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

[Dieter B. <die...@me...>]

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


###################################################

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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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