Hi Nicolas,
RELION will make a system call to "gs" to combine the EPS files into a
single logfile.pdf. If it fails, it should write to stderr. Did you see
such an error in the run.err of those directories? You could try executing
the command from the command line to find out what the problem on your
system is.
HTH,
Sjors
PS: I am pasting the relevant code from src/CPlot2D.cpp in case it helps
below:
FileName fn_list = fn_pdf + ".lst";
std::string command = "gs -sDEVICE=pdfwrite -dNOPAUSE -dBATCH -dSAFER
-dDEVICEWIDTHPOINTS=800 -dDEVICEHEIGHTPOINTS=800 -sOutputFile=";
command += fn_pdf + " @" + fn_list;
std::ofstream filelist(fn_pdf + ".lst");
bool have_at_least_one = false;
for (int i = 0; i < fn_eps.size(); i++)
{
// fn_eps[i] could be a Linux wildcard...
std::vector<FileName> all_eps_files;
fn_eps[i].globFiles(all_eps_files);
fn_eps[i].globFiles(all_eps_files);
for (long int j= 0; j < all_eps_files.size(); j++)
{
if (exists(all_eps_files[j]))
{
filelist << all_eps_files[j] << "\n";
have_at_least_one = true;
}
}
}
filelist.close();
> Hi -
>
>
> We are currently testing Relion 3 and have some weird behavior with the
> pdf files generated during the motion-correction they are empty.
>
>
> We are using the tutorial dataset and we ran several very similar Motion
> Correction jobs; 11 out of 15 runs gave empty "logfile.pdf" file (it
> seems to not depend on the number of GPU or CPUs - it happens for both
> motioncor and "relioncor" - main parameters in the I/O and Motion tabs
> were not changed). Also, the eps files of the movies all seem ok though
> (non-empty, can be converted to pdf with ps2pdf and can be open
> properly) and none of the run generate any error message.
>
>
> Does anyone know how to solve this issue or how we could track down its
> origin?
>
>
> Thanks,
>
> Best,
>
> Nicolas
>
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--
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
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