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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 19:24:21
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Thank you all, good to know :-) just to add: What might be the reason for the error (see below for my original post)? 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 24.02.2021 19:41, Carlos Oscar Sorzano wrote: > > Dear all, > > I totally agree. The most convenient way to create these volumes is > through the protocol. > > Cheers, Carlos Oscar > > On 2/24/21 4:31 PM, Pablo Conesa wrote: >> >> Hi Dieter, people from xmipp team is reading this list. So is the >> right email to be used. Although maybe a xmipp specific email could >> be more clearer. >> >> My line was, more than a clarification for you, a call for xmipp team >> to come to the rescue!. Which Carlos Oscar did. >> >> The way you used xmipp through scipion is fine. You could even do it >> in one line: >> >> *scipion3 **xmipp_volume_from_pdb* >> >> scipion3 will redirect command starting with "xmipp_*" to xmipp , >> "e2" or "sx" to eman, and "relion" to relion. >> >> I do not know a better way from the command line, unless you want to >> avoid scipion and use directly xmipp. There is a way, but then you >> need to install xmipp on its own, which might be more complex. >> >> The other way would be using scipion itself, you have a protocol for >> that, that its calling xmipp program in the backgound: >> >> >> On 24/2/21 13:30, Dieter Blaas wrote: >>> >>> 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 >>> >>> >>> _______________________________________________ >>> 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 > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
