Hi,
Simply perform "Join star files" job as usual.
Best regards,
Takanori Nakane
On 2020/09/13 14:15, Laurence Pearl wrote:
> How do I recombine the surviving particles into a single set for 3D classification after the seperate 2D classification and selection ?
>
> Laurence
>
> ----------------------------------------------------
> Laurence H. Pearl PhD FRS FMedSci
>
> Professor of Structural Biology
> Genome Damage and Stability Centre
> University of Sussex, Brighton, BN1 9RQ, UK
>
> Phone +44-(0)1273 <tel:+44-(0)1273%20876%20544>678 349
> ----------------------------------------------------
> "Live Modestly and do Serious Things .. "
> - Dorothy Crowfoot Hodgkin
> ----------------------------------------------------
>
>
> On 13 Sep 2020, at 13:53, Takanori Nakane <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>
>> Hi,
>>
>> I would split the dataset into batches of 0.5 - 1 M particles and run
>> Class2D separately.
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>> On 2020/09/13 11:28, Laurence Pearl wrote:
>> > We have a large dataset - > 9 million particles - and are encountering problems in RELION 3.1 trying to do 2D classification. A small subset of 15k
>> > particles classifies beautifully with the same settings, giving clear secondary structure in the 2D classes, but feeding it the full 9M particles
>> > causes a crash immediately after the calculation of initial noise spectra.
>> >
>> > The error suggest we are going out of addressed memory (see below) which my old hackers brain interprets as exceeding some array bound or other.
>> >
>> > Are there physical limits to the number of particles to that RELION 3.1 can handle, and if so, can we override these ? Alternatively, can anyone
>> > suggest a rational approach to 2D classification of a dataset this size in chunks, so that it can be recombined at a later stage, once the junk has
>> > been eliminated.
>> >
>> > Laurence
>> >
>> > [juniper:42273] *** Process received signal ***
>> > [juniper:42273] Signal: Bus error (7)
>> > [juniper:42273] Signal code: Non-existant physical address (2)
>> > [juniper:42273] Failing at address: 0x7f91ac5f5f70
>> > [juniper:42273] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x128a0)[0x7f91c4e7b8a0]
>> > [juniper:42273] [ 1] /lib/x86_64-linux-gnu/libc.so.6(+0x16d927)[0x7f91c4077927]
>> > [juniper:42273] [ 2] /usr/local/relion-3.1-200730/bin/relion_refine_mpi(opal_convertor_pack+0xc9)[0x55e21d70b5b9]
>> > [juniper:42273] [ 3] /usr/local/relion-3.1-200730/bin/relion_refine_mpi(mca_btl_smcuda_prepare_src+0xb1)[0x55e21d7a4921]
>> > [juniper:42273] [ 4] /usr/local/relion-3.1-200730/bin/relion_refine_mpi(mca_pml_ob1_send_request_start_rndv+0x1a6)[0x55e21d59a786]
>> > [juniper:42273] [ 5] /usr/local/relion-3.1-200730/bin/relion_refine_mpi(mca_pml_ob1_send+0x8c3)[0x55e21d58f103]
>> > [juniper:42273] [ 6] /usr/local/relion-3.1-200730/bin/relion_refine_mpi(MPI_Send+0xdf)[0x55e21d54f3cf]
>> > [juniper:42273] [ 7]
>> > /usr/local/relion-3.1-200730/bin/relion_refine_mpi(_ZN7MpiNode15relion_MPI_SendEPvlP15ompi_datatype_tiiP19ompi_communicator_t+0x127)[0x55e21d3600f7]
>> > [juniper:42273] [ 8] /usr/local/relion-3.1-200730/bin/relion_refine_mpi(_ZN14MlOptimiserMpi22combineAllWeightedSumsEv+0x3d2)[0x55e21d33f2b2]
>> > [juniper:42273] [ 9]
>> >
>> /usr/local/relion-3.1-200730/bin/relion_refine_mpi(_ZN14MlOptimiserMpi41calculateSumOfPowerSpectraAndAverageImageER13MultidimArrayIdE+0x185)[0x55e21d33fb15]
>> > [juniper:42273] [10] /usr/local/relion-3.1-200730/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0xae6)[0x55e21d343ed6]
>> > [juniper:42273] [11] /usr/local/relion-3.1-200730/bin/relion_refine_mpi(main+0x6b)[0x55e21d30c1db]
>> > [juniper:42273] [12] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f91c3f2bb97]
>> > [juniper:42273] [13] /usr/local/relion-3.1-200730/bin/relion_refine_mpi(_start+0x2a)[0x55e21d30f2ca]
>> > [juniper:42273] *** End of error message ***
>> >
>> > --------------------------------------------------------------------------------
>> > Laurence H. Pearl PhD FRS FMedSci
>> >
>> > Professor of Structural Biology
>> > Genome Damage and Stability Centre
>> > School of Life Sciences, University of Sussex
>> > Brighton, BN1 9RQ, UK
>> >
>> > +44-(0)1273 678349
>> > --------------------------------------------------------------------------------
>> > "Live Modestly and do Serious Things .. "
>> > - Dorothy Crowfoot Hodgkin
>> > --------------------------------------------------------------------------------
>> >
>> >
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------------------------------------------------------------------------------
>> >
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