Frealign

In the resolution file generated by v8.11, there is a column "Part_FSC". How to use this to evaluate resolution of the reconstruction? Thanks.

Hi,

I have been trying to run the multiprocessor reconstruction using the "_mp" version of the frealign executable. Am I right to say that the control script between the non _mp version and the _mp version is almost the same? I have seen discussion at http://emlab.rose2.brandeis.edu/node/1230, and learnt that the IFLAG should be set to 0 and the NCPUS parameter must be set. Leaving these aside, is there any other change that needs to be made to how the parameters are passed to the _mp version? Spider was used to do a coarse refinement for the angles prior to the run.

Hi,

from the website it looks like the latest version of the the GPU-enabled version (8.06) precedes the version that includes helical averaging (8.09 and beyond). Is that correct? Is is possible to use helical symmetrization with the GPU-enabled code?

Best, ~Adam
frost@biochem.utah.edu

I have a question about padding. Can I just set IBLOW=2 to get 2x padding during 3D reconstruction? Thanks.

Hi,

I have some problems how to give parameters to impose helical symmetries in Frealign

Readme says: " #SUBUNITS = #STARTS x D / RISE" My interpretation is that #STARTS then is a function of the overlapping in segment picking and that 90% overlap gives #STARTS=0.1. On the other hand "The number of starts in the helix" would be 10. When I use 0.1 I get reasonable results but in the resulting parameter file I get "C Number of starts . . . . . . . . . 1".

Thankful for any clarifications/Martin

Hello,

This is a bit of a continuation to the "map does not refine" entry to the forum where I was trying to get mode "3" or "4" to arrive to a 3d model similar to the given reference. I was adviced to try to convert my alignment parameters from spider and try then. And here is what I found:

I manage to obtain a reasonanle good model when I use as input stack file a file that has been already aligned by spider. In that case, the PSI angle is left as zero and everything works well.

Hi,

I'm trying to install the latest version of frealign (8.10_120517) on a Mac running Snow Leopard server (10.6.8). I have used the latest intel compilers (composer_xe_2011_sp1.10.328, ifort v. 12.1.4).
I tried to compile frealign using the Makefile_OSX_86-64_intel file, but this results in these errors:

Undefined symbols:
  "_omp_get_num_procs_", referenced from:
      _MAIN__ in frealign_v8.o
  "_omp_set_num_threads_", referenced from:
      _MAIN__ in frealign_v8.o
ld: symbol(s) not found

(a whole capture of the stdin/stderr of make is attached)

Hello,

Not sure this goes well in the forum as I don't have a specific question. The problem that I am encountering is that all maps I am getting with Frealing are extremely low-pass filtered versions of the map that I am using as reference. In the first instance I would like to see Frealing producing the same map that I am giving as a reference and then refine the model to higher resolution. The model was obtain by ML (Xmipp).

I'm having problems getting the GPU version of frealign working. It compiles without error, but running frealign_v8.exe_ref always results in crashes, with a variety of Segmentation faults, Aborts, and silent crashes. The errors, when any errors are reported in the logs, are memory-related: "free(): invalid next size (normal)" or "double free or corruption (!prev)", for example. The errors are not consistent, even with the same input data (which would tend to reinforce the hypothesis of memory errors). Most but not all of the errors produce core files.