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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 19:37:12
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Dear Dieter, if you send me the pdb I can try myself and I will try to check where the problem is. Kind regards, Carlos Oscar El 24/02/2021 a las 20:23, Dieter Blaas escribió: > > 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 > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
