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 1. [[EMAN1/FAQ/DfiltOption|Advice on using classiter= in iterative refinement rounds?]]  1. [[EMAN1/FAQ/Classiter|Advice on using classiter= in iterative refinement rounds?]]

FAQ

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The Questions:

  1. What paper should I cite if I use EMAN1 in published results ?

Installing EMAN:

  1. I installed EMAN 1.8, all command line programs work OK. But if I run GUI program, it gives me error: "error while loading shared libraries: libXinerama.so.1: cannot open shared object file: No such file or directory "?

  2. After I installed EMAN 1.8 on Fedora Core 6, I get this error message when I type eman: "EMAN/lib/libqsci.so cannot restore segment prot after reloc: Permission denied"?

  3. I am trying to install CMAKE from source, but I only get three program cmake, cpack and ctest, I do not have ccmake. But no error message in compilation process. What am I missing here?

  4. I download the EMAN 1.8 binary for linux, the file unpacked fine, but the installer does not seem to run. It returns immediately and print out message like this: "Please add the following line to the end of your /home/gtang/.bashrc: source /home/gtang/EMAN/eman.bashrc." Is this normal?

  5. Can I compile EMAN with qt4?

  6. Can I compile EMAN with fftw3?

  7. What is fftwgel, should I use it instead of fftw2?

  8. I build eman on my Ubuntu 7.04, when I type 'eman', before the window shows up, I see the error message dispalys 'X Error: BadDevice, invalid or uninitialized input device 169'. I installed the binary release for Ubuntu, the same thing happens. What is it?

  9. I compiled EMAN on Mac OS X, and set up the environment variables. But when I import EMAN in Python prompt, I got error "ImportError: No module named libpyAligner2". I checked my EMAN/lib directory, there is a libpyAligner2.dylib file in it.

  10. How do I compile EMAN for OSX(Mac) ?

  11. After successfull installation (WinXP) of EMAN I get the following error-message: 'This application has failed to start because MSVCR80.dll was not found. Re-installing the application may fix this problem.', when trying to start boxer (or any of the other programs). Re-installation does not resolve the problem. What can I do to get EMAN to run?

  12. I installed EMAN 1.8 on RHEL 4.0, I get error when I open any GUI programs: "couldn't open fontconfigs chose font with Xft!!!", what should I do?

Preprocessing, Particle Picking & CTF:

  1. Boxer - How can I use boxer to evaluate and clean up the automatically selected particles from batchboxer ?

  2. What process should I follow to do CTF correction in EMAN1

  3. How does CTF correction work in EMAN (technical)

  4. CTF Correction - I Don't have a structure factor and can't do a solution scattering experiment. What should I do ?

  5. I'm trying to do manual CTF correction. Did I understand it right, that the aim of the sliders it to get the theoretical curve and the "data-curve" congruent? If so, to what extent should this be done? I am curently playing around with that feature and am not sure how curves should match as I did not succeed to get everything congruent

  6. If I have particles already picked and 'extracted' using a picking software other than 'boxer', how can I put them all into a '.hed' file so as to use them with EMAN?

  7. I want to simulate noise and CTF to generate "real" EM-pictures from the projections of my molecule, just as you did in the orginal EMAN-paper for the BTV trimer. When I measure the carbon-film and use ctfit to determine the ctf, are the noise-levels determined simultaneously? How do I apply these parameters to the pictures?

  8. I would like to shift a stack of particles according to a x,y document (whole integers to avoid interpolation), and I wonder if it is possible with eman ?

2-D Analysis/Classification:

  1. Centering - Should my data set be well centered before I run refine2d.py?

  2. How do I extract images from specific classes after running refine2d.py ?

  3. How can I align and average a set of particles in 2-D with symmetry ?

  4. Symmetry determination - Do you have a facility for calculating rotational power spectra ? How can I determine the symmetry of my particles ?

  5. Some of the classsums look a bit off centered and it gets worse as I do more rounds of refinement. Our structure looks more funny as I refine further ... what should I do?

  6. When I look at the results of startnrclasses in matrix view and select show # of particles per class, the number is not displayed. Any suggestions?

  7. Whatever number of classes is chosen always 10 classes are produced

Initial 3-D Models:

  1. I have an asymmetric particle. How do I get a starting model and refine it

  2. 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 ?

Refinement

  1. What do all of the options in 'refine' mean

  2. How does CTF correction work in EMAN

  3. My FSC curve looks funny

  4. How can I find out how many particles were used in a reconstruction ? How can I look at the particles that were discarded ?

  5. Is there anywhere that explains the text output of the classification and model construction routines? being impatient and having calculated several completely bogus models of my asymmetric particle, I am hoping there is a way to tell fromt he numbers when it might be better to stop the procedure than to let it run on.

  6. If I have a good template and a bunch of raw particles, is there a way to determine the particle center and orientation by some EMAN programs? In our reconstruction programs, we can get a set of parameters for each particle during refinement again a single reference. Including the x, y shift and 3 angle rotation. We are thinking about getting those parameters from EMAN.

  7. Some of the classsums look a bit off centered and it gets worse as I do more rounds of refinement. Our structure looks more funny as I refine further ... what should I do?

  8. What does the "shrink=n" do in Refine commmand? It doesn't look like changing the size of subfiles like proc2d shrink=n does

  9. Explain the contents of the 'cls*.lst' files (how can I easily extract particles in a particular orientation with 2D alignment ?)

  10. Explain the contents of the 'particle.log' file (how can I figure out which particle went in which class, and with what alignment parameters ?)

  11. How do I choose the correct parameters for the xfiles argument?

  12. How do I choose the correct parameters for the amask argument?

  13. What in the heck is the dfilt option and how does it work ?

  14. Advice on using classiter= in iterative refinement rounds?

After Reconstruction - Structure Analysis

  1. How can I make a difference map between two structures ?

  2. 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.

  3. 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 ?

  4. What is the fsc.eotest file ?

Specimen Heterogeneity

  1. I want to use phase residual data to identify the number of heterogeneous populations in my data set

  2. I have a good reconstruction, but my data is heterogeneous. How can I separate my data to better process it ?

  3. How do I extract images from specific classes after running refine2d.py ?

  4. I have heard that EMAN can process heterogeneous data sets and produce multiple models, for example, to study dynamics or ligand binding

  5. How do I determine the handedness of my single particle reconstruction ?

General Questions

  1. What paper should I cite if I use EMAN1 in published results ?

  2. Where can I download the DVD from the last EMAN workshop ?

  3. Support for icosahedral symmetry

  4. I want to learn how to use EMAN, where can I get some sample data to try a reconstruction ?

  5. using e2scannereval - what is wrong with this image?

  6. problems reading maps created by CCP4 in EMAN

  7. I read the documentation, and I still don't know what to do. How can I get more help ?

  8. I've heard that (insert favorite program) runs much faster than EMAN. Is this true ?

  9. I heard that someone did a refinement in (insert favorite program) and got a higher resolution structure than they did in EMAN. Is this true ?

  10. I'm running EMAN in parallel on a cluster, and it seems to lock up when it reaches the class-averaging step (classalign2).

  11. I'm trying my first EMAN refinement, but the refine command crashes or produces black images in classes.1.hed. What's going on?

  12. How can I read images in format ABC ? What file formats does EMAN support ?

  13. I'd like to process a really big data set with EMAN. Is it up to the task ?

  14. I have a bunch of MRC convention Euler angles and need to generate projections of a model in EMAN

Bugs:

  1. In EMAN 1.8 my class-averages have very strange numbers of particles listed, and this breaks the reconstruction

  2. I'm trying my first EMAN refinement, but the refine command crashes or produces black images in classes.1.hed. What's going on?

  3. Our jobs are crashing because the stdout file is too big...

  4. refine2d.py error: segmentation fault...

EMAN1/FAQ (last edited 2010-05-26 19:25:24 by gtang)