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Re: [scipion-users] localrec not present in scipion and what version of relion neede
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From: Dieter B. <die...@me...> - 2017-06-04 06:43:52
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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... <mailto: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... <mailto: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...
>>>> <mailto: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
>>>>> <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...
>>>>> <mailto:die...@me...>
>>>>> ------------------------------------------------------------------------
>>>>>
>>>>>
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