FSC raw data download

3D Refinement
1

Hi, Where can I found FSC raw data if I can’t open the windows of Cryosparc?I processed the dataset on the cryosparc which is on the server I failed to login in now. But I have all the output of the processed dataset. I can’t found where is the FSC raw data.

2

Also interested. Editors are asking for “source data files” (usually in .csv or .xls format) for everything these days. - which I find a good idea, but we need to adapt.

3

In the result webpage, the data file links are above the FSC plots. The PDF allows for making higher-res figures. The txt file contains all curves. The XML file contains the corrected FSC curve (ready for PDB deposition).

1 Like
4

If you do not have access to the webpage:

1. save the following as “dump_gridfs_data.py”

#!/usr/bin/env python3

import pickle,sys,os

def read_grid_fs_to_dic(fn):
    with open(fn, 'rb') as f:
        a = pickle.load(f)
    return a

def write_pickle_contents(a, od):
    assert os.path.isdir(od)
    count = 0
    listtxt = "{}\t{}\t{}\t{}\t{}\n".format(
        'count', '_id', 'job_uid', 'filename', 'Bytes')
    for i in a:
        listtxt += "{}\t{}\t{}\t{}\t{}\n".format(count, i['_id'], i['job_uid'], i['filename'], len(i['data']))
        fn = fn_ori = i['filename']
        if fn_ori[-4:] in ['.png', '.txt', '.pdf']:
            count += 1
            fn = f"{fn_ori[:-4]}_{i['_id']}{fn_ori[-4:]}"
        with open(os.path.join(od, fn), 'wb') as f:
            f.write(i['data'])
    print(listtxt)
    with open(os.path.join(od, 'unpickled_file_list.txt'), 'w') as f:
        f.write(listtxt)


def dump_gridfsdata_0(fn='gridfsdata_0', outputdir=None):
    od = os.path.dirname(os.path.abspath(fn))
    if outputdir is not None:
        od = os.path.abspath(outputdir)
    assert os.path.isdir(od)

    dic = read_grid_fs_to_dic(fn)
    write_pickle_contents(dic, od)


dump_gridfsdata_0(sys.argv[1])

2. Find the “gridfs_file/gridfsdata_0” file in your saved refinement directory.
3. run as

dump_gridfs_data.py  gridfsdata_0

This dumps all data files from “gridfsdata_0”. These are the same data files referred to by the web interface.

The XML file to deposit is “Jxxx_fsc_iteration_00x_after_fsc_mask_auto_tightening_corrected_mask.xml”.
The txt, png and pdf files are also among the extracted files.

5

True! it’s aways been there! Thanks ZhijieLi