Frealign

Hello,
I have a problem compiling the GPU version of frealign on our system.

Background:
1) GeFREALIGNv8.06_110514.tar.gz - latest GPU version (CUDA 3.2)
2) gcc:
Configured with: ../configure --prefix=/home/soft/gcc340 --enable-languages=c,f77,c++
Thread model: posix
gcc version 3.4.0

3) Nvidia Driver Version: 310.44
4) Cuda compilation tools, release 5.0, V0.2.1221
5) 2x GPU Tesla K20m

I have modified Makefile a little to use old GCC:
COMP = /home/soft/gcc340/bin/g77


Hi,

In frealign, to save time, how can I only do global search (mode=3) for the particles with worse phase residual? for example, how to only search angles for particles with phase residuals > 75.0, and skip the particles with phase residual <= 75.0? Thanks.

Xing

Hi, I have download frealign_v8.11 and try to do the helical example in the extract folder examples/helical_refinement. When I didn't modify anything, it works, just run 1 iteration.But when I revised tha end_process to 5, something went wrong. It has run 2 iterations successfully, from the 3nd iteration, it will have a message saying "segmentation fault". Also the same situation for my own data. So what should I do to let it run smoothly? Thanks!

Hi,

What's new in FREALIGN v8.11 in terms of helical processing?

And when doing FREALIGN local refinement (mode 1), what's the difference between setting ASYM to H and 0 (C1)?

Thanks!

Rui

Hi,
Is there anyone who has ever seen the problem "Number of parallel processors too large,Resetting IMP =12"? The programme has detected 24 CPUs, which echoes "Parallel Processing: NCPUS=24" in the beginning. The version I used is 8.11(the latest version of helical reconstruction). And I was trying to run it on our DELL T7600 workstation.

Hello,

I am very new to Frealign, but I found the the recently published 3D classification paper very intresting and would like to give it a try. However after downloading, I am not really sure how to start any job and the readme was not really clear to me.
So I was wondering wether there is some kind of tutorial somewhere, which explains how to use Frealign especially with the new classification feature.

kind regards

David

I was trying to run some Sparx functionalities on a stack of particles that were refined in FREALIGN, and I want to convert the FREALIGN angles and translations over to Sparx.

I used the "frealign_to_sparx.py" script on the website and I'm pretty sure something's going wrong. I can see the alignment metadata as values for the xform.projection tag, but when I do a back-projection to get a volume in Sparx (sxrecons3d_n.py), it looks like pure noise (especially when compared with the FREALIGN volume.)

Hi, I am trying to convert parameters from sparx alignments to frealign, in order to use the tiltdiff software for tilt validation. I am in particular at loss with the Euler angles conversion.
I have found various solutions on this and other websites, all of them different, and all of them not working in my hands...

Hopefully someone can help me out of this very frustrating task I got into?

Thanks
Giulia

Dear All,

I am using Frealign for carrying out reconstruction of helical filaments of a reasonably large dataset. I split my data in several parts , determine the orientation with iFlag set to 1 and the termination value to negative & then combine all of them to finish the reconstruction (with iFlag set to 1 & termination value to 0).

During the course of the process I keep the Magnification refinement as T.

Hi All,

I want to mask the input stack of images (overlapping segments of filaments). While I can mask them from the sides, many of the filaments that are orientated diagonally in the box are cut off. How can I mask the filaments in such a situation?

Thanks.