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| The Questions: | === The Questions: === 1. [[FAQ_EMAN_USING_13|What paper should I cite if I use EMAN1 in published results ?]] '''Installing EMAN:''' |
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| 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 "?]] 1. [[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"? ]] 1. [[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? ]] 1. [[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?]] 1. [[EMAN_QT4|Can I compile EMAN with qt4?]] 1. [[EMAN_FFTW3|Can I compile EMAN with fftw3?]] 1. [[EMAN_FFTWGEL|What is fftwgel, should I use it instead of fftw2?]] 1. [[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?]] 1. [[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.]] 1. [[FAQ_EMAN_USING_17|How do I compile EMAN for OSX(Mac) ?]] 1. [[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?]] 1. [[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?]] '''Preprocessing, Particle Picking & CTF:''' |
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| 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 "?] 1. [: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"? ] 1. [: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? ] 1. [: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?] 1. [:EMAN QT4:Can I compile EMAN with qt4?] 1. [:EMAN FFTW3:Can I compile EMAN with fftw3?] 1. [:EMAN FFTWGEL:What is fftwgel, should I use it instead of fftw2?] 1. [: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?] Bugs: |
1. [[EMAN1/FAQ/MultipleBoxer|Boxer - How can I use boxer to evaluate and clean up the automatically selected particles from batchboxer ?]] 1. [[EMAN1/FAQ/CtfHowTo|What process should I follow to do CTF correction in EMAN1]] 1. [[EMAN1/FAQ/Ctf|How does CTF correction work in EMAN (technical)]] 1. [[EMAN1/FAQ/StructureFactor|CTF Correction - I Don't have a structure factor and can't do a solution scattering experiment. What should I do ?]] 1. [[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]] 1. [[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?]] 1. [[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?]] 1. [[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:''' |
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| 1. [:EMAN1/FAQ/Median:In EMAN 1.8 my class-averages have very strange numbers of particles listed, and this breaks the reconstruction] Using EMAN: |
1. [[EMAN1/FAQ/Refine2dpy_centering|Centering - Should my data set be well centered before I run refine2d.py?]] 1. [[EMAN1/FAQ/Refine2d_classes|How do I extract images from specific classes after running refine2d.py ?]] 1. [[EMAN1/FAQ/D2_Symmetry|How can I align and average a set of particles in 2-D with symmetry ?]] 1. [[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 ?]] 1. [[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?]] 1. [[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?]] 1. [[EMAN1/FAQ/Refine2dNinitcls|Whatever number of classes is chosen always 10 classes are produced]] '''Initial 3-D Models:''' |
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| 1. [:EMAN1/FAQ/Dvd2007:I want to learn how to use EMAN, where can I get some sample data to try a reconstruction ?] 1. [:EMAN1/FAQ/Heterogeneous:I have a good reconstruction, but my data is heterogeneous. How can I separate my data to better process it ?] 1. [:EMAN1/FAQ/Refine2dpy centering:Centering - Should my data set be well centered before I run refine2d.py?] 1. [:EMAN1/FAQ/e2scannereval results:using e2scannereval - what is wrong with this image? ] 1. [:EMAN1/FAQ/Ctf:How does CTF correction work in EMAN] 1. [:EMAN1/FAQ/Refine2d classes:How do I extract images from specific classes after running refine2d.py ?] 1. [:EMAN1/FAQ/D2 Symmetry:How can I align and average a set of particles in 2-D with symmetry ?] 1. [:EMAN1/FAQ/FSC FSC:My FSC curve looks funny] 1. [:EMAN1/FAQ/CCP4 maps:problems reading maps created by CCP4 in EMAN] 1. ["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."] 1. [:EMAN1/FAQ/StructureFactor:CTF Correction - I Don't have a structure factor and can't do a solution scattering experiment. What should I do ?] 1. [/eman/eman1/faq.html#a1 I read the documentation, and I still don't know what to do. How can I get more help ?] 1. '''[/eman/eman1/faq.html#a2 What paper should I cite if I use EMAN1 in published results ?]''' 1. '''[/eman/eman1/faq.html#a2a I've heard that (insert favorite program) runs much faster than EMAN. Is this true ?]''' 1. '''[/eman/eman1/faq.html#a2b 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 ?]''' 1. '''[/eman/eman1/faq.html#a2c I'm running EMAN in parallel on a cluster, and it seems to lock up when it reaches the class-averaging step (classalign2).]''' 1. '''[/eman/eman1/faq.html#a3 How do I compile EMAN for OSX(Mac) ?]''' 1. '''[/eman/eman1/faq.html#a4 I'm trying my first EMAN refinement, but the refine command crashes or produces black images in classes.1.hed. What's going on?]''' 1. '''[/eman/eman1/faq.html#a5 How can I read images in format ABC ? What file formats does EMAN support ?]''' 1. '''[/eman/eman1/faq.html#a6 Symmetry determination - Do you have a facility for calculating rotational power spectra ? How can I determine the symmetry of my particles ?]''' 1. '''[/eman/eman1/faq.html#a7 CTF Correction - I can't do an x-ray solution scattering experiment on my specimen. Is there some way I can get an apporoximate structure factor to use in fitting and CTF correction ?]''' 1. [/eman/eman1/faq.html#a8 How can I find out how many particles were used in a reconstruction ? How can I look at the particles that were discarded ?] 1. '''[/eman/eman1/faq.html#a9 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]''' 1. '''[/eman/eman1/faq.html#a10 I'd like to process a really big data set with EMAN. Is it up to the task ?]''' 1. '''[/eman/eman1/faq.html#a11 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?]''' 1. '''[/eman/eman1/a12 I have a particle which might have a c5, c6 or c7 symmetry. How can I find out which it is ?]''' 1. '''[/eman/eman1/faq.html#a13 Is there anywhere that explains the text output of the classification and model construction routines? being impatient an dhaving 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.]''' 1. '''[/eman/eman1/faq.html#a14 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?]''' 1. [/eman/eman1/faq.html#a15 I have a bunch of MRC convention Euler angles and need to generate projections of a model in EMAN] 1. '''[/eman/eman1/faq.html#a16 I have heard that EMAN can process heterogeneous data sets and produce multiple models, for example, to study dynamics or ligand binding]''' 1. '''[/eman/eman1/faq.html#a17 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 ?]''' 1. '''[/eman/eman1/faq.html#a18 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.]''' |
1. [[EMAN1/FAQ/Asymmetric|I have an asymmetric particle. How do I get a starting model and refine it]] 1. [[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/Refine|What do all of the options in 'refine' mean]] 1. [[EMAN1/FAQ/Ctf|How does CTF correction work in EMAN]] 1. [[EMAN1/FAQ/FSC_FSC|My FSC curve looks funny]] 1. [[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 ?]] 1. [[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.]] 1. [[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.]] 1. [[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?]] 1. [[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]] 1. [[EMAN1/FAQ/ClsLstFiles|Explain the contents of the 'cls*.lst' files (how can I easily extract particles in a particular orientation with 2D alignment ?)]] 1. [[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 ?)]] 1. [[EMAN1/FAQ/XFiles|How do I choose the correct parameters for the xfiles argument?]] 1. [[EMAN1/FAQ/Refineamask|How do I choose the correct parameters for the amask argument?]] 1. [[EMAN1/FAQ/DfiltOption|What in the heck is the dfilt option and how does it work ?]] '''After Reconstruction - Structure Analysis''' 1. [[EMAN1/FAQ/Diffmap|How can I make a difference map between two structures ?]] 1. [[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.]] 1. [[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 ?]] 1. [[FAQ_EMAN_USING_34|What is the fsc.eotest file ?]] '''Specimen Heterogeneity''' 1. [[EMAN1/FAQ/HeterogeneousPhase|I want to use phase residual data to identify the number of heterogeneous populations in my data set]] 1. [[EMAN1/FAQ/Heterogeneous|I have a good reconstruction, but my data is heterogeneous. How can I separate my data to better process it ?]] 1. [[EMAN1/FAQ/Refine2d_classes|How do I extract images from specific classes after running refine2d.py ?]] 1. [[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]] 1. [[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 ?]] 1. [[EMAN1/FAQ/WorkshopDVD|Where can I download the DVD from the last EMAN workshop ?]] 1. [[EMAN1/FAQ/icos|Support for icosahedral symmetry]] 1. [[EMAN1/FAQ/Dvd2007|I want to learn how to use EMAN, where can I get some sample data to try a reconstruction ?]] 1. [[EMAN1/FAQ/e2scannereval_results|using e2scannereval - what is wrong with this image? ]] 1. [[EMAN1/FAQ/CCP4_maps|problems reading maps created by CCP4 in EMAN]] 1. [[FAQ_EMAN_USING_12|I read the documentation, and I still don't know what to do. How can I get more help ?]] 1. [[FAQ_EMAN_USING_14|I've heard that (insert favorite program) runs much faster than EMAN. Is this true ?]] 1. [[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 ?]] 1. [[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).]] 1. [[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?]] 1. [[FAQ_EMAN_USING_19|How can I read images in format ABC ? What file formats does EMAN support ?]] 1. [[FAQ_EMAN_USING_24|I'd like to process a really big data set with EMAN. Is it up to the task ?]] 1. [[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]] 1. [[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?]] 1. [[FAQ_EMAN_USING_stdouttoobig|Our jobs are crashing because the stdout file is too big...]] 1. [[FAQ |refine2d.py error: segmentation fault...]] |
FAQ
This is the new EMAN Frequently Asked Questions page :
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The Questions:
Installing EMAN:
Preprocessing, Particle Picking & CTF:
2-D Analysis/Classification:
Centering - Should my data set be well centered before I run refine2d.py?
How do I extract images from specific classes after running refine2d.py ?
How can I align and average a set of particles in 2-D with symmetry ?
Whatever number of classes is chosen always 10 classes are produced
Initial 3-D Models:
Refinement
How do I choose the correct parameters for the xfiles argument?
How do I choose the correct parameters for the amask argument?
After Reconstruction - Structure Analysis
Specimen Heterogeneity
I want to use phase residual data to identify the number of heterogeneous populations in my data set
How do I extract images from specific classes after running refine2d.py ?
How do I determine the handedness of my single particle reconstruction ?
General Questions
What paper should I cite if I use EMAN1 in published results ?
I want to learn how to use EMAN, where can I get some sample data to try a reconstruction ?
I read the documentation, and I still don't know what to do. How can I get more help ?
I've heard that (insert favorite program) runs much faster than EMAN. Is this true ?
How can I read images in format ABC ? What file formats does EMAN support ?
I'd like to process a really big data set with EMAN. Is it up to the task ?
I have a bunch of MRC convention Euler angles and need to generate projections of a model in EMAN
Bugs: