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:
mean: -0.003090 sigma: 0.078643 threshold: 0.100000 dimensions:22,22,22
Warning: Incomplete data read 14/484 blocks
-12.0 12.0 Segmentation fault (core dumped)
I have also tried to convert with situs but without success. Is there any way I can get a ccp4 map converted to an mrc that is readable by eman?
CCP4 maps should be directly readable by EMAN. You shouldn't need to convert anything. If you have a map EMAN won't read properly, please send us an example, and we will fix the problem.
The 'Incomplete data read' message you got on the converted image means something went wrong in the conversion process or the transfer process from one computer to another. Is the size of the file 22*22*22*4+1024 ?
yes, the size of the mrc was the one you calculated.
Now, I am using the ccp4 map and I am getting at some point a segmentation fault. I cannot find out where it comes from. It is in the pseudoatoms.py script. The reading of the map looks OK. I checked using EMdata.valueAt and the values look raisonnable to me. (here I have one more question. If the size of map is 46 46 46, how is it that one can get values at pixels outside this range like at -1000 1 1. Shouldn t it be outside the map). Then the program is starting. The first cycle of the while loop seems to go Ok, but then at the second cycle, I get a segmentation core error inside the update_map function (I think). I don t know if it is a problem with the map or not.
The map I am using is at http://marie.epfl.ch/besnard (best.ccp4) It is samples with 1 A/pix. If you have any idea where that can come from, it would really help me.
Answer: For what purpose are you running pseudoatoms.py ? That was really just a quick hack by Matt Baker for a specific purpose. It likely makes assumptions about the data in the map that your map doesn't meet. segment3d can do much the same thing with the correct options, you might give that a try.
I would still be interested in seeing one of your 'converted' MRC files that cannot be read properly. While it wasn't necessary, it should have worked. Note that you can attach images and other files directly to these Wiki pages with the attachments link above, or by putting a link directly on the page (see HelpOnEditing).
Here is the mrc map I got problems with : marmap.mrc
Answer: Ok. That file (marmap.mrc) is corrupt. The number of bytes in symmetry elements is set to 640, and should be zero. Some programs may still be able to read it, but if they do, then they will be unable to read properly formatted CCP4 files with symmetry elements. For a while many in the cryoEM community were (incorrectly) just ignoring this field in the header. Anyway, this is a bug in whatever program you used to do the conversion...