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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...> - 2017-05-19 06:40:24
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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...
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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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