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Re: [scipion-users] xmipp_volume_from_pdb "-i" "all_atoms.pdb" "-o" "all_test" "--blobs" "--fixed_Gaussian"
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From: Carlos O. S. <co...@cn...> - 2021-02-23 19:14:43
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Dear Dieter, I see two possible reasons: 1. --blobs and --fixed_Gaussian are mutually exclusive. Use only one of them as they point to different kinds of atom models. 2. --fixed_Gaussian if there is no parameter afterwards is taking the Gaussian sigma from the type of atom. If there is a type of atom in the PDB that is not explicitly encoded in the program, then the result may be undefined and that is why you are getting a segmentation fault. To me, the best atom conversion is the one without these two parameters. It is taking the electron atomic scattering factors. Kind regards, Carlos Oscar On 2/23/21 12:37 PM, Pablo Conesa wrote: > > 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... >> ------------------------------------------------------------------------ >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
