequently work with complex data sets assembled from diverse experimental sources, public resources, and analysis methods. Archiving and mining these data sets with their complicated interrelationships remains a persistent challenge, particularly with ?open science? initiatives to make entire workflows, including all raw and intermediate data, available with publications.

emen2_api

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:38:54+00:00
EMEN2 Public API Time * time.difference * time.now Utilities * version * ping Auth * auth.login * auth.logout * auth.check.context * auth.check.admin * auth.check.readadmin * auth.check.create Generic methods

emen2_backups

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:26:06+00:00
EMEN2 Backups An EMEN2 environment contains a number of things: BerkeleyDB files: * _db.* (environment backing files) * data/ (databases) * journal/ (transaction journal) EMEN2-managed file attachments: * binary/ (file storage) * preview/ (thumbnails and other derived data)

emen2_dependencies

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:23:13+00:00
EMEN2 Dependencies To run the EMEN2 server, Berkeley DB, bsddb3, and dateutil are required for basic functionality. If you want to run the web server, you will also need Twisted, Markdown, Mako, and jsonrpc. Additional server features, such as thumbnails and image analysis, are provided by EMAN2 and ImageMagick.

emen2_emdash_install

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:40:24+00:00
EMDash Installation EMDash can be installed using “easy_install” or you may download the source and use “setup.py” Download EMDash sources Dependencies * PyQt4 * Python bindings for Nokia's Qt toolkit * You will want to install the Qt Library using Nokia's installer package.

emen2_emdash_tutorial

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:40:51+00:00
EMDash EMDash is an EMEN2 client program for uploading images during a microscopy session. It includes tools for session management, commenting, viewing records, uploading, and watching data directories for new files. <> This is a screenshot of an active EMDash session. Each component in the interface will be described in the following sections.

emen2_emen2ctl

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:24:27+00:00
EMEN2 control script (emen2ctl) Similar to Apache's “apachectl” script, EMEN2 includes an “emen2ctl” script. This can be used to start and stop the server and perform some basic administration tasks. Running emen2ctl Note: Depending on how you installed EMEN2, emen2ctl may not be in your $PATH. On Linux, using the recommended installation, it will probably be $$HOME/test.db") or by setting the $

emen2_extensions

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:39:58+00:00
# EMEN2 Extensions # Note: More to come... The EMEN2 web interface can be extended fairly easily. First, create a directory with the following structure: / /%%__%%init%%__%%.py /views/ /views/%%__%%init%%__%%.py /views/example.py /templates/ /templates/example/ /templates/example/example.mako

emen2_hardware

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:25:18+00:00
Planning hardware requirements EMEN2 runs well on commodity servers running recent versions of Linux. For a typical lab, a 4-core machine with 16gb of memory and running CentOS 6.x or RedHat Linux should be adequate. The more important consideration is storage. If you plan to use EMEN2 as a long term solution for archiving data from your lab, you will need to consider how much raw data is produced. The cost of storage tends to decrease every year, so you may want to plan on an initial 2-3 year…

emen2_install

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:23:53+00:00
Installing and configuring EMEN2 EMEN2 has a number of dependencies, which are described on the dependencies page. However, because EMEN2 is often used with EMAN2, we have packaged all of the EMEN2 dependencies along with binary builds of EMAN2, which greatly simplifies installation. See the $HOME/EMAN2; make sure to run the "EMAN2/eman2-installer" script and add the resulting EMAN2 init script (EMAN2/eman2.bashrc) to your shell rc (usually $$HOME/EMAN2, you would use $

emen2_public_data_server

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:20:59+00:00
EMEN2 (Electron Microscopy Electronic Notebook) EMEN2 Home Page EMEN2 is an object oriented database and electronic lab notebook. It is designed to store scientific data in a freeform way without limiting the ability to search/mine the results. Unlike a traditional database, where the contents of each record type (table) must be defined by a database administrator and strictly adhered to, each individual record in EMEN2 can have arbitrary additional parameters outside the record definition, a…

emen2_rpc

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:39:23+00:00
Accessing the EMEN2 Public API using JSON-RPC and XML-RPC All public API methods are available via JSON-RPC, which is a language-neutral Remote Procedure Call protocol based on the JSON standard. We have published a simple JSON-RPC module for Python and JavaScript (described below) that can be used with EMEN2. In the future, we plan to provide similar access via a simpler REST

emen2_startup

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:24:49+00:00
Running EMEN2 at system boot For systems that will run EMEN2 continuously, I highly recommend creating a dedicated “emen2” account. This will run EMEN2 using regular user-level permissions instead of as root. Please see your operating system documentation for creating a new account.

eotest

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T18:46:37+00:00
e2eotest This program supplements e2refine.py by splitting the data into even and odd halves and computing (semi)independent reconstructions for computing the resolution of a reconstruction. The parameters it takes are a subset of the parameters that e2refine.py takes. You should generally use exactly the same parameters (for the subset accepted) used for e2refine.py when running this command. The result is even/odd class-averages and models for one iteration of a refinement as well as correspo…

faq_eman_using_13

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:31:29+00:00
Question: What paper should I cite if I use EMAN1 in published results ? Answer: This one: Ludtke, S.J., Baldwin, P.R., and Chiu, W. (1999). EMAN: semiautomated software for high-resolution single-particle reconstructions. J Struct Biol 128, 82-97.

faq_eman_using_31

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T15:49:54+00:00
Question: What sort of problems will EMAN have with initial model bias ? What if I can't get my structure to converge to something sensible in EMAN, but I can in another program ? Answer: This is largely answered in the question above relating to resolution of reconstructions. If you are not using optimal options with the refine command, you may, indeed, not get optimal results. The basic options provided by the EMAN tutorial do not give the entire picture. For example, if you continue to use c…

lstcat

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T18:53:03+00:00
lstcat.py Generates a 'lst' file from a set of input image stacks Usage lstcat.py ... Parameters Output file, MUST BE SPECIFIED FIRST ...Input file(s), may be images of any type Typical usage: lstcat.py start.lst orig.1.hed orig.2.hed orig.3.hed

macosxbuildfiles

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T03:14:58+00:00
Script files Patches Info.plist files

makeinitialmodel

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:00:46+00:00
makeinitialmodel.py Interactively allows the user to make an initial model for iterative reconstruction Usage makeinitialmodel.py Parameters None Description Interactive prompts, no documentation. ---------- EMAN Manual page, generated Mon Jan 8 17:35:59 2007

orphans

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T22:28:19+00:00

pdbtomrc

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T18:55:22+00:00
pdb2mrc This program will generate a 3D electron density map from PDB files Usage pdb2mrc [info] [apix=] [res=] [box=] [het] [center] [solvate] [full] [sym=] [rot=] [gen1] [sf=]

ptcltrace

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:06:14+00:00
ptcltrace Trace how classification of a single particle changes Usage ptcltrace [ptcl=[,]] [iter=[,][-]] [sym=] [simple] [report] [zap=] Parameters [ptcl=[,]]Particle number to evaluate (range 0-n)[iter=[,][-]]

segment3d

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:08:45+00:00
segment3d Split a 3d map into several pieces. Usage segment3d [watershed[=[,]] [nseg=] [morph=] [ampw] [thr=] [split] [maxit=] [itxp=] [vector=] [apix=] [chimeraout=] [pdb=] [gaussmod=] [randomize] [stats] [segmaxv] [resegbystats=] [sym=]

start

Anonymous (anonymous@undisclosed.example.com) — 2025-08-07T12:17:18+00:00
Ludtke Lab - Baylor College of Medicine This is the main webserver for the Ludtke Lab. It documents several NIH supported projects, provides educational materials and has a range of historical resources, including some from the National Center for Macromolecular Imaging, a NIGMS P41 center which was at BCM for ~30 years.

startany

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:05:47+00:00
startAny This program will generate a 3D model from a set of class averages, using cross common lines. Usage startAny [sym=] [proc=] [rounds=<2-5>] [mask=] [lp=] Parameters File containing class averages to be used

startcsym

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:01:09+00:00
startcsym This program generates a preliminary 3d model for objects with Cn or Dn symmetry. Usage startcsym <# to keep> [sym=] [imask=] [nosym] [fixrot=] Parameters Raw centered particles to use to build a model

starticos

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:05:09+00:00
starticos This program generates a preliminary 3d model for objects with icosahedral symmetry. Usage starticos <# to keep> [imask=] [nosym] Parameters Raw centered particles to use to build a model

startoct

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T19:05:28+00:00
startoct This program generates a preliminary 3d model for objects with octahedral symmetry. Usage startoct <# to keep> [nosym] Parameters Raw centered particles to use to build a model <# to keep>Number of particles to use for each view

volume

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T18:58:15+00:00
volume This program calculates the volume/mass of a 3D map Usage volume [thr=] [calc=] [set=] [plot] Parameters 3D map to work with Angstroms/voxel in the map[thr=]Calculate the volume/mass at a given threshold

ws2011

Anonymous (anonymous@undisclosed.example.com) — 2025-06-19T12:10:07+00:00
Material for NCMI 2011 Workshop on CryoEM Single Particle Analysis This page contains several links (in the table below) to the software and data you need to download for each of the specific tutorials at the workshop. People using the on-site desktop PCs do not need to install anything in advance, unless they wish to do something on their laptops as well.

ws2011_agenda

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T20:42:07+00:00
NCMI Workshop on Single Particle Reconstruction, Validation and Analysis March 14 - 17, 2011 This page contains the workshop schedule, and will contain the PDFs of each of the presentations at the workshop. Speakers are asked to upload their presentations sometime before the beginning of their talk (preferably as far in advance as possible).

ws2011_chimera

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T20:30:39+00:00
Chimera Tuesday Morning Practical Chimera is a comprehensive tool for molecular/macromolecular visualization. It will be used as a complementary tool throughout the workshop, and will be required to fully participate in the practical sessions. Tom Goddard, developer of Chimera volume capabilities will give the tutorial.

ws2011_direx

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T20:33:33+00:00
DireX Thursday AM Talk/Practical DireX is a tool for real-space refinement of atomic models against (low-resolution) density maps. You can download a copy from the SimTK website: You should use the latest development version 0.5-devel (rev124). This is not a full release yet, there are still quite some things that need further testing, in particular some new recently added features. However, the basic functionality should work as in the previous (0.4) ver…

ws2011_eman2

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T20:26:20+00:00
EMAN2 This page contains an EMAN2 single particle reconstruction tutorial using real data. This page is part of the 2011 workshop. Tutorial Here are the two parts of the tutorial (linked from the workshop agenda page): Part 1 Part 2 You MUST use a current version of EMAN2 for these tutorials, not an older release. If you have an old version installed, please upgrade to 2.01 or newer, and be sure to run 'e2bdb.py -c' under the old version BEFORE installing the new version !

ws2011_emen2

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T20:34:18+00:00
EMEN2 Thursday PM Practical EMEN2 is a web-based electronic notebook and object oriented database. While it has so-far been used primarily for cyro-EM, it is completely flexible and can easily be adapted to other disciplines. We are gradually building connectivity between EMEN2 and EMAN2, as will be demonstrated.

ws2011_frealign

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T20:34:47+00:00
Frealign Overview Frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles, originally developed at the MRC/LMB. It is now developed and maintained by the Grigorieff lab at Brandeis. The main Frealign documentation can be

ws2011_gorgon

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T20:32:20+00:00
Gorgon Thursday PM Practical Gorgon is an interactive molecular modeling system specifically geared towards near-atomic resolution density maps of macromolecular assemblies. It is being developed as a collaboration between Washington University in St. Louis (Tao Ju) and Baylor College of Medicine (Matthew Baker).

ws2011_location

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T20:39:19+00:00
All the workshop activities are taking place at the University of Houston in rooms 232 and 200 of Philip G. Hoffman Hall. A full campus map is available here. We have arranged for free parking in a reserved section of the stadium lot (see map). As with any other urban area, we suggest using caution if walking alone at night.

ws2011_rosetta

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T20:32:45+00:00
Rosetta Thursday PM Practical Rosetta is an object-oriented software suite which provides a robust system for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions. For the tutorial, you can download binaries of Rosetta for:

ws2011_segger

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T20:37:46+00:00
Segger Wed AM Practical Segger is a tool for segmenting density maps and for quick rigid-body docking of structures into density maps [1]. The software is distributed as part of Chimera which will already be installed for the workshop. Segmentation

ws2011_sparx

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T20:36:57+00:00
SPARX Tutorial Session Note Please download file codim.tar.gz using link on page prior to Tuesday session, preferable before arriving to the workshop. The file is ~600Mb and may take awhile to upload. Tuesday afternoon By Tuesday, you should have EMAN2 installed and running. SPARX is part of the same installation package. To make sure it runs properly, at a prompt type .

ws2011_spt

Anonymous (anonymous@undisclosed.example.com) — 2025-07-05T20:38:09+00:00
Single Particle Tomography in EMAN2, 2011 WORKSHOP in Houston, TX The SPT page has move to This is just an archaic page with the version of the tutorial used in the EMAN2 Workshop in March 2011. OLD E2SPT USERS' GUIDE * Single particle tomography USER'S GUIDE (March 2011).

ws2012

Anonymous (anonymous@undisclosed.example.com) — 2025-06-19T12:10:48+00:00
EMAN2 This page contains an EMAN2 reconstruction tilt validation tutorial using real data. Tutorial In this tutorial, we will validate the Ip3R structure or the PRD1 Virus(your choice): You MUST use the EMAN2 nightly build for this tutorial. In the future, we will put out EMAN2.1, which will be sufficient for EM validation. Follow this link to download the EMAN2 Nightly build:

ws2013

Anonymous (anonymous@undisclosed.example.com) — 2025-06-19T12:12:52+00:00
International Workshop of Advanced Image Processing of Cryo-Electron Microscopy Institute of Biophysics, Chinese Academy of Sciences, Beijing These tutorial materials are for the workshop hosted by the Chinese Academy of Sciences in Beijing in July 2013. Each day of the workshop is devoted to a different software package. The material on this page is the training material for EMAN2.

ws2015

Anonymous (anonymous@undisclosed.example.com) — 2025-06-19T12:13:58+00:00
NCMI Workshop on Single Particle Reconstruction, Structural Variability and Modeling Oct 30 - Nov 2, 2015 We strongly recommend bringing a 3 button (or 2 button+scroll) mouse. While it is possible to survive with a trackpad or one button mouse, there are many things in EMAN and Chimera where having additional mouse buttons is VERY useful.