Frealign

Hi,

I wonder whether it is possible to monitor the class-assignment of all individual particles during a full multi model refinement (many iterations)? What I would like to see is different from frealign_calc_stats which gives you the occupancy.
Is there a way that I can simply grep the classnumber of each particle for each iteration after the run has finished?

many thanks
Arne

Hi all,

I would like to recenter my particles to see if I have overlapping particles in my refinement.

Do you know if the conventions for EMAN boxer files and the FREALIGN parameter files are the same after conversion from Angstroms to pixels (e.g. the shifts can just be added to the box coordinates)?

Best,

Axel

Hi everyone,

Could you please share some of your experience on how do you pick the best reconstruction parameters for a given map, notably, thresh_reconst and PBC?

Although I try to optimize these parameters following some kind of systematic search while assessing the map visually and by the FSC, I am concerned whether my reconstructions are the best they can be. I'd like to know how do people pick these values and whether there is any "optimal" way of setting them.

Thanks a lot.

Hi, I have a question about gun tilt refinement in FREALIGN.
I tried different values for TX and TY (even at 0.2 mrad instead of 0.02), but always got exactly the same resolution number and FSC curve.

In mult_hreconstruct_n.com file, I put in:
1.,${dstep},60.0,${thresh},${cs},${kV},0.2,0.2 !RELMAG,DSTEP,TARGET,THRESH,CS,AKV,TX,TY

How can I be sure the program actually reads in the TX and TY values I specified?

Thanks!

Rui

Hi,

I would like to know how the splitting of particles is performed in Frealign in order to calculate the FSC and if the data is refined independently as in the "gold-standard" approach.

Thank you very much!

Dear All,

I've been trying to modify the qsub_string_ref of mparameters to specify a queue and the number of nodes and ppn for our PBS cluster. I'm using the following:

qsub_string_ref "-q mpi -l nodes=3:ppn=64"

It's recognising the -q command and sending the job to our mpi queue but it's ignoring the -l nodes=3:ppn=64 and sends the job to other nodes. Does anyone have a successfully working qsub_string_ref for PBS clusters?

Thanks,

Andrea

Hi,

Hi everyone,

Reading the latest article about Frealign in the Methods in Enzymology, I have two questions about the "generating initial map" part:
1. Do you change the high-resolution limit to calculate class membership with the refinement resolution limit?
2. If I understood it well Mode 3 is used in the whole process, do you change the value of DANG during the cycles? If not what value do you use?

Thank you!

Best regards,
Gabor

Hi everybody,

is there any documentation for frealign_calc_variance? It sounds like a helpful tool but I don't fully understand how it works and how to interpret the results.

Cheers
Lukas

Hi Niko and Alexis,

I recently started working with Frealign (v9.11), which did so far an excellent job in separating a simulated dataset using my local machine (6 cores). I especially liked the easy set-up and the organization with the mparameter and the .par-files. Now, I would like to scale up the process and hence moved to a large PBS-cluster (HLRN, https://www.hlrn.de/home/view). Here, I installed Frealign and started running it. I have the following files in my folder:

RNAP_80.par #already refined parameter
RNAP_80.mrc #refined volume