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Re: [scipion-users] localrec not present in scipion and what version of relion neede
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From: Jose M. de la R. T. <del...@gm...> - 2017-06-05 07:17:01
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Dear Dieter, Take a look at the help of xmipp_transform_filter, I think the raised_cosine should not be there. The command line should be like: scipion xmipp_transform_filter -i my.vol -o my_filtered.vol --fourier low_pass 30 0.05 --sampling 0.97 Regarding the pixel size, Xmipp does not use or store information in the header of the images/volumes, so that's the reason why still your output volume has pixel size of 1 instead of 0.97 Bests, Jose Miguel On Sun, Jun 4, 2017 at 8:43 AM, Dieter Blaas <die...@me...> wrote: > Dear Pablo and all, > > thanks a lot, I got it! Now I am having the next problem: Trying to > prepare a mask by using a pdb file I first looked for an example with: > > "scipion xmipp_volume_from_pdb" > > and got the following: > > "EXAMPLES > Sample at 1.6A and limit the frequency to 10A > xmipp_volume_from_pdb -i 1o7d.pdb --sampling 1.6 > xmipp_transform_filter -i 1o7d.vol -o 1o7dFiltered.vol --fourier > low_pass 10 raised_cosine 0.05 --sampling 1.6" > > based on this I tried: > > xmipp_volume_from_pdb -i my.pdb --sampling 0.97 > > and got: my.vol > > Next I did: > > scipion xmipp_transform_filter -i my.vol -o my_filtered.vol --fourier > low_pass 30 raised_cosine 0.05 --sampling 0.97 > > and got: > > ** Running command: xmipp_transform_filter "-i" "my.vol" "-o" > "my_filtered.vol" "--fourier" "low_pass" "30" "raised_cosine" "0.05" > "--sampling" "0.97" > XMIPP_ERROR 1: Errors on command line parameters > Too many arguments for parameter --fourier > > File: software/em/xmipp/libraries/data/argsparser.cpp line: 1036 > > *Furthermore:* the generated volume has a sampling of 1 instead of 0.97 > as specified in both commands above. > > Thanks for hints! > > Dieter > > > ------------------------------------------------------------------------ > Dieter Blaas, > Max F. 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, > Fax: 0043 1 4277 9616, > e-mail: die...@me... > ------------------------------------------------------------------------ > > Am 22.05.2017 um 08:13 schrieb Pablo Conesa: > > Dear Dieter, you are almost there: > > > after a: > > 1.- git clone https://github.com/I2PC/scipion.git > > 2.- cd scipion > > 3.- git checkout release-1.1 > > you should have release-1.1 code checked out. > > Then continue from here: step2-dependencies > <https://github.com/I2PC/scipion/wiki/How-to-Install-1.1-sources#step2-dependencies> > . > > > If you had previous version installed you will need to adjust > configuration files, there are several way to do this, I'll explain the > easiest, this is: > > 1.- Back up your *user config file*. From the console type: *mv > ~/.config/scipion/scipion.conf ~/.config/scipion/scipion.conf.v1.0.backup* > > 2.- Run *scipion config* (this will regenerate you user config file > compatible with release 1.1) > > 3.- run *scipion config --update* (this will update your existing > scipion_home config file with missing new variables) > > 4.- Review EM software folders name, at *<SCIPION_HOME>/software/em/*, > this is the main change from release 1.0 to 1.1. Here you have 2 options: > > A) Simplest way would be to remove all folders there *except xmipp*. > And install EM software needed again using scipion install > <package-version>. Most of them are just a tar.gz extraction. It should be > quick. And some versions have been updated like motioncor2. > > B) RenameEM packages folders (or create links) to match new naming > convention (package-version). As an example, in release 1.0 the folder > for frealign was named "frealign". Now, in release 1.1 it should have the > version also in the name--> frealign-9.07 > > 5.- Compile Xmipp with new code: *scipion install -j 5* > > That should be all to install and migrate configuration from Scipion 1.0 > to Scipion 1.1. > > Let us know how it goes and if you need any further assistance. > > All the best, Pablo. > > Scipion Team. > > On 19/05/17 17:24, Dieter Blaas wrote: > > Hi Juha, Miguel & all, > > please forgive me my ignorance but what is the command for installing > scipion *release-1.1?* Can it be installed via git clone or do I have to > use the tar.gz file? I cannot find the correct name in github! > > Dieter > > > ------------------------------------------------------------------------ > Dieter Blaas, > Max F. 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, > Fax: 0043 1 4277 9616, > e-mail: die...@me... > ------------------------------------------------------------------------ > > Am 19.05.2017 um 08:40 schrieb Dieter Blaas: > > Dear all, > > thank you very much for these explanations, I shall do as suggested! > > Best wishes, Dieter > > ------------------------------------------------------------------------ > Dieter Blaas, > Max F. 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, > Fax: 0043 1 4277 9616, > e-mail: die...@me... > ------------------------------------------------------------------------ > > Am 19.05.2017 um 08:11 schrieb Juha Huiskonen: > > Dear Dieter, > > I just checked and Jose Miguel is right, when run localrec from Scipion, > localrec needs to have Relion 1.4 present. So when you install Scipion, > please install both. However, 1.4 is used only internally for some > functions - you can still classify, refine and reconstruct the sub-paricles > in Relion 2.0. > > Please double check that you have this line in your > .config/scipion/scipion.conf file: > LOCALREC_RELION_HOME=%(EM_ROOT)s/relion-1.4 > > Best wishes, > Juha > > > On Fri, May 19, 2017 at 7:02 AM, Jose Miguel de la Rosa Trevin < > del...@gm...> wrote: > >> Dear Dieter, >> >> As Juha suggested, it would be better to use branch release-1.1, which is >> going to be the next official release. >> >> Juha, correct me if I'm wrong, but I think that localrec would need >> Relion 1.4, and currently does not work with 2.0. In Scipion, both versions >> can live together. Indeed, you don't need to modify your environment, >> Scipion will do it for you when launching Relion jobs (the same for other >> packages). It is also possible to reuse package installations (if the >> version is the one used in Scipion). You just need to create a symbolic >> link in the scipion/software/em folder with the proper name >> (package-version). >> >> Cheers, >> Jose Miguel >> >> >> On Fri, May 19, 2017 at 7:31 AM, Juha Huiskonen <ju...@st...> >> wrote: >> >>> Dear Dieter >>> >>> Please update your Scipion to 1.1 beta (balbino) from github branch >>> release-1.1-fixes. Localrec is part of that version and will be in the >>> official release 1.1 when that comes out. It is also compatible with Relion >>> 2.0. >>> >>> Best wishes, >>> Juha >>> >>> On 19 May 2017, at 08:14, Dieter Blaas <die...@me...> >>> wrote: >>> >>> Dear colleagues, >>> >>> I tried to install localrec in scipion (Scipion v1.0.1 >>> (2016-06-30) Augusto) following this instruction: >>> https://github.com/OPIC-Oxford/localrec/wiki/How-to-install but >>> 'scipion >>> --help' does not show this software and 'scipion install localrec' does >>> not find it. >>> >>> 1) how do I install localrec? >>> >>> 2) once installed will it run also by using the latest relion version >>> (i.e. relion-2.0.x, which I have as a separate and independent install) >>> or do I have to use the old relion (v-1.4) and if so, can both version >>> live side by side (for example relion-1.4 within scipion and >>> relion-2.0.5 outside scipion? >>> >>> Thanks a lot for hints, >>> >>> Dieter >>> >>> >>> >>> ------------------------------------------------------------------------ >>> Dieter Blaas, >>> Max F. 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, >>> Fax: 0043 1 4277 9616, >>> e-mail: die...@me... >>> ------------------------------------------------------------------------ >>> >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> >> > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
