Re: [scipion-users] xmipp_volume_from_pdb "-i" "all_atoms.pdb" "-o" "all_test" "--blobs" "--fixed_Gaussian"

[Pablo C. <pc...@cn...>]

Hi Dieter!

I think xmipp team should know more about the current status.

One question, how are you invoking the xmipp command, though scipion3?, 
like scipion3 run xmipp_volume_from_pdb

On 18/2/21 19:20, Dieter Blaas wrote:
> Hi,
>
> I am trying to make a kind of mean volume from many aligned pdb files. 
> I appended all the pdbs and removed everything that is not a 
> coordinate record. This file I feed into xmipp like so: 
> xmipp_volume_from_pdb "-i" "all_atoms.pdb" "-o" "all_test" "--blobs" 
> "--fixed_Gaussian". I am using an old version of this script but I 
> believe that it has not have changed over the years. I get this:
>
> ############################################
>
> PDB file:           all_atoms.pdb
>
> Sampling rate:      1
> High sampling rate: 0.0833333
> Size:               -1
> Center PDB:         0
> Do not Hetatm:      0
> Use blobs:          1
> Use poor Gaussian:  0
> Use fixed Gaussian: 1
> Intensity Col:      occupancy
> Sigma:              -1
>
> Bus error (core dumped)
> Traceback (most recent call last):
>   File "/home/blaas/.local/anaconda3/envs/scipion3/bin/emprogram", 
> line 8, in <module>
>     sys.exit(main())
>   File 
> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/cmd/program.py", 
> line 43, in main
>     runProgram(program, params)
>   File 
> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/utils.py", 
> line 64, in runProgram
>     pwutils.runJob(None, program, params, env=env)
>   File 
> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", 
> line 51, in runJob
>     return runCommand(command, env, cwd)
>   File 
> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", 
> line 66, in runCommand
>     check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
>   File 
> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", 
> line 364, in check_call
>     raise CalledProcessError(retcode, cmd)
> subprocess.CalledProcessError: Command 'xmipp_volume_from_pdb "-i" 
> "all_atoms.pdb" "-o" "all_test" "--blobs" "--fixed_Gaussian"' returned 
> non-zero exit status 135.
>
> ###############################################
>
> What is wrong? What would be the best way for doing so? I want to use 
> this volume to finally make a soft mask in relion....
>
> Thanks a lot, best, Dieter
>
>
> ###################################################
>
> ------------------------------------------------------------------------
> Dieter Blaas,
> Max Perutz Laboratories
> Medical University of Vienna,
> Inst. Med. Biochem., Vienna Biocenter (VBC),
> Dr. Bohr Gasse 9/3,
> A-1030 Vienna, Austria,
> Tel: 0043 1 4277 61630,
> Mobile: 0043 699 1942 1659
> e-mail: die...@me...
> ------------------------------------------------------------------------
>
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*