RuntimeError

[Liang Chen]

HI everyone,

I am a new user of EMAN2. I am trying to learn the official tutorial. I installed EMAN2 on my windows 10. When I tried to reconstruct tomograms, I always stuck with the following message:

RuntimeError: InvalidValueException at D:\Miniconda3\conda-bld\eman2_1615225643321\work\libEM\emdata_metadata.cpp:844: error with '0': 'x size <= 0' caught

I do not even have a D:\ disk. I tried to load a virtual D:\ and installed Miniconda3 on it, but it didn't work. Anyone has any ideas?

[Ludtke, Steven J.]

Hi. Did you install the native windows version or use the (strongly recommended) LSW approach?

I believe this message is complaining about an image file it's trying to open, and has nothing to do with the D:\ you see in the path...   Saying you are getting stuck with a certain message isn't very useful unless you tell us what you were trying to do when you get the error.

cheers

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

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[Liang Chen]

Hi Steven,

Thank you for your reply. I installed the "Native Win7/10 64 bit" according to the "Binary Installation Instructions v2.31".

I tried to follow the official "EMAN2 Tomography Workflow Tutorial". I just reached the second step "3D Reconstruction -> Reconstruct Tomograms". After I clicked "launch", there came the message. I tried the same on Mac without any problems, but my Mac is a little old and slow.

By the way, what is LSW approach? Is there an official link to explain it? Sorry about my ignorance. I am a complete novice.

[Ludtke, Steven J.]

Hi,

you should be installing the current 2.91 version, not 2.31 (especially if you are doing the tomography tutorial):

http://eman2.org/Install/BinaryInstallAnaconda/2.91

the section under windows installation has a separate link for the WSL approach. 

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/574ed66d-86c5-4f18-bf34-9e85f293830dn%40googlegroups.com.

[Liang Chen]

Thank you the instructions. I tried to follow the tutorial carefully, but I did download the latest v2.91. I will try the WSL approach as you recommended.

[Ludtke, Steven J.]

Hi, 

the point is that we have not tested the tomography tutorial using the native windows 10 install. There are a number of things which do not work properly on native Win 10. The WSL approach fixes most of these problems.

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/0ba470b4-569d-4bf2-adc7-4640c2f84c42n%40googlegroups.com.

[Liang Chen]

Hi Steven,

I tried the WSL approach and installed the latest 2.91 version of EMAN2. When I input e2version.py, it worked. However, when I tried e2display.py, it showed "QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-lclinux'

qt.qpa.screen: QXcbConnection: Could not connect to display :0

Could not connect to any X display."

I have installed the "Xming X Server for Windows" and it was running while I tried e2display.py.

Another error I got was when I input " glxinfo|grep OpenGL", an error appeared "Error: unable to open display :0". Is the failure caused by the setting of OpenGL in WSL?

[Steve Ludtke]

It sounds like the X-server isn't working properly...

-----------------------------------------
Steven Ludtke, slud...@gmail.com 

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/df4f2e49-1a54-4b90-9204-881e06768f8cn%40googlegroups.com.