Questions about Frealix

Submitted by charleswain on Wed, 2017-04-12 17:19

Forums

Frealix

Hi guys,

I want to try Frealix to hopefully get better resolution for one set of our filament
data.

This website did post a tutorial, Ab(40) using Frealix, however, it is
outdated file. I am wondering whether I could obtain an updated tutorial about
Frealix. In addition, may I get an example input file to Frealix and the
scripts needed in Frealix?

Thank you very much!

Bing

Alexis Wed, 2017-04-12 19:04

Hi Bing,

I'm afraid I haven't written a proper tutorial for this, but please go ahead and download frealix 1.2.0, which I have just added to the frealix page.

After downloading, you should be able to build frealix in the usual manner (i.e. configure; make) using the GCC compiler suite.

Once you have it installed, the first step is to run the frealix_template.sh script, which is distributed in the scripts/folder. This creates a local file called parameters.flx and prints out some instructions on getting started.

You will need to edit the parameters.flx file so that frealix knows where to find your micrographs, defocus estimates, filament coordinates etc. Once this is all ready, you can then use the flx_wrap.rb script to get started with refinement (start by doing flx_wrap.rb --help).

Hope this is sufficient to get you started.

Thanks,
Alexis

charleswain Thu, 2017-04-13 09:05

Hi Alexis,

Thank you for your reply! Seems we got problems when installing the frealix either for 1.1 or 1.2. Some errors showed up about the compiler when we installed 1.1 either in Ubuntu or Mac. When I try to install the new 1.2 in Ubuntu, there are still some problems. Sorry for my less background about this! Could I have your email?

The following log was produced when I installed 1.2.

./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
/home/bingwang/Softwares/frealix-1.2.0/missing: Unknown '--is-lightweight' option
Try '/home/bingwang/Softwares/frealix-1.2.0/missing --help' for more information
configure: WARNING: 'missing' script is too old or missing
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for g77... no
checking for xlf... no
checking for f77... f77
checking whether the Fortran 77 compiler works... yes
checking for Fortran 77 compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU Fortran 77 compiler... rm: cannot remove 'core': Is a directory
yes
checking whether f77 accepts -g... rm: cannot remove 'core': Is a directory
yes
checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... rm: cannot remove 'core': Is a directory
yes
checking whether gfortran accepts -g... rm: cannot remove 'core': Is a directory
yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... rm: cannot remove 'core': Is a directory
yes
checking whether gcc accepts -g... rm: cannot remove 'core': Is a directory
yes
checking for gcc option to accept ISO C89... rm: cannot remove 'core': Is a directory
none needed
checking whether gcc understands -c and -o together... rm: cannot remove 'core': Is a directory
yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for Fortran flag to compile .f90 files... none
checking for Fortran flag to compile .f files... none
checking for Fortran flag needed to accept free-form source... rm: cannot remove 'core': Is a directory
-ffree-form
checking for library containing cblas_sswap... rm: cannot remove 'core': Is a directory
rm: cannot remove 'core': Is a directory
no
configure: error: Could not find your installation of the GSL CBLAS library
rm: cannot remove 'core': Is a directory

Alexis Thu, 2017-04-13 12:15

Hi,

You need to have installed on your system the development files for GSL and FFTW. On Ubuntu, the following should do it:

sudo apt install libgsl-dev libgsl2 libfftw3-dev libfftw3-single3 libfftw3-bin

I think you should be able to configure on Ubuntu after that.

I am not able to help you with Mac installation.

Cheers,
Alexis

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