| Next revision | Previous revision |
| eman1_faq [2025/07/05 03:25] – created steveludtke | eman1_faq [2025/07/05 14:46] (current) – steveludtke |
|---|
| |
| ==== The Questions: ==== | ==== The Questions: ==== |
| 1. [[FAQ_EMAN_USING_13|What paper should I cite if I use EMAN1 in published results ?]] | - [[FAQ_EMAN_USING_13|What paper should I cite if I use EMAN1 in published results ?]] |
| |
| **Installing EMAN:** | **Installing EMAN:** |
| |
| 2. [[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 "?]] | - [[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 "?]] |
| 3. [[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"?]] | - [[EMAN1:FAQ: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"?]] |
| 4. [[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?]] | - [[EMAN1:FAQ: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?]] |
| 5. [[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?]] | - [[EMAN1:FAQ: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?]] |
| 6. [[EMAN_QT4|Can I compile EMAN with qt4?]] | - [[EMAN1:FAQ:QT4|Can I compile EMAN with qt4?]] |
| 7. [[EMAN_FFTW3|Can I compile EMAN with fftw3?]] | - [[EMAN1:FAQ:FFTW3|Can I compile EMAN with fftw3?]] |
| 8. [[EMAN_FFTWGEL|What is fftwgel, should I use it instead of fftw2?]] | - [[EMAN1:FAQ:FFTWGEL|What is fftwgel, should I use it instead of fftw2?]] |
| 9. [[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?]] | - [[EMAN1:FAQ: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?]] |
| 10. [[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.]] | - [[EMAN1:FAQ:MacOSLibrary|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.]] |
| 11. [[FAQ_EMAN_USING_17|How do I compile EMAN for OSX(Mac) ?]] | - [[EMAN1:FAQ:USING_17|How do I compile EMAN for OSX(Mac) ?]] |
| 12. [[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?]] | - [[EMAN1:FAQ: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?]] |
| 13. [[EMAN_RHEL4|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?]] | - [[EMAN1:FAQ:RHEL4|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:** | **Preprocessing, Particle Picking & CTF:** |
| |
| 14. [[EMAN1/FAQ/MultipleBoxer|Boxer - How can I use boxer to evaluate and clean up the automatically selected particles from batchboxer ?]] | - [[EMAN1:FAQ:MultipleBoxer|Boxer - How can I use boxer to evaluate and clean up the automatically selected particles from batchboxer ?]] |
| 15. [[EMAN1/FAQ/CtfHowTo|What process should I follow to do CTF correction in EMAN1]] | - [[EMAN1:FAQ:CtfHowTo|What process should I follow to do CTF correction in EMAN1]] |
| 16. [[EMAN1/FAQ/Ctf|How does CTF correction work in EMAN (technical)]] | - [[EMAN1:FAQ:Ctf|How does CTF correction work in EMAN (technical)]] |
| 17. [[EMAN1/FAQ/StructureFactor|CTF Correction - I Don't have a structure factor and can't do a solution scattering experiment. What should I do ?]] | - [[EMAN1:FAQ:StructureFactor|CTF Correction - I Don't have a structure factor and can't do a solution scattering experiment. What should I do ?]] |
| 18. [[FAQ_EMAN_USING_23|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]] | - [[EMAN1:FAQ:USING_23|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]] |
| 19. [[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?]] | - [[EMAN1:FAQ: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?]] |
| 20. [[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?]] | - [[EMAN1:FAQ: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?]] |
| 21. [[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 ?]] | - [[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:** | **2-D Analysis/Classification:** |
| |
| 22. [[EMAN1/FAQ/Refine2dpy_centering|Centering - Should my data set be well centered before I run refine2d.py?]] | - [[EMAN1:FAQ:Refine2dpy_centering|Centering - Should my data set be well centered before I run refine2d.py?]] |
| 23. [[EMAN1/FAQ/Refine2d_classes|How do I extract images from specific classes after running refine2d.py ?]] | - [[EMAN1:FAQ:Refine2d_classes|How do I extract images from specific classes after running refine2d.py ?]] |
| 24. [[EMAN1/FAQ/D2_Symmetry|How can I align and average a set of particles in 2-D with symmetry ?]] | - [[EMAN1:FAQ:D2_Symmetry|How can I align and average a set of particles in 2-D with symmetry ?]] |
| 25. [[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 ?]] | - [[EMAN1:FAQ:USING_20|Symmetry determination - Do you have a facility for calculating rotational power spectra ? How can I determine the symmetry of my particles ?]] |
| 26. [[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?]] | - [[EMAN1:FAQ: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?]] |
| 27. [[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?]] | - [[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?]] |
| 28. [[EMAN1/FAQ/Refine2dNinitcls|Whatever number of classes is chosen always 10 classes are produced]] | - [[EMAN1:FAQ:Refine2dNinitcls|Whatever number of classes is chosen always 10 classes are produced]] |
| |
| **Initial 3-D Models:** | **Initial 3-D Models:** |
| |
| 29. [[EMAN1/FAQ/Asymmetric|I have an asymmetric particle. How do I get a starting model and refine it]] | - [[EMAN1/FAQ/Asymmetric|I have an asymmetric particle. How do I get a starting model and refine it]] |
| 30. [[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 ?]] | - [[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** | **Refinement** |
| |
| 31. [[EMAN1/FAQ/Refine|What do all of the options in 'refine' mean]] | - [[EMAN1:FAQ:Refine|What do all of the options in 'refine' mean]] |
| 32. [[EMAN1/FAQ/Ctf|How does CTF correction work in EMAN]] | - [[EMAN1:FAQ:Ctf|How does CTF correction work in EMAN]] |
| 33. [[EMAN1/FAQ/FSC_FSC|My FSC curve looks funny]] | - [[EMAN1:FAQ:FSC_FSC|My FSC curve looks funny]] |
| 34. [[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 ?]] | - [[EMAN1:FAQ: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 ?]] |
| 35. [[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.]] | - [[EMAN1:FAQ: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.]] |
| 36. [[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.]] | - [[EMAN1:FAQ: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.]] |
| 37. [[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?]] | - [[EMAN1:FAQ: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?]] |
| 38. [[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]] | - [[EMAN1:FAQ: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]] |
| 39. [[EMAN1/FAQ/ClsLstFiles|Explain the contents of the 'cls*.lst' files (how can I easily extract particles in a particular orientation with 2D alignment ?)]] | - [[EMAN1:FAQ:ClsLstFiles|Explain the contents of the 'cls*.lst' files (how can I easily extract particles in a particular orientation with 2D alignment ?)]] |
| 40. [[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 ?)]] | - [[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 ?)]] |
| 41. [[EMAN1/FAQ/XFiles|How do I choose the correct parameters for the xfiles argument?]] | - [[EMAN1:FAQ:XFiles|How do I choose the correct parameters for the xfiles argument?]] |
| 42. [[EMAN1/FAQ/Refineamask|How do I choose the correct parameters for the amask argument?]] | - [[EMAN1:FAQ:Refineamask|How do I choose the correct parameters for the amask argument?]] |
| 43. [[EMAN1/FAQ/DfiltOption|What in the heck is the dfilt option and how does it work ?]] | - [[EMAN1:FAQ:DfiltOption|What in the heck is the dfilt option and how does it work ?]] |
| 44. [[EMAN1/FAQ/Classiter|Advice on using classiter= in iterative refinement rounds?]] | - [[EMAN1:FAQ:Classiter|Advice on using classiter= in iterative refinement rounds?]] |
| 45. [[EMAN1MpiMake3d|How to use mpi version of make3d?]] | - [[EMAN1:FAQ:MpiMake3d|How to use mpi version of make3d?]] |
| |
| **After Reconstruction - Structure Analysis** | **After Reconstruction - Structure Analysis** |
| |
| 46. [[EMAN1/FAQ/Diffmap|How can I make a difference map between two structures ?]] | - [[EMAN1:FAQ:Diffmap|How can I make a difference map between two structures ?]] |
| 47. [[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.]] | -[[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.]] |
| 48. [[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 ?]] | - [[EMAN1:FAQ: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 ?]] |
| 49. [[FAQ_EMAN_USING_34|What is the fsc.eotest file ?]] | - [[EMAN1:FAQ:USING_34|What is the fsc.eotest file ?]] |
| |
| **Specimen Heterogeneity** | **Specimen Heterogeneity** |
| |
| 50. [[EMAN1/FAQ/HeterogeneousPhase|I want to use phase residual data to identify the number of heterogeneous populations in my data set]] | - [[EMAN1:FAQ:HeterogeneousPhase|I want to use phase residual data to identify the number of heterogeneous populations in my data set]] |
| 51. [[EMAN1/FAQ/Heterogeneous|I have a good reconstruction, but my data is heterogeneous. How can I separate my data to better process it ?]] | - [[EMAN1:FAQ:Heterogeneous|I have a good reconstruction, but my data is heterogeneous. How can I separate my data to better process it ?]] |
| 52. [[EMAN1/FAQ/Refine2d_classes|How do I extract images from specific classes after running refine2d.py ?]] | - [[EMAN1:FAQ:Refine2d_classes|How do I extract images from specific classes after running refine2d.py ?]] |
| 53. [[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]] | - [[EMAN1:FAQ:USING_30|I have heard that EMAN can process heterogeneous data sets and produce multiple models, for example, to study dynamics or ligand binding]] |
| 54. [[EMAN1/FAQ/Handedness|How do I determine the handedness of my single particle reconstruction ?]] | - [[EMAN1:FAQ:Handedness|How do I determine the handedness of my single particle reconstruction ?]] |
| |
| **General Questions** | **General Questions** |
| |
| 55. [[FAQ_EMAN_USING_13|What paper should I cite if I use EMAN1 in published results ?]] | - [[EMAN1:FAQ:USING_13|What paper should I cite if I use EMAN1 in published results ?]] |
| 56. [[EMAN1/FAQ/WorkshopDVD|Where can I download the DVD from the last EMAN workshop ?]] | - [[EMAN1:FAQ:WorkshopDVD|Where can I download the DVD from the last EMAN workshop ?]] |
| 57. [[EMAN1/FAQ/icos|Support for icosahedral symmetry]] | - [[EMAN1:FAQ:icos|Support for icosahedral symmetry]] |
| 58. [[EMAN1/FAQ/Dvd2007|I want to learn how to use EMAN, where can I get some sample data to try a reconstruction ?]] | - [[EMAN1:FAQ:Dvd2007|I want to learn how to use EMAN, where can I get some sample data to try a reconstruction ?]] |
| 59. [[EMAN1/FAQ/e2scannereval_results|using e2scannereval - what is wrong with this image?]] | - [[EMAN1:FAQ:e2scannereval_results|using e2scannereval - what is wrong with this image?]] |
| 60. [[EMAN1/FAQ/CCP4_maps|problems reading maps created by CCP4 in EMAN]] | - [[EMAN1:FAQ:CCP4_maps|problems reading maps created by CCP4 in EMAN]] |
| 61. [[FAQ_EMAN_USING_12|I read the documentation, and I still don't know what to do. How can I get more help ?]] | - [[EMAN1:FAQ:USING_12|I read the documentation, and I still don't know what to do. How can I get more help ?]] |
| 62. [[FAQ_EMAN_USING_14|I've heard that (insert favorite program) runs much faster than EMAN. Is this true ?]] | - [[EMAN1:FAQ:USING_14|I've heard that (insert favorite program) runs much faster than EMAN. Is this true ?]] |
| 63. [[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 ?]] | - [[EMAN1:FAQ: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 ?]] |
| 64. [[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).]] | - [[EMAN1:FAQ: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).]] |
| 65. [[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?]] | - [[EMAN1:FAQ: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?]] |
| 66. [[FAQ_EMAN_USING_19|How can I read images in format ABC ? What file formats does EMAN support ?]] | - [[EMAN1:FAQ:USING_19|How can I read images in format ABC ? What file formats does EMAN support ?]] |
| 67. [[FAQ_EMAN_USING_24|I'd like to process a really big data set with EMAN. Is it up to the task ?]] | - [[EMAN1:FAQ:USING_24|I'd like to process a really big data set with EMAN. Is it up to the task ?]] |
| 68. [[FAQ_EMAN_USING_29|I have a bunch of MRC convention Euler angles and need to generate projections of a model in EMAN]] | - [[EMAN1:FAQ:USING_29|I have a bunch of MRC convention Euler angles and need to generate projections of a model in EMAN]] |
| |
| **Bugs:** | **Bugs:** |
| |
| 69. [[EMAN1/FAQ/Median|In EMAN 1.8 my class-averages have very strange numbers of particles listed, and this breaks the reconstruction]] | - [[EMAN1:FAQ:/Median|In EMAN 1.8 my class-averages have very strange numbers of particles listed, and this breaks the reconstruction]] |
| 70. [[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?]] | - [[EMAN1:FAQ: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?]] |
| 71. [[FAQ_EMAN_USING_stdouttoobig|Our jobs are crashing because the stdout file is too big...]] | - [[EMAN1:FAQ:USING_stdouttoobig|Our jobs are crashing because the stdout file is too big...]] |
| 72. [[FAQ|refine2d.py error: segmentation fault...]] | - [[EMAN1:FAQ:Segfault|refine2d.py error: segmentation fault...]] |
| |
