yes it is. thanks, Ludo!
> You need to put .box in the script not *.box
> I think that's the problem.
>
> Ludo
>
> sent from mobile - excuse typos - darn autocorrect!
> On 5 Oct 2015 14:52, "Joshua Lobo" <[log in to unmask]> wrote:
>
>> Hi Dr. Scheres
>>
>> I am attaching a file which shows a small test with a subset of
>> Micrographs (of a different data set )done using Relion 1.4 . I have
>> relion
>> 1.3 on the cluster and relion 1.4 on the local cluster so I cannot
>> perform
>> exact tests. In the logfile I have included the command version of what
>> I
>> ran. I have shown that the size of the star file created is 0k and I
>> have
>> listed a sample of my Micrographs folder showing that I have .box
>> files.Lastly I have double checked the path about which relion points to
>> in
>> the does not exist warning message and that path seems to pint to the
>> right
>> file.I am also attaching my gui.settings for the particle extract job.
>>
>> As mentioned earlier the CTF job ran normally.
>>
>> I should also mention that the Particles folder (containing the .mrcs
>> and
>> star files ) is not created at all . I'm not sure how to troubleshoot
>> the
>> problem. Any suggestions are welcome
>>
>> Sincerely
>> Joshua Lobo
>>
>> On Sun, Oct 4, 2015 at 3:55 PM, Sjors Scheres
>> <[log in to unmask]>
>> wrote:
>>
>>> Hi Joshua,
>>> What should happen is that relion indeed warns you about missing
>>> coordinate files, but then it should still extract the micrographs for
>>> which there is a coordinate file. Did you check whether the output
>>> particle.star file and the particle stacks were indeed created?
>>> HTH,
>>> Sjors
>>>
>>> > Hi CCPEM
>>> >
>>> > I am trying to extract particles from .box files using relion 1.3 . I
>>> have
>>> > done this successfully in the past on another test data set.
>>> >
>>> > I performed the CTF correction and that ran fine and generated a
>>> proper
>>> > file with all my micrographs. Now I am providing the file
>>> > "all_micrographs_ctf.star" as input to the Particle extraction job.
>>> The
>>> > Micrographs folder contains the .box suffixed cordinate files from
>>> boxer .
>>> > However I have picked them from random micrographs in my dataset (
>>> i.e a
>>> > cordinate file does not exist for each Micrograph listed in
>>> > all_micrographs_ctf. I want to generate a template so that I can use
>>> > autopick to pick all the particles. On running the particle
>>> extraction
>>> job
>>> > relion complains that there arent cordinate files for each micrograph
>>> in
>>> > the all_micrograph_ctf.star file Whch is true . So how do I proceed
>>> with
>>> > the extraction step so that i can eventually make a template for
>>> autipick
>>> > to pick  everything.
>>> >
>>> > please advise any inputs will be appreciated
>>> >
>>> > Sincerely
>>> > Joshua Lobo
>>> >
>>>
>>>
>>> --
>>> Sjors Scheres
>>> MRC Laboratory of Molecular Biology
>>> Francis Crick Avenue, Cambridge Biomedical Campus
>>> Cambridge CB2 0QH, U.K.
>>> tel: +44 (0)1223 267061
>>> http://www2.mrc-lmb.cam.ac.uk/groups/scheres
>>>
>>>
>>
>>
>> --
>> *Joshua Lobo*
>> *Biomedical Engineering *
>> *Virginia Commonwealth University*
>>
>>
>


-- 
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres