FAQ

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The Questions:

1. [:FAQ EMAN USING 13:What paper should I cite if I use EMAN1 in published results ?]

Installing EMAN:

1. [:EMAN1/FAQ/GUI1: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. [:SELinux: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. [:CMAKE1: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. [:EMAN INSTALLER1: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. [:EMAN QT4:Can I compile EMAN with qt4?]
6. [:EMAN FFTW3:Can I compile EMAN with fftw3?]

7. [:EMAN FFTWGEL:What is fftwgel, should I use it instead of fftw2?]

8. [:Ubuntu baddevice error: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. [:EMANMacOSLibrary: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. [:FAQ EMAN USING 17:How do I compile EMAN for OSX(Mac) ?]
11. [:FAQ EMAN MSVCR80.dll: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?]

Preprocessing, Particle Picking & CTF:

1. [:EMAN1/FAQ/MultipleBoxer:Boxer - How can I use boxer to evaluate and clean up the automatically selected particles from batchboxer ?]

2. [:EMAN1/FAQ/StructureFactor:CTF Correction - I Don't have a structure factor and can't do a solution scattering experiment. What should I do ?]

3. [:EMAN1/FAQ/Ctf:How does CTF correction work in EMAN]

4. [:FAQ EMAN USING 23:I'm trying to do 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]
5. [:FAQ EMAN USING 25: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?]
6. [:FAQ EMAN USING 28: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?]

7. [:EMAN1/FAQ/TranslateParticles: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. [:EMAN1/FAQ/Refine2dpy centering:Centering - Should my data set be well centered before I run refine2d.py?]
2. [:EMAN1/FAQ/Refine2d classes:How do I extract images from specific classes after running refine2d.py ?]

3. [:EMAN1/FAQ/D2 Symmetry:How can I align and average a set of particles in 2-D with symmetry ?]

4. [:FAQ EMAN USING 20:Symmetry determination - Do you have a facility for calculating rotational power spectra ? How can I determine the symmetry of my particles ?]
5. [:FAQ EMAN USING 26:I have a particle which might have a c5, c6 or c7 symmetry. How can I find out which it is ?]
6. [:FAQ EMAN USING 33: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?]
7. [:EMAN1/FAQ/Startnrclasses: 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?]
8. [:EMAN1/FAQ/Refine2dNinitcls: Whatever number of classes is chosen always 10 classes are produced]

Initial 3-D Models:

1. [:EMAN1/FAQ/Asymmetric:I have an asymmetric particle. How do I get a starting model and refine it]

2. [:FAQ EMAN USING 26:I have a particle which might have a c5, c6 or c7 symmetry. How can I find out which it is ?]
3. [:FAQ EMAN USING 31: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. [:EMAN1/FAQ/Ctf:How does CTF correction work in EMAN]

2. [:EMAN1/FAQ/FSC FSC:My FSC curve looks funny]

3. [:FAQ EMAN USING 22:How can I find out how many particles were used in a reconstruction ? How can I look at the particles that were discarded ?]
4. [:FAQ EMAN USING 27: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.]
5. [:FAQ EMAN USING 32: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.]
6. [:FAQ EMAN USING 33: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?]
7. [:FAQ EMAN USING refine shrink:What does the "shrink=n" do in Refine commmand? It doesn't look like changing the size of subfiles like proc2d shrink=n does]

8. [:EMAN1/FAQ/ClsLstFiles:Explain the contents of the 'cls*.lst' files (how can I easily extract particles in a particular orientation with 2D alignment ?)]

9. [:EMAN1/FAQ/ParticleLogFile:Explain the contents of the 'particle.log' file (how can I figure out which particle went in which class, and with what alignment parameters ?)]

10. [:EMAN1/FAQ/XFiles:How do I choose the correct parameters for the xfiles argument?]

11. [:EMAN1/FAQ/Refineamask:How do I choose the correct parameters for the amask argument?]

After Reconstruction - Structure Analysis

1. [:EMAN1/FAQ/Diffmap: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. [:FAQ EMAN USING 31: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 ?]

Specimen Heterogeneity

1. [:EMAN1/FAQ/HeterogeneousPhase:I want to use phase residual data to identify the number of heterogeneous populations in my data set]

2. [:EMAN1/FAQ/Heterogeneous:I have a good reconstruction, but my data is heterogeneous. How can I separate my data to better process it ?]

3. [:EMAN1/FAQ/Refine2d classes:How do I extract images from specific classes after running refine2d.py ?]
4. [:FAQ EMAN USING 30:I have heard that EMAN can process heterogeneous data sets and produce multiple models, for example, to study dynamics or ligand binding]

5. [:EMAN1/FAQ/Handedness:How do I determine the handedness of my single particle reconstruction ?]

General Questions

1. [:FAQ EMAN USING 13:What paper should I cite if I use EMAN1 in published results ?]

2. [:EMAN1/FAQ/WorkshopDVD:Where can I download the DVD from the last EMAN workshop ?]

3. [:EMAN1/FAQ/icos:Support for icosahedral symmetry]
4. [:EMAN1/FAQ/Dvd2007:I want to learn how to use EMAN, where can I get some sample data to try a reconstruction ?]
5. [:EMAN1/FAQ/e2scannereval results:using e2scannereval - what is wrong with this image? ]
6. [:EMAN1/FAQ/CCP4 maps:problems reading maps created by CCP4 in EMAN]
7. [:FAQ EMAN USING 12:I read the documentation, and I still don't know what to do. How can I get more help ?]
8. [:FAQ EMAN USING 14:I've heard that (insert favorite program) runs much faster than EMAN. Is this true ?]
9. [:FAQ EMAN USING 15: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. [:FAQ EMAN USING 16:I'm running EMAN in parallel on a cluster, and it seems to lock up when it reaches the class-averaging step (classalign2).]
11. [:FAQ EMAN USING 18: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. [:FAQ EMAN USING 19:How can I read images in format ABC ? What file formats does EMAN support ?]
13. [:FAQ EMAN USING 24:I'd like to process a really big data set with EMAN. Is it up to the task ?]
14. [:FAQ EMAN USING 29:I have a bunch of MRC convention Euler angles and need to generate projections of a model in EMAN]

Bugs:

1. [:EMAN1/FAQ/Median:In EMAN 1.8 my class-averages have very strange numbers of particles listed, and this breaks the reconstruction]

2. [:FAQ EMAN USING 18: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. [:FAQ EMAN USING stdouttoobig:Our jobs are crashing because the stdout file is too big...]