e2display.py - click in the middle

[Yuliya Miloslavina]

I just installed the latest EMAN 2, but the control panel in display doesn't open at all after clicking in the middle. Is there another way to activate this panel? I have this problem on both Mac Sierra and Windows 7 platforms.

[Steve Ludtke]

The windows release hasn't been updated in a very long time, due to compilation problems. If you have another option I suggest using that. The Mac version should be OK although on Sierra there may be some strange issues with window decorations being shifted a little we haven't dealt with that problem yet.

When you say you middle clicked, What type of window did you click on? What was it displaying?

On the mac ,were you using a 3 button mouse?

Can you provide the full output of the e2version.py command?

Sent from my iPad

On Nov 9, 2016, at 4:14 PM, Yuliya Miloslavina <milos...@gmail.com> wrote:

I just installed the latest EMAN 2, but the control panel in display doesn't open at all after clicking in the middle. Is there another way to activate this panel? I have this problem on both Mac Sierra and Windows 7 platforms.

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[Yuliya Miloslavina]

Thank you very much for the fast response! I have a molecule in pdb, with the help of EMAN2 I created 3D density map as .mrc file. It worked perfectly well. And now I want to make XYZ projection of it, FFT and measure distances, also to adjust the contrast - this is all what I want. I apply e2display.py and I see several options how I can open the .mrc file. When I go for 3D or 2D options I see a black window with my molecule, I can rotate it in any direction. That works great! I can also do projXYZ - it opens another window and shows the perfect image. The problem is that the middle click doesn't work. I tried it with a three button mouse and with a trackpad, on my big mac and on laptop [both have Sierra], than I also tried on my work windows computer with a different mouse and windows 7 and still I can't activate the control panel to measure the distances and make FFT. It just doesn't open it somehow.

Here is the output, if I understand it correctly what you want to see:

Yuliyas-iMac:~ Yummi$ e2version.py

EMAN 2.12 (GITHUB: Thu Nov  3 12:20:34 2016)

Your EMAN2 is running on: Mac OS 10.12.1 x86_64

Your Python version is: 2.7.10

Yuliyas-iMac:~ Yummi$ e2display.py

Traceback (most recent call last):

  File "/Applications/EMAN2/lib/emscene3d.py", line 786, in paintGL

    glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT)

  File "/Applications/EMAN2/extlib/site-packages/OpenGL/error.py", line 208, in glCheckError

    baseOperation = baseOperation,

OpenGL.error.GLError: GLError(

err = 1286,

description = 'invalid framebuffer operation',

baseOperation = glClear,

cArguments = (16640,)

)

Traceback (most recent call last):

  File "/Applications/EMAN2/lib/emimage2d.py", line 214, in paintGL

    self.render()

  File "/Applications/EMAN2/lib/emimage2d.py", line 1069, in render

    glCallList(self.main_display_list)

  File "/Applications/EMAN2/extlib/site-packages/OpenGL/error.py", line 208, in glCheckError

    baseOperation = baseOperation,

OpenGL.error.GLError: GLError(

err = 1286,

description = 'invalid framebuffer operation',

baseOperation = glCallList,

cArguments = (3L,)

)

Mouse Double Click Event

Mouse Double Click Event

[Steve Ludtke]

Hi Yuliya,

Ok. It looks like you are doing everything correctly, and have a good version. I just tried this myself on a Mac running Sierra, and downloaded a fresh binary, and it worked as expected. On the Mac, sometimes new Python windows show up behind the other windows, and you need to hit the rocketship icon or view all open windows to find it.  If that isn't the problem, it seems like it must be something about your mouse or mouse config. As an alternative, you can try holding down 'alt' and using the left mouse button.

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

[Yuliya Miloslavina]

Hi Steve,

Thank you for the answer. It finally worked with a different keyboard and with pressing "Alt".

Why is that I can't save images, like FFT or projection, as .tiff format, which would be read by any other application reading tiff? The same is about png or jpg...

With best regards,

Yuliya

[Steve Ludtke]

Seems likely that you have some sort of utility or assistive tool installed on the machine which is interfering with the normal behavior of the standard buttons. Not sure why you'd need a different keyboard, but glad you found a solution.

The TIFF format is actually quite complicated, and most programs support only a small subset of its capabilities. TIFF can support floating point greyscale images, for example, but only certain scientific image processing programs tend to use this. That is the purpose for TIFF format within EMAN2, exchanging raw data among other programs rather than taking "screenshot" style images.  

PNG and JPG writing support should be fine. I just tested it within at least one context and it worked ok, and the resulting images could be displayed in other software. So, you may have to give a more detailed explanation of specifically what you're trying to do that fails. 

cheers

----------------------------------------------------------------------------

Steven Ludtke, Ph.D.

Professor, Dept of Biochemistry and Mol. Biol.         (www.bcm.edu/biochem)

Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu)

Co-Director CIBR Center                          (www.bcm.edu/research/cibr)

Baylor College of Medicine                             

slu...@bcm.edu

[Yuliya Miloslavina]

I use Corel Draw to work with .tiff images and shows an error... I also tried with Photoshop and got the same result.

[Jason K]

Yuliya,

If you want to convert the whole micrograph, you can also use e2proc2d.py input.hdf output.png and you can open in Photoshop or any utility.

With tiff having so many different specifications, I also have experienced this problem which looks like a bug but is not actually a bug: scientific image software like ImageJ can open the EMAN2 tiffs and then you can change the bit depth and color type to whatever you want to re-save. For purposes of figures, I suggest using "Snapshot" and outputing png. If you use "Save Img" you can't write a png correctly for whatever reason, at least in my old version.

Jason

[Steve Ludtke]

Hmm, the save buttons on the single 2d image display widget work properly for me. Anyway, that's why I was asking the purpose of the coversion

Sent from my iPad

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