Frealign

Hi,

I am running FrealignX_run_refine. It seems that it ran at the beginning but stopped at the merge3d step. Here is the error message in the merge_3d_frealignx_r1.log:

        **   Welcome to Merge3D   **

            Version : 1.00
           Compiled : Jul 26 2016
               Mode : Scripted

I would like to repeat classification using the same number of classes but from a different randomization of parameters to test the robustness of class occupancy. I vaguely recall there was a random number seed option in an older version of frealign but I'm not sure if this applied to rsample or not. Is there still such an option in the newer versions? Is there a description of rsample.exe somewhere so I could implement similar randomization on my own?
Thanks in advance

Hello-

I am attempting to process a (true) helical filament (symmetry H) with Frealign v9.11. The processing is being performed locally on a workstation.

After initial alignment of segments with RELION, I was able to port my data to Frealign and generate a believable 3.5 A reconstruction (based on comparison to known structures of the protomer) with Frealign utilizing the RELION alignment parameters with mode 0, running the provided frealign_calc_reconstructions script.

I am getting these warnings:

Warning: ieee_invalid is signaling
Warning: ieee_divide_by_zero is signaling
Warning: ieee_inexact is signaling
Normal termination, no output data-files

The job seems to be running however. Should I be worried?

Currently I'm using Frealign for my proteins. My normal workflow is:
- Refine all the particles
- Classification into 2 conformations/states (C1 and C2)
- Split the stack, to get all the particles from class 1 into 1 new stack (C1 stack)
- Refine the particles belonging to class 1 above
- Further classify class 1 into 3 subclass C1_1, C1_2, C1_3
- Split the C1 stack to get all the particles from class C1_1 into C1_1 stack
- Refine particles belonging to C1_1 class

Hi,

I'm trying to run a refinement in MODE 3 using PMASK="0 0 1 0 0" and DANG=90.0 in Frealign v9.11.
While the vast majority of particles behave as I expect (changes in the angle PHI are multiples of 90 degrees, with some deviations due to the subsequent refinement in MODE 1), a few particles end up having changes in the other parameters, which should be blocked by PMASK.
Interestingly, in these cases the blocked parameters seem to "acquire" the values from the particle located immediately before it in the .par file, which makes it even more strange.

Here is one example:

Dear Frealign experts,

I hope this was not asked before, at least I couldn't find any documentation about that...
How do you track your particles during classification?
Since there is no information about the original part.no in the par file after several iterations the link to the original part.no. is easily lost.

I am using additional index-files at the moment but I was wondering if someone has a different solution.

What about introducing another column into the par file?

Dear Niko,

I am wondering how can I judge the resolution? Should I use part_FSC or FSC? In your paper 2016, your suggest to use part_FSC. If I use part_FSC, it is still above 0.143 at 6A. But I can not see transmembrane alpha helix in my map.

Best regards,
Chao

C  NO.  RESOL  RING RAD   FSPR    FSC  Part_FSC  Part_SSNR  Rec_SSNR       CC   EXP. C    SIG C  ERFC  TOTVOX
C   2  264.50    0.0040   0.56  1.000     1.000    47.8584    573.35   0.0000   0.0000   0.0000  0.00      17

I am wondering the appropriate range for the BSC number. Does it have to be within 0-20? Or we can use any number which could make the FSC curve best, even it is larger than 20?

Hi Frealign Developers,

I wish to plot the part-FSC curves for 30 cycles together to see the progress of my 3D-reconstruction. Could it be done with frealign_plot_fsc command? I could only get plots for individual cycles using the same.

Any advice will be highly appreciated.
Thanks in advance.