WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
I0000 00:00:1725864668.678668 236592 service.cc:145] XLA service 0x55626c166d90 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:
I0000 00:00:1725864668.678936 236592 service.cc:153] StreamExecutor device (0): Tesla V100-PCIE-16GB, Compute Capability 7.0
I0000 00:00:1725864669.765751 236592 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.
WARNING:tensorflow:You are casting an input of type complex64 to an incompatible dtype float32. This will discard the imaginary part and may not be what you intended.
EMAN 2.99.62 ( GITHUB: 2024-08-27 01:33 - commit: NOT-INSTALLED-FROM-GIT-REPO )
Your EMAN2 is running on: Linux-3.10.0-957.el7.x86_64-x86_64-with-glibc2.17 3.10.0-957.el7.x86_64
Your Python version is: 3.12.5
Finally, the resultant map called threed_05.hdf was as a resolution of 8 Å without any improvement. The commands and map have been provided below. Thank you in advance for any advice or suggestions you may have regarding this matter!
Dear Muyuan,
<Screen Shot 2024-09-09 at 20.31.46.png>
<Screen Shot 2024-09-09 at 20.30.09.png>
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<Screen Shot 2024-09-09 at 20.31.46.png><Screen Shot 2024-09-09 at 20.30.09.png>
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On Sep 10, 2024, at 2:56 AM, Muyuan Chen <g5v...@gmail.com> wrote:
1. --thr is the isosurface threshold level. It is just EMAN compress the hdf files, and chimera cannot read them properly. If you open the map with "show3d" in e2display browser, 4 should be the right number.2. Normally it should do the post-processing by itself, and you should get a sharpened map in threed_05. In fact, now you ran the e2spt_structfac program once, if you repeat the same e2gmm_refine_iter run, you should get correct maps in threed_xx.hdf in the new gmm folder. I don't know what went wrong in your case in the first place. I would guess there was some error message in the first e2convertrelion command that was missed that led to this, or some intermediate files was moved or deleted during the refinement...Muyuan
On Mon, Sep 9, 2024 at 11:12 PM Clotho <cloth...@gmail.com> wrote:
Dear Muyuan,Cheers! The high resolution features now can be seen clearly. There are still questions needed to be clarify.
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IndexError: index 0 is out of bounds for axis 0 with size 0
On Sep 12, 2024, at 10:08 AM, Clotho <cloth...@gmail.com> wrote:
Hi, I just tested e2gmm on my own dataset. It is quite strange that the proper isosurface threshold value for the threed_00.hdf generated by e2convertrelion cmd would reach ~2000 in e2display. If I typed in "--thr 2000" for e2gmm_guess_n.py , the program reported error as follow:dm=np.sort(d)[len(d)//2]IndexError: index 0 is out of bounds for axis 0 with size 0
<Screenshot from 2024-09-12 16-47-17.png>
And the output log for the e2convertrelion cmd was displayed here. Are there any difference from your case?
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<Screenshot from 2024-09-12 16-47-17.png><Screen Shot 2024-09-13 at 01.05.29.png>
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On Sep 13, 2024, at 12:14 PM, Muyuan Chen <g5v...@gmail.com> wrote:
Yes I find it quite strange too. There has been quite a few strange things lately after the python upgrade. Hopefully they get fixed soon...It is probably sharpened, but the default sharpening parameters may not be as aggressive as some other software. Running e2spt_structfac with --sharper will probably help.That said, the sharpening only affect the visual appearance but not the alignment results. So you can run the sharpening in the end, then re-run the e2refine_postprocess with the new sf.txt and the threed_raw files (i.e. copy the threed_raw_even to the last threed_0X_even, and rerun the last e2refine_postprocess command). Or just bring it to other software for sharpening, since there are quite a few protein feature based fancy sharpening tools out there as well.
On Fri, Sep 13, 2024 at 8:24 AM Clotho <cloth...@gmail.com> wrote:
Hi Muyuan,
I checked the info of "threed_00.hdf" and the value of mean and sigma is 0.025 and 1, respectively. I also make a copy using provided command and the threshold value seems to be normal this time. It is quite strange.
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On Sep 24, 2024, at 10:58 PM, Clotho <cloth...@gmail.com> wrote:Sorry for reply late.I have posted the tensorflow warning snaphot here:<Screenshot from 2024-09-25 11-14-51.png>Also, I have checked my eman2 envrionment. The cuda version is 12.3. The version of tensorflow and numpy is 2.16.1 and 1.26.4, respectively.<Screen Shot 2024-09-25 at 11.47.21.png>If you need more detailed information, please feel free to ask here. Thank you again for your reply.
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<Screen Shot 2024-09-25 at 11.47.21.png><Screenshot from 2024-09-25 11-14-51.png>