Hi Takanori,
Thanks for your reply—I was also able to confirm that --pad 1 works out, thanks for also looking into this.
Also, thanks for directing me to the resources to help me further my understanding, much appreciated!
best,
jonny
> On Feb 4, 2020, at 4:20 AM, Takanori Nakane <[log in to unmask]> wrote:
>
> Hi,
>
> I confirmed that a padding factor less than 1 causes
> several problems. So I updated the program to disallow
> such option.
>
> Best regards,
>
> Takanori Nakane
>
>
> On 2020/02/03 23:28, Jonathan Flores wrote:
>> Hi all,
>>
>> I wanted to check that a set of signal-subtracted particles I generated
> corresponds to the volume I expect.
>> To do this, I am trying to run relion_reconstruct_mpi (RELION3.1-beta)
> with the following command:
>>
>> relion_reconstruct_mpi --i job1870_particles_subtracted.star --sym c1
> --maxres 3.0 --angpix 0.649 --ctf --verb 2 --pad 0.5 --skip_gridding
> true
>>
>> (I am aware that --skip_gridding true and --pad 0.5 are not conventional
> options, but I wanted to see if I could speed things up a bit. I am
> currently running --pad 1, but waiting to see what results)
>>
>> It seems that the image back-projection step proceeded without issue,
> but when the reconstruction started, the following error popped up:
>>
>> in:
> /home/exacloud/lustre1/reichowlab/RELION/relion/src/backprojector.cpp,
> line 1449
>> ERROR:
>> BUG: zeros in counter or radavg_weight!
>> === Backtrace ===
>> /home/exacloud/lustre1/reichowlab/RELION/relion/build/bin/relion_reconstruct_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41)
> [0x42af81]
>> /home/exacloud/lustre1/reichowlab/RELION/relion/build/bin/relion_reconstruct_mpi(_ZN13BackProjector11reconstructER13MultidimArrayIdEibRKS1_ddibP5ImageIdE+0x20b3)
> [0x4bbc43]
>> /home/exacloud/lustre1/reichowlab/RELION/relion/build/bin/relion_reconstruct_mpi(_ZN13Reconstructor11reconstructEv+0x667)
> [0x45a077]
>> /home/exacloud/lustre1/reichowlab/RELION/relion/build/bin/relion_reconstruct_mpi(_ZN16ReconstructorMpi3runEv+0x49)
> [0x44b129]
>> /home/exacloud/lustre1/reichowlab/RELION/relion/build/bin/relion_reconstruct_mpi(main+0x31)
> [0x423bf1]
>> /usr/lib64/libc.so.6(__libc_start_main+0xf5) [0x7fc2e7bf4445]
>> /home/exacloud/lustre1/reichowlab/RELION/relion/build/bin/relion_reconstruct_mpi()
> [0x42464f]
>> ==================
>> ERROR:
>> BUG: zeros in counter or radavg_weight!
>> --------------------------------------------------------------------------
>>
>> I have little experience using relion_reconsruct from the command line,
> so I'm not sure what "zeros in counter or radavg_weight" is referring
> to. I would really like to gain a bit more understanding of what's going
> on "under the hood" here, and to hear from anyone who has encountered
> this error before.
>>
>> Thanks in advance for any/all insight!
>>
>> best,
>> jonny
>>
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>
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