Frealign

I am trying Frealign 8.09. The options FPART and DFSIG are for defocus refinement of individual particles. I used FPART=T and DFSIG=150.0, however, the defocus parameters for each particle did not change at all after refinement.
Should I turn on FDEF and/or FASTIG options at the same time in order to refine the defocus values? I remember FDEF and FASTIG can only be done based on each film (the particles from the same film are being refined together).

I have generated a pretty good density map using IHRSR with the following parameters.

(1) Rotation between subunits=25.63deg (2) Axial rise=31.14A (3) Rotational symmetry=5 (4) Step size=68A

Now I am trying to get a map using Frealign.
I calculated values of some parameters in the file, mparameters.

ALPHA=360/5+25.63
RISE=31.14A
START=5
SUBUNITS = STARTS x D / RISE = 11

Unfortunately, the reconstruction didn't converage to a correct map and there are no helical arrays on the map. Are the values above wrong? What is the correct way to impose rotational symmetry?

Thanks.

mrefine_sge.com splits up particles into batches without taking their micrograph number into account.

Hi there!

Has anyone ever tried converting xmipp angles/shifts from a doc file to frealign.
In my case, I would get the other necessary information (micrograph id, defocus, astigmatism, ...) and the images themselves by imagic-to-frealign.

doc file:

; Headerinfo columns: rot (1), tilt (2), psi (3), Xoff (4), Yoff (5) , Ref (6), Flip (7), maxCC (8)
; prot/p000001.xmp


I am trying to run frealign on helical segments and have a couple of problems with it and am hoping you might be able to help.

Hi,

I am trying to refine several initial models obtained from negative-stain data using ~20,000 low-tilt (15 deg) negatively stained particles. My previous attempts with Spider and EMAN2 could not improve the resolution (0.5 FSC at 50-45 angstroms). I tried to run a few FREALIGN sessions (Mode 1) yesterday with particle parameters obtained from previous projection matching done with a Spider script and CTFTILT. The resolution seemed to stabilize at 49 A after 3 iterations. I would like to try FREALIGN again and have a few questions,

Hi niko,
I am trying do a Eular angle(output from frealign) comparison. Could you confirm the angle setting for me?
I always think FREALIGN takes the same Z-Y-Z rotation setting as SPIDER, that is, first rotate "phi" around Z, and then "theta" around Y, finally "psi" around Z. So, if writng in a matrix formula, it is
r1=R(psi)*R(theta)*R(phi)*r0 . (1)
But in FREALIGN, I found the formula is
r1=r0*R(psi)*R(theta)*R(phi) . (2)

After running a 3D projection matching refinement using SPARX, I am trying to convert my data into FREALIGN to do the final amplitude correction. I have seen the script posted in the FREALIGN download page describing how to convert FREALIGN parameters to SPARX parameters, but when I apply the inverse transformations (described below) I keep getting a ball.

Transforming data from SPARX to FREALIGN:

Phi (SPARX) = Psi (FREALIGN)
Theta (SPARX) = Theta (FREALIGN)
Psi (SPARX) = Phi (FREALIGN)

SHx (SPARX) = -SHx (FREALIGN)
SHy (SPARX) = -SHy (FREALIGN)

Hi,

I'm new to Frealign and trying to make a refinement for my RCT model. Among many other parameters I'm actually interested in RMAX1 & RMAX2. As far as I understood they determine the resolution range in Angstroms for search/refinement cycles. My question is do they correlate with RREC param? I mean, in README file RREC=10 looks good for initial search and RMAXs are 25-200A. What does this range mean?

How can I determine good values for rmax?

Thanks.

Dear all,

I've unsuccesfully tried to get GeFREALIGN (v.8.06) working with newer versions of CUDA (3.2.16 / 4.0.11 / 4.0.13) on a Tesla M2070 based system.

Changing of '__devices__' to 'static __devices__' resolves an immediate problem on compiling that is due to pre-3.1 CUDA assuming implicitly static __device__ functions. Alas, the resulting program is non-functional for reasons that are still unclear to me. Has anyone else tried (and hopefully succeeded in) using a 3.x CUDA?

Or better yet, is there an updated version of GeFREALIGN available that will work on modern hardware?