Frealign

Hi,

Is there a new script which splits per micrograph for ctf/mag refinement, or should I modify Xing's old script?

Axel

Hi Everybody,

I have been noticing some "lagging" in Frealign individual frealign refinement jobs. When a new round of refinement is submitted to the cluster, I noticed that the submitted refinement tasks differ greatly in execution time. So even though all jobs start running at roughly the same time, the first one can be done before the last one is half way through.

Hi specialists,

I try to reconstruction a map with GeFrealign_v8.exe_rec and when I finished the card 1 input, it came out with a message "CARD 1: Error. Trying old CARD 1 input...".
I don't know which options are used in 'old CARD 1 input'. And anyone would like to help me? Thank you!

Regards,
Jianhao

Hi,

I downsampled my particle stack by a factor of 2, using the resample.exe program, and refined my map up to the point where the FSC is high up to the Nyquist frequency of this downsampled dataset. My refinement resolution limit is at a much lower resolution to avoid overfitting.

Then, I performed reconstruction using the original stack, and because the resample.exe program performs cropping in Fourier space, I expected my FSC to be good up to at least the highest resolution shell of the downsampled dataset, but it's actually worse than that. How can that be explained?

Dear FREALIGN developers,

I'm trying helical refinement with frealign (V9.11 build on 151031), and now I need a conclusion about the STIFFNESS parameter.

In the default mparameters file produced by frealign_helical_template, the STIFFNESS parameter is explained as 'Stregth of straightness restraint (small value = strong restraint).'.

But in README.txt (included in frealign_v9.11), and also in some past posts in this forum, the STIFFNESS parameter is explained as the opposite (small value = weak restraint).

Could you tell me which is correct? I will appreciate your help.

Hi,

When starting a refinement with frealign using only:
- a stack
- a .par file (XXX_1_r1.par)
- a mparameter file including start_process=2 and end_process=2
it first generates a map with index 1, refine and generate a new map and a new .par file with index 2 (XXX_2_r1).
Is the first map with index 1 (XXX_1_r1.xxx) used in the actual refinement or just an output?
Is is possible to replace this first reconstruction map by another map to be used in the refinement?

Thanks

Dear All,

We have two datasets for which data has been collected at different magnifications. Now, we want to merge stacks from both the datasets.

I have query to how to introduce more than one stack with different pixel size in mparameter file. We are using frealign_v9.11.

Your help will be highly appreciated.

Thanks and Regards

I have noticed a recurring error where, on occasion (thankfully rarely), a giant .par file gets written that, when undetected at an early enough time point, can easily creep up to many TB in size. The first time I saw this, the file was 4.2 TB, now second time 2.4 TB.

Hi all,

Most jobs on our cluster are large MPI jobs reserving anywhere from 96 to several hundred cpus. Submitting a large number of one cpu jobs as Frealign does makes it difficult for these users to schedule their jobs sometimes.

I was wondering if anyone had suggestions on how to submit a Frealign job which reserves a block of cpus on an sge cluster, and submits frealign jobs to those cpus without letting those cpus return to the pool of cpus until the job is finished (preferably without having to rewrite too many of the submission scripts).

Best,

Axel

Hi everyone,

I was wondering if there were any plans to implement frealign refinement with phase plate data.

Best,

Axel