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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: Dieter B. <die...@me...> - 2021-02-24 12:31:03
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Hi Pablo, thanks! I thought that this list was the successor of the xmipp list. Sorry! Actually, I created the scipion3 environment with " conda activate scipion3" and invoked it with "scipion xmipp_volume_from_pdb". I am not sure whether this makes sense as I have been using the old fashioned command line xmipp commands until I recently had to move to scipion. I was wondering whether there was a better way of getting from pdb files to volume files to be used as a starting map for relion refinements or making masks etc. In fact, I appended a number of pdb files and removed everything not being a coordinate. This file I then tried to use for making a volume including all atoms.... 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... ------------------------------------------------------------------------ On 23.02.2021 12:37, 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 |
