EMAN Release Notes (1.7)

Welcome to EMAN 1.7.  Remember the full online help for EMAN is always available by pressing the "HELP" button in eman. Most of our development effort is now focused on the completely revamped EMAN 2.0, though another release in the 1.x series is likely.

EMAN 1.7 has some major enhancements over 1.61.

• Major overhaul of parallelism infrastructure (runpar). Now uses fileserver for both reads and writes in the cluster versions. Fault tolerance has also improved. If a node dies during a run, the run will continue, and simply stop using that node. Better job distribution to nodes.
  
• Binary release for AMD64, and better support for OSX (still imperfect).
• New program refine2d.py for generating reference-free class-averages from a set of particles. Uses a combination of SVD and alignment. MUCH better than startnrclasses.
• New program makeinitialmodel.py for constructing 3D models from blobs, good for making random or deterministic shapes.
• Greatly expanded and improved AIRS software with Chimera bindings. This includes tools for locating secondary structure in intermediate resolution maps (ssehunter.py), docking crystal structures (foldhunter.py), and many other useful tools.
  
• Support for both full and 1/2 maps for icosahedral reconstructions
• Support for exponential envelope functions in CTF correction (normally Gaussian), email if to ask about this.
  
• Major improvements to experimental 2D crystallography preprocessing program (qindex)

• PIF writer fixed
• Reader for 3D .dm3 files added (Digital Micrograph)
• AMIRA file format support (r/w)
• Fixed MRC/CCP4 compatibility problem
• Fixed SPIDER read for 1 image stacks
• Problem with A/pix adjustment when scaling fixed
• Improvements to tiltseries (simple tomography program), though the EMAN2 equivalent is much better.
  

• dfilt option in refine works now. This is the major cause for the 1.6 release. This option was used for our recent 6 A reconstruction of GroEL, and we have been touting it as the best current approach for doing EMAN reconstructions (which it is). Unfortunately, due to an unfortunate error on my part, a critical change never got updated in the EMAN source repository. So, essentially, this option worked very well for me, but not for anyone else. Anyone who was experimenting with the dfilt option should give it another try. On the bright side, the bug wasn't causing any harm, specifying dfilt in the buggy version was almost equivalent to not specifying it at all. I apologize for this nasty snafu.
• Better support for icosahedral reconstructions and for reconstructions of large models (contact wjiang@bcm.tmc.edu for more info)
• Some programs didn't like EMAN's MRC files. They should now be properly CCP4 compliant.
• EM file format support was minimal in last version, now properly handles stack files and byte-ordering
• New program qplot utility for plotting 2 column text files.
• EMAN can now compile and run on Macs (again). OS 10.3 only, with appropriate fink packages installed. This is still not officially supported.
• The >2G file support was apparently broken in v1.5. This has been fixed.
• Improved 64-bit support for use on Athlon-64's and Opterons. This is currently the fastest platform available for EMAN refinements (and the most cost-effective)
• Support for KDE 3.2/Mandrake 10.0
• Fixed funny narrow display in some cases in asymmetric triangle viewer
• fitctf improved to work on a wider range of images, including particles from CCD frames
• usefilt support in multirefine
• MRC file i/o improved for use with chimera

Known bugs:

• While we've fixed the majority of the lockup problems that occured under OSX and a few other specific systems, there still seem to be some problems running under RH9 with Gnome. KDE has no problems. This seems to be a wierd incompatibility between QT and Gnome on this platform.

• dfilt option in refine (great results, but requires ctfcw=)
  
• Prototype of animation module and other tools for Chimera
  
• Chimera output in segment3d, autosegmentation of symmetric structures
• Fixed bug in PNG image writing
  
• Better PGM image writing
  
• Chimera-compatible MRC header information on all MRC file writes
• Improvements to procpdb.py
  
• Fixed bugs with alignments in images not divisible by 4
• realfilter 110 and 111 for iterative expansion of masks
  
• Binaries for more Linux platforms
  

Here's a list of the major changes in version 1.40:

• 3dit/3dit2 - A number of recent problems have been associated with these options, and we have found that they are actually not necessary in many cases. If you experience strange problems with your 3D models containing horizontal bands, or being completely black, try not using these options. We are working to resolve this issue in a more satisfactory way. If they are necessary for your project (try running clean3d manually on a model and see if there is a substantial impact), look for an upcoming nightly release version to address this problem.
• Substantial improvements were made to EMAN's parallelism. When used on small particles on a large number of processors, the previous versions of EMAN would run at less than 100% capacity on each processor. The new version should run at 100% on fairly large numbers of CPUs.
• Python support - EMAN now officially supports Python scripting. Some very powerful operations can be performed with some very simple (and easy) scripts. Just to give you the flavor, here's a quick example which will compare class-averages to projections:

python
from EMAN import *
img=readImages("classes.1.hed",-1,-1)
for i in range(0,len(img),2):
    print i," vs. ",i+1," -> ",img[i].lcmp(img[i+1],1,0)[0]

• New options in the refine command:
  • setsf=<res> - Will apply the user defined 1D structure factor to the final reconstructed model after each iteration. This represents the ultimate in CTF amplitude correction. While the 'ctfcw=' option does a very good job of CTF correction, it does make certain assumptions which aren't valid in all cases. If you have a reliable structure factor (from x-ray solution scattering, or generated from a set of micrographs), this option is highly recommended.
  • refine - How confusing, an option with the same name as the command. Normal alignments in EMAN classification are +- 1 pixel. This option will refine all 2D alignments to +-.05-.1 pixels. This can signficantly improve classification accuracy for certain structures, and hence improve resolution. In some cases it will have little or no effect. There is a significant speed penalty associated with this option.
  • phasecls - This option will use signal to noise ratio weighted phase residual as a classification criteria (instead of the default optimized real space variance). Over the last year or so, people working on cylindrical structures (like GroEL), have noticed that 'side views' of this particle seem to frequently get classified as being tilted 4 or 5 degrees from the side view. While apparently this didn't effect the models significantly at the obtained resolution, it is quite irritating. This problem turns out to be due to resolution mismatch between the 3D model and the individual particles. Using phase residual solves this problem, although it's unclear if there is any resolution improvement. This option has a slight speed penalty
  • fscls - An improvement, albeit an experimental one, over phasecls. phasecls basically ignores Fourier amplitude when making image comparisons. fscls will use a SNR weighted Fourier shell correlation as a similarity criteria. Preliminary tests have shown that this produces slightly better results than phasecls, but it should still be used with caution.
  • slow - This option tries to do an even better job of 2D particle alignment. Used with the 'refine' option above, this option uses fsc as a criteria during alignment. This is quite slow, but theoretically even more accurate.
  • axialfilt=<val> - In theory, direct Fourier reconstruction algorithms, such as the one used in EMAN are not susceptible to problems with an excess of images in a particular set of orientations. However, there are certain circumstances under which this is not the case, and a certain amount of 'axial blurring' can occur. This largely occurs with cylindrical particles where virtually all of the data is in side views. Axialfilt can perform some empirical corrections for this effect.
• qindex - a program for very basic indexing of 2D crystal images was added. This program may be enhanced in future, depending on community response.
• fitctf - improvements in fitting quality and accuracy. May still have problems with some CCD data.
• procpdb.py - a script for basic manipulation of PDB files, designed largely for use with foldhunter
• foldhunter - new option added to generate rotated/translated PDB files corresponding to the best fits
• multirefine - now permits a different symmetry to be specified for each model. This is still an experimental option.
• building EMAN from source - We previously used GNU configure to easily configure EMAN on any platform. Due to a variety of problems with this system, we are now switching to 'CMake'. This is the cross-platform configuration tool written as part of the ITK project. If you wish to compile EMAN from source, please download and install the cmake version provided on the EMAN required libraries download page. The INSTALL text file will describe how to use it. GNU configure is still present, but is deprecated.
  

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Steven Ludtke, PhD              |        Baylor College of Medicine
sludtke@bcm.tmc.edu             |              Co-Director
stevel@alumni.caltech.edu       | National Center For Macromolecular Imaging
V: (713)798-6989                |    Dept of Biochemistry and Mol. Biol.
instant messenger: sludtke42    |           * Those who do ARE *
http://ncmi.bcm.tmc.edu/~stevel |         The converse also holds