Frealign

Hi,

If we have a icosahedral virus, under mode=3,
setting search angle, does program still search whole space or only search asymmetric unit (half triangle)?

If still search the whole space, is there a way to provide a list of angles for frealign to search?

Thanks

Dear all,

We have problems over here in Finland... We have managed to successfully install frealign on our in-house cluster, and the pdh test data set works fine. When we try to run our own data - parameter files created either from scratch and run in modes -4 or -3, or alternatively parameter files generated in imagic using imagic-to-frealign - we get this error message:

At line 54 of file card10.f
Fortran runtime error: No such file or directory
INPUT PARAMETER FILE ?
my_virus.par_1_53

I'm getting discontinuities (mainly extra density) between helical section repeats using FBEAUT. These discontinuities only show up in Chimera when viewing with a step size of 1.

If I turn FBEAUT off there are no discontinuities, but the helical densities blur out and fade away toward the ends. I presume this would seriously impair the next round of refinement??

I'm running the latest Frealign.

I am wondering if I can impose a two fold symmetry on a helical reconstruction using frealign.

Thanks a lot.

I was wondering if there is a way to make Frealign restrict it's angle / shift refinement to within certain limits. For instance, is it possible to tell Frealign to only refine theta to within 15 degrees.

Frealign is running nicely in Appion, with one exception. The densities of the resulting volumes and class averages are flipped. A quick fix is to flip it back after each iteration. However I am concerned that this is a symptom for something being messed up within the code and that Frealign might not run correctly. At this point we can't tell if this is an Appion issue, or if that is something Frealign does. That's why I want to ask, if you have an idea and/or if that happened to you before?

I had a couple Frealign questions that I'm hoping someone can help me with:

1. How does "set_polarity.exe" calculate the 'score' after adjusting a parameter file and how does it choose which polarity to select initially?

Has anybody met such a problem?
I use frealign to process a helical tube. It works perfectly for binned data (332X332 pixels). Once I start processing unbinned data (664X664), the alignment works fine, but the reconstruction did not generate any density in the map.The program ends normally, did not give any error information. I later found out this was due to the FBEAUT function. If I turn FBEAUT off, the reconstruction is fine.

Hi Niko,

You say that you apply a mask with a cosine edge to the images. What width do you give to you give to your edge? I can't find it in your publication. Also, what mask radius do you use? The particle radius?

Best,

Amedee

Hi,