https://blake.bcm.edu/emanwiki/ 2026-04-17T02:28:38+00:00 https://blake.bcm.edu/emanwiki/ https://blake.bcm.edu/emanwiki/lib/exe/fetch.php?media=wiki:dokuwiki.svg text/html 2025-07-05T18:07:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:ccp4_maps&rev=1751738854&do=diff Question: I am having problems reading mrc maps in EMAN. I have a ccp4 map which I convert to mrc using em2em. The map looks fine in chimera. when I am trying to use this file by lauching ssehunter3.py, the reading of the map is starting OK but then I got this error message: text/html 2025-07-05T16:05:44+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:classiter&rev=1751731544&do=diff Q: What value should I use for classiter ? A: Large (4-8) values of classiter do an excellent job of preventing model/noise bias, but slightly degrade resolution and sharpness (different things) of the reconstruction. I suggest using 4-8 for a few rounds until convergence, then do your high resolution refinement with 3 (which actually does only 1 iteration for historical reasons). 3 is still reasonably consevative with respect to inducing model bias. Then at the end, if you want to 'sharpen up'… text/html 2025-07-05T15:53:47+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:clslstfiles&rev=1751730827&do=diff Q: Explain the contents of the cls*.lst files, and how they relate to extracting individual oriented particles. A: There is one of these files for each projection within a specific orientation. The results from each iteration are combined into a cls.#.tar file in case they are needed later. However, the same information is also present in the particle.log file (for all iterations). text/html 2025-07-05T14:55:27+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:cmake1&rev=1751727327&do=diff Your system does not have a library named “ncurses”. Install this package first, then compile cmake again, you will get ccmake. (or configure isn't finding ncurses properly, you may need to manually tell configure in the cmake package where curses is) text/html 2025-07-05T15:28:00+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:ctf&rev=1751729280&do=diff CTF Correction in EMAN1 EMAN's model was outlined in the 1999 paper introducing EMAN This model was confirmed accurate with experimental data in the 2001 paper on GroEL at 11.5 A resolution The derivation of EMAN's CTF correction model was in a rather obscure IEEE proceedings paper Finally, you can the updated details from the 1999 paper in the static EMAN1 documentation EMAN2 is going to use a new model for easier CTF correction text/html 2025-07-05T15:27:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:ctfhowto&rev=1751729228&do=diff Q: How do I go about doing CTF correction in EMAN1 A: Much of this is described in the 4 step tutorial interface, but the description here is more up to date. CTF correction in EMAN1, is, unfortunately, a somewhat time-consuming process. This has been massively simplified in EMAN2, but as EMAN2 still remains 'experimental' you may wish to stick with EMAN1 for a while longer for serious refinement work. It is a VERY good idea to make sure you are using a current snapshot version of EMAN1, rathe… text/html 2025-07-05T15:44:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:d2_symmetry&rev=1751730286&do=diff Question: I need to do a 2D average with symmetry using all my particles. I could not find a command in the manual. “startnrclasses” is no symmetry. And “startcsym” is for 3D reconstruction and could only use 1/3 of my particles. Is there such a command in EMAN? Thank you. text/html 2025-07-05T16:02:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:dfiltoption&rev=1751731333&do=diff Q: What is this 'dfilt' option for the refine command, and how does it work ? How does it compare to phasecls and fscls ? A: In ~2002 when we were first moving to subnanometer resolution, we were struggling with some problems with similarity criteria. It turned out that for GroEL, for some reason, using simple a weighted correlation coefficient to compare raw particles to model projections produced a bias, which tended to shift the side views of GroEL to orientations a few degrees away from th… text/html 2025-07-05T17:49:01+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:diffmap&rev=1751737741&do=diff Q: I have two structures with different ligands or in different functional states. How do I make a difference map between two structures ? A: Hi. Difference maps are always tricky in cryoEM. Very subtle differences in CTF can cause large artifacts in difference maps. One trick you can use, if you expect the 2 structures to be almost the same, with just a few subtle differences, is to take the radial structure factor from one map and impose it on the other map. In EMAN, this can be accomplished … text/html 2025-07-05T18:06:15+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:dvd2007&rev=1751738775&do=diff EMAN1 Sample Data Here is an image of the DVD handed out at the 2007 NCMI EMAN/Visualization workshop. Download here To use this file, use a DVD burning program (like k3b under linux or Nero, etc. under windows) to burn the image to a DVD. Alternatively under linux (as root), you can mount the image file directly: text/html 2025-07-05T17:52:44+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:eman1_faq_heterogeneous&rev=1751737964&do=diff I have processed my data set to high resolution, but I'm sure the raw data is heterogeneous. Is there any way for me to resolve this heterogeneity to get a better resolution structure out, or to produce multiple models from my single data set ? Two approaches have evolved in EMAN for dealing with heterogeneous data sets. text/html 2025-07-05T14:57:01+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:fftw3&rev=1751727421&do=diff No. EMAN1 can not be compiled with fftw3. In EMAN2, we support both fftw2 and fftw3, you can choose one of them to compile EMAN2. text/html 2025-07-05T15:01:53+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:fftwgel&rev=1751727713&do=diff FFTW-GEL is an architecture-specific version of FFTW. Compile EMAN with FFTW-GEL will have some performance gain on older Athlon machines. This does not apply to newer 64-bit chips, and the intel specific version is not useful for EMAN. text/html 2025-07-05T15:51:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:fsc_fsc&rev=1751730673&do=diff Question: I am having an issue with the eotest and FSC curves. When the particles are low pass filtered, the FSC curve produced by eotest starts to come up sometimes quite significantly, to around 0.5, at about the resolution frequency that the particles were filtered at. Also, the same thing happens when the models are CTF corrected. I have tested the effect of specifying different CTF correction cutoffs on the FSC curve at 20, 30, and 40A. Each time the curve produced by eotest starts to incr… text/html 2025-07-05T14:52:28+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:gui1&rev=1751727148&do=diff The reason for this error is that you are running a very old Linux system. The X window libraries are not compatible with the one I used to compile EMAN1.8. If you don't want to upgrade your Linux, you can download the daily release of EMAN. It is built on an old Linux system. This daily release copy will not run on most current Linux system. That's the reason we build the EMAN 1.8 binary on a newer system to cover current Linux release and some older system (but not too old). text/html 2025-07-05T17:55:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:handedness&rev=1751738117&do=diff Q: How do I determine the handedness of my single particle reconstruction A: Unfortunately the normal experiment, many images of untilted specimens, doesn't provide any experimental data permitting you to determine handedness. That is, the image of a particle in a particular orientation is exactly identical to the image of the particle rotated 180 degrees with flipped handedness. text/html 2025-07-05T17:52:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:heterogeneousphase&rev=1751737930&do=diff Q: I have a heterogeneous data set and want to know where I can find information on the phase residuals of the data set in EMAN to see if it can reveal the extent of the heterogeneity of my data. A: What do you mean by 'the phase residuals of the data set' ? text/html 2025-07-05T18:05:56+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:icos&rev=1751738756&do=diff Question: What about the support for icosahedral viruses? Answer: EMAN supports icosahedral symmetry similarly to other symmetries. Basically you will follow the same procedures as for particles of other symmetries. Of course, you need to specify sym=icos text/html 2025-07-05T14:56:01+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:installer1&rev=1751727361&do=diff This is normal. eman-installer is a simple script to detect your system shell then create corresponding lines to add necessary enviroment variables for EMAN. What you downloaded is binary package, nothing need to compile. It is ready to use by set up three environmental variables. text/html 2025-07-05T15:13:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:macoslibrary&rev=1751728412&do=diff For all .dylib files in EMAN/lib directory, you need a symbolic link .so. For example: libpyAligner.dylib -> libpyAligner.so text/html 2025-07-05T18:43:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:median&rev=1751741017&do=diff *Question: In EMAN 1.8 I run a refinement, and when I look at the number of particles in my class averages I get really weird values that obviously aren't correct. Answer:** It appears that there is a bug with the “median” option in EMAN 1.8. It is fixed in current snapshots. If you are using the 1.8 release without CTF correction, simply omit the 'median' option. This will perform an average rather than a median, which is fine. The only thing to be aware of with this, is if you are using CCD… text/html 2025-07-05T16:06:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:mpimake3d&rev=1751731571&do=diff Question: How can I use mpi version of make3d? Answer: First of all, you need a mpi package to compile a mpi version of EMAN(make3d). We use mpich1.2.7. You need compile mpich1.2.7 as following: $./configure -prefix=/usr/local -rsh=ssh $make CXXFLAGS='-O2 -fPIC' $su $make install text/html 2025-07-05T15:17:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:msvcr80.dll&rev=1751728630&do=diff Q: I have downloaded the Windows installer and installed as administrator under C: and the installation finishes without any error message. When I want to run any of the EMAN programs, I get the error message about the missing msvcr80.dll. I found the file in a few folders on my system (e.g. ADOBE, and Windows\SxS text/html 2025-07-05T15:26:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:multipleboxer&rev=1751729186&do=diff Q: Boxer - I used a reference and batchboxer to pick particles from cryo-micrographs using a script. I did not use the minidist option to remove touching particles. Q: Boxer - I used the GUI boxer and the .box files to delete selected particles on the carbon file. I saved these new .box files text/html 2025-07-05T15:55:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:particlelogfile&rev=1751730912&do=diff This page is missing text/html 2025-07-05T14:56:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:qt4&rev=1751727392&do=diff No, EMAN can not be compiled with qt4. Qt3 and Qt4 have totally different API. The most current qt3 package tested to be compatible with EMAN is qt-x11-free-3.3.7.tar.gz. text/html 2025-07-05T15:50:36+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:refine&rev=1751730636&do=diff Refine command options The refine command is at the heart of using EMAN1 for single particle reconstructions, and it has many options, some of which can produce truly awful results, so it is important not to simply go into the process blindly. This is an overview of the various parameters: text/html 2025-07-05T15:47:51+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:refine2dninitcls&rev=1751730471&do=diff Q: I have run refine2d.py on different datasets with different number of particles (2000 to 4000) as follow: refine2d.py start.hed --iter=8 --ninicls=30 As a result it was produced always 10 classes for each dataset I have tested. Even I changed ninitcls= to 50 , 5, or 20 always 10 classes were created. According wiki there is possible to specify number of classes. text/html 2025-07-05T15:39:15+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:refine2dpy_centering&rev=1751729955&do=diff Should the data set be centered before subjecting it to refine2d.py? No. The only impact centering will have is on the quality of the 'bootstrap' averages (iter.1.img). If they are roughly centered, the impact will be negligible. Even if there is impact on the first set of averages, after a few iterations, this would be eliminated. So, basically, no, they don't need to be precentered, and it's possible (depending on the precentering method) that precentering would actually have a negative effec… text/html 2025-07-05T15:39:43+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:refine2d_classes&rev=1751729983&do=diff Question: After running refine2d.py there are some good classes in several of the iter.#.img files that I would like to use in other programs (spider and IMAGIC). I would like to be able to extract the individual images that made up these class averages - is this possible, and if so how would I go about this? text/html 2025-07-05T15:56:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:refineamask&rev=1751730983&do=diff Q: How do I choose the correct arguments for the amask argument in refine? I see that it ultimately is used to run the amask2 argument in proc3d, but I'm still a little unsure as do how to choose the parameters. I take it that the 'r' is the approximate radius where the density of the molecule falls off, and thr is the value of text/html 2025-07-05T15:17:48+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:rhel4&rev=1751728668&do=diff Q: 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? A: You need update your RHEL to its most recent state. Or run “fc-cach -vf” as root(not sudo). text/html 2025-07-05T18:44:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:segfault&rev=1751741075&do=diff Q: I compiled EMAN2 on Mandriva 2009, everything looks OK, but I got segmentation fault when I try to run e2display.py or e2boxer.py. A: It's a bug in one of the qt4 package, which is for foreign language input method. Use Mandiva's package manager to remove package scim-bridge-qt4 should solve this problem. text/html 2025-07-05T14:52:57+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:selinux&rev=1751727177&do=diff Q: 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”? The solution comes from this link: http://www.ittvis.com/services/techtip.asp%3Fttid%3D%33%30%39%32. The best way is: chcon -t texrel_shlib_t YOUR_EMAN_DIR/lib/*.so text/html 2025-07-05T15:46:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:startnrclasses&rev=1751730368&do=diff Q: The class-averages produced by startnrclasses don't seem to show the number of particles in each class when displayed in the matrix view. How can we fix this ? A: Hi. Two points here. First, you should really consider using refine2d.py rather than startnrclasses. startnrclasses is really only suitable for bootstrapping the refine2d.py process, or getting a very rough view of characteristic views of your particles. text/html 2025-07-05T15:34:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:structurefactor&rev=1751729685&do=diff Q: 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 A: The documentation really needs to address this, but doesn't. There are two reasons for this, though. First, it is really difficult to describe this adequately textually. Second, you need to have a sound understanding of the mathematics being used in CTF correction to use this method properly and avoid doing b… text/html 2025-07-05T15:38:16+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:translateparticles&rev=1751729896&do=diff Q: 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 ? A: This isn't how EMAN usually does things, so none of the canned command-line programs will do this, but this simple script should do: text/html 2025-07-05T15:02:39+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:ubuntu_baddevice_error&rev=1751727759&do=diff This error is not harmful. You can ignore it without any trouble to use eman. But to compile EMAN on Ubuntu (>7.04), you need set ENABLE_UBUNTU in ccmake, type 't' for advanced setting. If you think this is annoying and want to get rid of it, please do as following: text/html 2025-07-05T18:08:16+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_12&rev=1751738896&do=diff Question: I read the documentation, and I still don't know what to do. How can I get more help ? Answer: Every other spring, the NCMI hosts a workshop on single particle reconstruction and post-processing (at least we have for a number of years thru March 2007). This workshop covers all of the basics of performing a CTF corrected single particle reconstruction and analyzing the results, and historically has been free of charge (though you must cover your own travel expenses). Check the text/html 2025-07-05T18:00:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_13&rev=1751738406&do=diff Question: What paper should I cite if I use EMAN1 in published results ? (NOT EMAN2) Answer: This one: Ludtke, S.J., Baldwin, P.R., and Chiu, W. (1999). EMAN: semiautomated software for high-resolution single-particle reconstructions. J Struct Biol 128, 82-97. text/html 2025-07-05T18:08:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_14&rev=1751738917&do=diff Question: I've heard that (insert favorite program) runs much faster than EMAN. Is this true ? Answer: The quick answer is: EMAN strives for the best, most accurate solution, not the fastest solution. That may sound like a 'yes', but it definitely is NOT. It is quite possible to make EMAN run very fast, indeed. It all depends on the options you use. In the early rounds of refinement, or when you are still trying to determine the quaternary structure of your object, you are strongly encouraged … text/html 2025-07-05T18:09:01+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_15&rev=1751738941&do=diff Question: 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 ? Answer: This is a very complicated issue, and depends a lot on your relative skill in using the different packages as well as your understanding of some very complicated issues. The first issue is what your friend meant by 'better resolution'. People in CryoEM often confuse resolvability with resolution. These are two VERY different terms. In s… text/html 2025-07-05T18:09:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_16&rev=1751738972&do=diff Question: I'm running EMAN in parallel on a cluster, and it seems to lock up when it reaches the class-averaging step (classalign2). Answer: This is known to occur on a few clusters, but not in a predictable fashion. It seems to be related to a bug in older versions of OpenSSH, or perhaps in the network kernel itself. If (while refine is locked up) you run 'netstat' on the node where the refine command was run, and see a number ssh processes in the CLOSE_WAIT state, this is the problem you are … text/html 2025-07-05T15:14:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_17&rev=1751728465&do=diff Question: How do I compile EMAN for OSX(Mac) ? Answer: We now offer partial support for OSX (current OSX version only). Still, to compile yourself, you need to know what you're doing if you want to make it work on that platform. Basically: use 'fink' to install required libraries: text/html 2025-07-05T18:09:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_18&rev=1751738995&do=diff Question: I'm trying my first EMAN refinement, but the refine command crashes or produces black images in classes.1.hed. What's going on? Answer: There are several possible causes for this. The first possibility is that your particles in start.hed and your initial 3D model in threed.0a.mrc aren't the same size. Do an 'iminfo start.hed' and 'iminfo threed.0a.mrc' and make sure they're the same size in pixels. text/html 2025-07-05T18:10:27+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_19&rev=1751739027&do=diff Question: How can I read images in format ABC ? What file formats does EMAN support ? Answer: EMAN supports a lot of different formats, and it does it transparently. That is, in general, all EMAN program can read any image in a wide variety of formats without you having to do anything special. EMAN currently supports reading SPIDER, IMAGIC, MRC, HDF5,Gatan DM2, Gatan DM3, PIF and ICOS formats. TIFF images are now natively supported using libtiff. You should now be able to directly read 16 bit … text/html 2025-07-05T15:45:15+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_20&rev=1751730315&do=diff Question: Symmetry determination - Do you have a facility for calculating rotational power spectra ? How can I determine the symmetry of my particles ? Answer: This can be done in EMAN, though it doesn't use rotational power spectra. While we have played with rotational power spectra in the past we didn't find them to be very reliable, and don't currently have an end-user tool for this. text/html 2025-07-05T15:51:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_22&rev=1751730701&do=diff Question: How can I find out how many particles were used in a reconstruction ? How can I look at the particles that were discarded ? Answer: Good questions! To find out how many particles were included in the class-averages, type (for example) 'iminfo classes.4.hed all'. The last number on each line is the number of particles included in that class-average. At the end a total number of particles included in the classes file will be shown. text/html 2025-07-05T15:35:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_23&rev=1751729735&do=diff Question: 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 text/html 2025-07-05T18:10:49+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_24&rev=1751739049&do=diff Question: I'd like to process a really big data set with EMAN. Is it up to the task ? Answer: Gosh, I hope so! Seriously, there are a few issues to be aware of. First, one factor often of concern is the fact that EMAN generally keeps the entire set of particles in a single image file stack A really big reconstruction might cause this file to become bigger than 2 gigabytes, which is a problem for some parts of certain operating systems and a lot of other software packages. While EMAN does the pr… text/html 2025-07-05T15:37:09+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_25&rev=1751729829&do=diff Question: 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? Answer: The answer depends on the source images. EMAN reads most EM file formats directly. If you have each particle in a separate image file, for example, img001.img, img002.img, etc., then the following command would do it (zsh, similar for other shells): text/html 2025-07-05T15:52:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_27&rev=1751730726&do=diff Question: 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. text/html 2025-07-05T15:37:38+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_28&rev=1751729858&do=diff Question: 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? text/html 2025-07-05T18:12:50+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_29&rev=1751739170&do=diff Question: I have a bunch of MRC convention Euler angles and need to generate projections of a model in EMAN Answer: Here is a python script that should give you something to start with. Don't forget the help() function in python, ie: import EMAN help(EMAN.EMData) help(EMAN.Euler) text/html 2025-07-05T17:54:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_30&rev=1751738095&do=diff Question: I have heard that EMAN can process heterogeneous data sets and produce multiple models, for example, to study dynamics or ligand binding Answer: Yes, EMAN does have software to do this. The software itself is no more difficult to use than the normal 'refine' command (in fact the syntax is almost identical). However the overall process you normally follow to produce reliable results can be somewhat involved, and hasn't been well documented. Also, note that it is much more computational… text/html 2025-07-05T17:51:30+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_31&rev=1751737890&do=diff Question: 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 ? Answer: This is largely answered in the question above relating to resolution of reconstructions. If you are not using optimal options with the refine command, you may, indeed, not get optimal results. The basic options provided by the EMAN tutorial do not give the entire picture. For example, if you continue to use c… text/html 2025-07-05T15:52:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_32&rev=1751730754&do=diff Question: 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. text/html 2025-07-05T15:45:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_33&rev=1751730334&do=diff Question: We have a bit of a problem with our refinement :( 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. We wonder if it's worth removing the bad classsums in the initial rounds of refinements to get the rough shape of the molecule (if yes, how?). text/html 2025-07-05T17:51:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_34&rev=1751737906&do=diff Q : I have done a few eotests on different reconstructions. Do you know how the information in the fsc.eotest output file relates to the bold black EOTEST line that shows up in the FSC curve? I could be wrong, but they don't seem to be the same in my reconstructions. A colleague seemed to think it could be something to do with the A/pix in the .mrc file being different to the one I am entering in EMAN to create the convergence plot and bring up the FSC curve text/html 2025-07-05T15:53:14+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_refine_shrink&rev=1751730794&do=diff Q: What does the “shrink=n” do in Refine commmand? It doesn't look like changing the size of subfiles like proc2d shrink=n does? A: (DavidWoolford) - I had a look at the source code and it looks like refine uses the shrink parameter to run classesbymra text/html 2025-07-05T18:43:59+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:using_stdouttoobig&rev=1751741039&do=diff Q: Our jobs are crashing on our cluster because the stdout file is too big (more than 20meg). Is there a way to tell eman to generate a “less verbose” output? A: Sorry. Not really. Clusters shouldn't really limit the size of stdout like that... The only real option I can think of would be to redirect stdout of the 'refine' command directly to a file, however, since it calls other subshells, I'm not 100% positive if the subprograms would also go to the file text/html 2025-07-05T18:00:30+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:workshopdvd&rev=1751738430&do=diff You can download the DVD image from the 2007 workshop here: <http://blake.bcm.edu/dl/workshop4.iso> Warning, this is a 3.5 gigabyte file. It may take a while to download. Suggest using a download program with resume capabilities. text/html 2025-07-05T15:55:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman1:faq:xfiles&rev=1751730945&do=diff Q: How can I figure out the correct parameters for the xfiles argument? I know that the first argument is the angstrom per pixel (which is, say, 2.1), and I know that my molecule weighs a certain amount (say, 1700 kDa). I am not sure of the third argument, but I am aware that it might be practically unused. Is it as simple as writing xfiles=2.1,1700,99?