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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...> - 2021-02-24 18:41:52
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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 |
