How to convert relion star files to bdb files

[Lei Chen]

Hi All,

I have used relion for 2D-classification and want to further use SPARX to do ISAC, which requires bdb files as input.

I am wondering if there is a guideline or script to convert star files to bdb files?

Thanks,

Lei

[Paul Penczek]

Hi

A fancy way is to use sxrelion2sparx, it has detailed description on sparx wiki pages.

You can also try to copy the file directly, using sxcpy.py

Regards,

Pawel

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[rainfieldcn]

Hi Pawel,
I have just installed EMAN 2.11 (CVS 2015/06/05 19:02:06) but I can't find sxrelion2sparx.py
Where can I get it?
Thanks,
Lei

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[Paul Penczek]

Hi

You should install the most recent snapshot, not the release.

Regards,

Pawel

[Paul Penczek]

We did not quite manage to get sparx ready for the last release of eman2.  Now we are ready though so maybe Steve will prepare an update to the last release. 

Regards,

Pawel

[rainfieldcn]

Hi Pawel,
I have reinstalled the new build: EMAN 2.11 (CVS 2015/08/21 09:00:06)
I still can't find sxrelion2sparx.py .
did you forget to put it into the daily build?
Thanks,
Lei

[Paul Penczek]

I'll send you the ode in an hour. 

Regards,

Pawel

[Paul Penczek]

Hi,

the program is in distribution since at least July 8th.  Are you sure your path is correct?

The program is in EMAN2/bin

Should you decide to use the attached version, please make sure you modify the first line,

the one that invokes python, so it matches your system.

Regards,

Pawel.

---

From: rainfieldcn <rainf...@gmail.com>
To: em...@googlegroups.com
Sent: Friday, August 21, 2015 4:30 PM
Subject: Re: [EMAN2] How to convert relion star files to bdb files

[rainfieldcn]

Hi Pawel,
Sorry, I didn't realize that I need to delete the old EMAN2 dir.
I did again and I found it.
By the way, what does  --star_section=data_images  mean?
What should I put here?

My star header looks like:

data_

loop_
_rlnVoltage #1
_rlnDefocusU #2
_rlnDefocusV #3
_rlnDefocusAngle #4
_rlnSphericalAberration #5
_rlnDetectorPixelSize #6
_rlnCtfFigureOfMerit #7
_rlnMagnification #8
_rlnAmplitudeContrast #9
_rlnImageName #10
_rlnCoordinateX #11
_rlnCoordinateY #12
_rlnNormCorrection #13
_rlnMicrographName #14
_rlnGroupNumber #15
_rlnOriginX #16
_rlnOriginY #17
_rlnAngleRot #18
_rlnAngleTilt #19
_rlnAnglePsi #20
_rlnAutopickFigureOfMerit #21
_rlnClassNumber #22
_rlnLogLikeliContribution #23
_rlnNrOfSignificantSamples #24
_rlnMaxValueProbDistribution #25

Thanks,
Lei

[Paul Penczek]

I think you should put data_
Regards,

Pawel

[Lei Chen]

Hi Pawel,
I have installed pydusa-1.15-sparx-8.tgz
But I run into another problem:
when I start ISAC:
sxisac.py bdb:data isac1 --radius=35 --CTF
I got those errors:
[:35409] mca: base: component_find: unable to open
/usr/lib64/openmpi/lib/openmpi/mca_shmem_mmap: perhaps a missing
symbol, or compiled for a different version of Open MPI? (ignored)
[medusa.ohsu.edu:35409] mca: base: component_find: unable to open
/usr/lib64/openmpi/lib/openmpi/mca_shmem_posix: perhaps a missing
symbol, or compiled for a different version of Open MPI? (ignored)
[:35409] mca: base: component_find: unable to open
/usr/lib64/openmpi/lib/openmpi/mca_shmem_sysv: perhaps a missing
symbol, or compiled for a different version of Open MPI? (ignored)
--------------------------------------------------------------------------
It looks like opal_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during opal_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

opal_shmem_base_select failed
--> Returned value -1 instead of OPAL_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

opal_init failed
--> Returned value Error (-1) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):

ompi_mpi_init: ompi_rte_init failed
--> Returned "Error" (-1) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[:35409] Local abort before MPI_INIT completed successfully; not able
to aggregate error messages, and not able to guarantee that all other
processes were killed!

Thanks,
Lei

[Paul Penczek]

Hi
Have you looked at examples on isac manual page?
You are missing mpirun directive. You also have to consider the number of CPUs you have and should use. This is explained on isac page of sparx Wikipedia. I cannot easily paraphrase it here in few sentences.

Regards,
Pawel

[rainfieldcn]

Hi Pawel,
I tried mpirun before, which didn't work.

Let me explain more detail:
I converted my star file into hdf : sxrelion2sparx.py 2D_3_15145.star
--output_dir=sparx --star_section=data_ --create_stack
Then I convert hdf into bdb: sxcpy.py sparx_stack.hdf bdb:H8_8x
both of the programs worked well:
e2bdb.py /m3/lei/H8.test/sparx_8x/ -l
H8_8x 15145 60x60x1 apix: 0.02 218.00 mb
TOTAL 15145 218.00 mb

Then I used isac:
mpirun -np 20 sxisac.py bdb:H8_8x isac1 --radius=35 --CTF indep_run=4
| tee isac.log

it gave me error:
usage: sxisac.py stack_file <output_directory> --radius=particle_radius
--img_per_grp=img_per_grp --CTF --restart_section<The remaining
parameters are optional --ir=ir --rs=rs --xr=xr --yr=yr --ts=ts
--maxit=maxit --dst=dst --FL=FL --FH=FH --FF=FF --init_iter=init_iter
--main_maxit=main_iter --iter_reali=iter_reali --match_first=match_first
--max_round=max_round --match_second=match_second --stab_ali=stab_ali
--thld_err=thld_err --indep_run=indep_run --thld_grp=thld_grp
--generation=generation --rand_seed=rand_seed>
Please run 'sxisac.py -h' for detailed options

Do I have to fill all the parameters?

By the way, when convert star to hdf using sxrelion2sparx.py, the apix
is wrong. is there a way to manually change the apix size?
Thanks,
Lei

[Steven Ludtke]

In addition to Pawel's comments, a very common cause for this sort of problem is an inconsistent environment. Most clusters have more than one version of MPI available. When you build an MPI application, you use 'mpicc' instead of 'cc' or 'gcc'. 'mpicc' is a script specific to a particular MPI installation, which makes sure your programs use the correct include files and libraries. However, if your LD_LIBRARY_PATH or other variable is causing a different MPI library to be used at runtime, you will get errors like this. Typically the problem can be diagnosed via:

which mpicc
echo $LD_LIBRARY_PATH

if that doesn't reveal a problem, you can continue with

ldd EMAN2/lib/mpi.so
and make sure that it's consistent with the result 'which mpicc' gives.

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

[Paul Penczek]

You forgot to put "--" in front of index_run, this is what the program parser is trying to tell in an awkward way.

You do not need this parameter anyway. 

Your images are 60^2, right?  If so, they are tad small.  The bigger problem is that I am not sure

how a circle with radius 35 can fit into a square of 60.  Most likely the program will crash.

sxisac can accept hdf file as an input.

You may also want to make sure CTF information is correct:

sxheader.py sparx_stack.hdf   --params=ctf  --export=myctfs.txt

and then simply scan the text file.

Regards,

Paweel.

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[rainfieldcn]

Hi Steven,
I did the test:
$ which mpicc
/usr/lib64/openmpi/bin/mpicc
$echo $LD_LIBRARY_PATH
/usr/local/IMOD/lib:/usr/local/cuda/lib64:/usr/lib64/openmpi/lib:/software/relion-1.3/lib
$ ldd lib/mpi.so
linux-vdso.so.1 => (0x00007fff9596e000)
libmpi.so.1 => /usr/lib64/openmpi/lib/libmpi.so.1
(0x00002ae62ebc0000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00002ae62eebb000)
libc.so.6 => /lib64/libc.so.6 (0x00002ae62f0d8000)
libopen-rte.so.7 => /usr/lib64/openmpi/lib/libopen-rte.so.7
(0x00002ae62f46c000)
libopen-pal.so.6 => /usr/lib64/openmpi/lib/libopen-pal.so.6
(0x00002ae62f6e4000)
libdl.so.2 => /lib64/libdl.so.2 (0x00002ae62f9ae000)
librt.so.1 => /lib64/librt.so.1 (0x00002ae62fbb2000)
libnsl.so.1 => /lib64/libnsl.so.1 (0x00002ae62fdbb000)
libutil.so.1 => /lib64/libutil.so.1 (0x00002ae62ffd4000)
libm.so.6 => /lib64/libm.so.6 (0x00002ae6301d7000)
libltdl.so.7 => /usr/lib64/libltdl.so.7 (0x00002ae63045c000)
/lib64/ld-linux-x86-64.so.2 (0x00000031da800000)
It looks OK to me.
Thanks,
Lei

On 8/22/2015 8:50 AM, Steven Ludtke wrote:
> which mpicc

[rainfieldcn]

Hi Pawel,
You are right. I missed "--".
right now when I run: mpirun -np 4 sxisac.py bdb:H8_8x --indep_run=4 | tee isac.log
It gives some errors about the library.
But I am checked /usr/lib64/openmpi/lib/openmpi/ folder, all of the libraries are there.
Thanks,
Lei


$mpirun -np 4 sxisac.py bdb:H8_8x --indep_run=4 | tee isac.log

[ :60794] mca: base: component_find: unable to open /usr/lib64/openmpi/lib/openmpi/mca_shmem_mmap: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[ :60792] mca: base: component_find: unable to open /usr/lib64/openmpi/lib/openmpi/mca_shmem_mmap: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[ :60792] mca: base: component_find: unable to open /usr/lib64/openmpi/lib/openmpi/mca_shmem_posix: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[ :60794] mca: base: component_find: unable to open /usr/lib64/openmpi/lib/openmpi/mca_shmem_posix: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[ :60794] mca: base: component_find: unable to open /usr/lib64/openmpi/lib/openmpi/mca_shmem_sysv: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[ :60792] mca: base: component_find: unable to open /usr/lib64/openmpi/lib/openmpi/mca_shmem_sysv: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[ :60793] mca: base: component_find: unable to open /usr/lib64/openmpi/lib/openmpi/mca_shmem_mmap: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[ :60793] mca: base: component_find: unable to open /usr/lib64/openmpi/lib/openmpi/mca_shmem_posix: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[ :60793] mca: base: component_find: unable to open /usr/lib64/openmpi/lib/openmpi/mca_shmem_sysv: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)

--------------------------------------------------------------------------
It looks like opal_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during opal_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  opal_shmem_base_select failed
  --> Returned value -1 instead of OPAL_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  opal_init failed
  --> Returned value Error (-1) instead of ORTE_SUCCESS
--------------------------------------------------------------------------

[ :60791] mca: base: component_find: unable to open /usr/lib64/openmpi/lib/openmpi/mca_shmem_mmap: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[ :60791] mca: base: component_find: unable to open /usr/lib64/openmpi/lib/openmpi/mca_shmem_posix: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[ :60791] mca: base: component_find: unable to open /usr/lib64/openmpi/lib/openmpi/mca_shmem_sysv: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)

[ :60791] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!

--------------------------------------------------------------------------
It looks like opal_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during opal_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  opal_shmem_base_select failed
  --> Returned value -1 instead of OPAL_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------

It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems.  This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):

  ompi_mpi_init: ompi_rte_init failed
  --> Returned "Error" (-1) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
***    and potentially your MPI job)

[ :60793] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!

*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
***    and potentially your MPI job)

[ :60792] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!

--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems.  This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):

  ompi_mpi_init: ompi_rte_init failed
  --> Returned "Error" (-1) instead of "Success" (0)
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems.  This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):

  ompi_mpi_init: ompi_rte_init failed
  --> Returned "Error" (-1) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
***    and potentially your MPI job)

[ :60794] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[35978,1],0]
  Exit code:    1
--------------------------------------------------------------------------


$ ls /usr/lib64/openmpi/lib/openmpi/
libompi_dbg_msgq.so      mca_db_hash.so               mca_grpcomm_bad.so       mca_pstat_linux.so        mca_scoll_basic.so
mca_allocator_basic.so   mca_db_print.so              mca_iof_hnp.so           mca_pubsub_orte.so        mca_scoll_mpi.so
mca_allocator_bucket.so  mca_dfs_app.so               mca_iof_mr_hnp.so        mca_ras_gridengine.so     mca_sec_basic.so
mca_atomic_basic.so      mca_dfs_orted.so             mca_iof_mr_orted.so      mca_ras_loadleveler.so    mca_sharedfp_individual.so
mca_bcol_basesmuma.so    mca_dfs_test.so              mca_iof_orted.so         mca_ras_simulator.so      mca_sharedfp_lockedfile.so
mca_bcol_ptpcoll.so      mca_dpm_orte.so              mca_iof_tool.so          mca_ras_slurm.so          mca_sharedfp_sm.so
mca_bml_r2.so            mca_errmgr_default_app.so    mca_io_ompio.so          mca_rcache_vma.so         mca_shmem_mmap.so
mca_btl_openib.so        mca_errmgr_default_hnp.so    mca_io_romio.so          mca_rmaps_lama.so         mca_shmem_posix.so
mca_btl_self.so          mca_errmgr_default_orted.so  mca_memheap_buddy.so     mca_rmaps_mindist.so      mca_shmem_sysv.so
mca_btl_sm.so            mca_errmgr_default_tool.so   mca_memheap_ptmalloc.so  mca_rmaps_ppr.so          mca_spml_yoda.so
mca_btl_tcp.so           mca_ess_env.so               mca_mpool_grdma.so       mca_rmaps_rank_file.so    mca_sshmem_mmap.so
mca_btl_vader.so         mca_ess_hnp.so               mca_mpool_sm.so          mca_rmaps_resilient.so    mca_sshmem_sysv.so
mca_coll_basic.so        mca_ess_singleton.so         mca_mtl_psm.so           mca_rmaps_round_robin.so  mca_state_app.so
mca_coll_hierarch.so     mca_ess_slurm.so             mca_odls_default.so      mca_rmaps_seq.so          mca_state_hnp.so
mca_coll_inter.so        mca_ess_tool.so              mca_oob_tcp.so           mca_rmaps_staged.so       mca_state_novm.so
mca_coll_libnbc.so       mca_fbtl_posix.so            mca_osc_rdma.so          mca_rml_oob.so            mca_state_orted.so
mca_coll_ml.so           mca_fcoll_dynamic.so         mca_osc_sm.so            mca_routed_binomial.so    mca_state_staged_hnp.so
mca_coll_self.so         mca_fcoll_individual.so      mca_plm_isolated.so      mca_routed_debruijn.so    mca_state_staged_orted.so
mca_coll_sm.so           mca_fcoll_static.so          mca_plm_rsh.so           mca_routed_direct.so      mca_state_tool.so
mca_coll_tuned.so        mca_fcoll_two_phase.so       mca_plm_slurm.so         mca_routed_radix.so       mca_topo_basic.so
mca_compress_bzip.so     mca_fcoll_ylib.so            mca_pml_bfo.so           mca_sbgp_basesmsocket.so  mca_vprotocol_pessimist.so
mca_compress_gzip.so     mca_filem_raw.so             mca_pml_cm.so            mca_sbgp_basesmuma.so
mca_crs_none.so          mca_fs_ufs.so                mca_pml_ob1.so           mca_sbgp_p2p.so

>> [ :35409] mca: base: component_find: unable to open

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[Paul Penczek]

I do not know about mpi, but now you are missing radius.

Regards,

Pawel

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