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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: Pablo C. <pc...@cn...> - 2021-02-24 15:31:31
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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* |
