frealign_v9 error
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Hi,Niko,I am graduate student in Tsinghua University, I am trying to use the latest version FREALIGN released on June 13th, 2014 to do helical reconstruction.But I have encountered a fatal error. When I use give the input parameters needed for frealign, it exits automatically only with a Warning: ieee_inexact is signaling. This warning appeared when I gave the image stack. But with the example for TMV, it ran successfully. So I am wondering is there anything wrong with my image stack file or something else? The image stack was converted from SPIDER format to IMAGIC format in EM2EM and change header to 3D volume with em2em header option then convert to MRC. And with the same image stack, it could run successfully in frealign_v8. What is the problem? Thank you so much!
Can you please run the
Can you please run the following command and post the output:
frealign_header
(the frealign_header command should be in the bin directory of the latest version of Frealign).
Yes,I have run the command.
In reply to Can you please run the by niko
Yes,I have run the command. And the result is pasted below.
Opening MRC/CCP4 file for READ...
File : test_stack.mrc
NX, NY, NZ: 256 256 9208
MODE : real
Min, max : -5.829934 5.498848
Mean, RMS : 0.3932341E-05 0.000000
TITLE 1: Created by IMAGIC: SPIDER image = test.spi 16-06-20 10:39:24
Your image stack looks OK.The
In reply to Yes,I have run the command. by Lingyun
Your image stack looks OK.The error is most likely due to some problem with the parameters you set in the file mparameters.
OK,let me try it again to
In reply to Your image stack looks OK.The by niko
OK,let me try it again to find the problem. If not,I would ask you for help. Thank you so much for your kindly help!
PGFIO-F-225/list-directed read/unit=5/lexical error
In reply to OK,let me try it again to by Lingyun
Hi,Niko,I am now trying to use the latest version frealign to do helical reconstruction.All the scripts I used were from the frealign package. But in mult_hrefine_n, we encountered a problem, which said PGFIO-F-225/list-directed read/unit=5/lexical error --unknown token type. File name =stdin formatted, sequential access record =6
In source file card5.f, at line number 47.
What may cause the problem? Thank you!
My guess is that you did not
In reply to PGFIO-F-225/list-directed read/unit=5/lexical error by Lingyun
My guess is that you did not add the required helical parameters to your mparameters file. I have added a new frealign command, frealign_helical_template, that will generate an mparameters file with all the required keys. You just have to edit it to enter the correct experimental details and symmetry for your dataset. You will have to download the latest frealign distribution and install it to get this new command.