{"EMPIAR-10008":{"imagesets":[{"segmentations":[],"name":"U115","directory":"data","category":"picked particles - multiframe - unprocessed","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":124478,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":0.74688,"pixel_height":0.74688,"micrographs_file_pattern":null,"picked_particles_file_pattern":null,"picked_particles_directory":null,"details":"U115dataset.mrcs: This is the particle set with the original pixel size. It is a subset of the larger dataset deposited as the *.dat SPIDER stack files (10007).\nU115D2dataset.mrcs: this was the particle stack used to reproduce the refinement in RELION starting from a Gaussian sphere. The dataset was two-fold binned from U115dataset.mrcs.\n\nWe made minor modifications to the RELION version 1.1 source code.\nThe purpose of these changes was two-fold: 1) to avoid pre-mature progression to finer angular sampling for images of lower contrast than those tested during the development of the original software, and 2) to solve a file resource interlocking issue that arises when a greater number of parallel nodes is employed. Three modifications were made in the file \"ml_optimiser.cpp\", as follows: (i) The function global_mutex.lock() was added at line 2220, global_mutex.unlock() at line 2242; (ii) 0.75 was changed to 0.05 at line 4684, allowing the finer angular sampling of lower contrast images in autoAdjustAngularSampling(); and (iii) Line 4656 was changed to \"max_nr_iter_wo_resol_gain = (do_split_random_halves) ? 0 : 6\" in autoAdjustAngularSampling(). These changes are not essential for successful refinement when one follows the author’s suggestion of starting from a 60-Å low-pass filtered model.\nHowever, we found the changes to be critical for successful refinement when a Gaussian sphere was used as a starting model.","image_width":"256","image_height":"256"}],"workflow_file":null,"grant_references":[],"version_history":[{"version_number":1,"date":"2015-10-27","status_code":"REL","details":"Restructured the entry directory to have \"data\" and \".private\"."}],"title":"Low-contrast particle stack for HIV-1 Env gp160 precursor (MRC stack)","principal_investigator":[{"author_orcid":null,"middle_name":null,"organization":"Dana-Farber Cancer Institute","street":null,"town_or_city":"Boston","state_or_province":null,"post_or_zip":"02215","telephone":null,"fax":null,"first_name":"Joseph","last_name":"Sodroski","email":"joseph_sodroski [at] dfci.harvard.edu","country":"United States","entry":"EMPIAR-10008"}],"status":"REL","deposition_date":"2014-02-20","release_date":"2014-02-21","obsolete_date":null,"update_date":"2014-02-21","corresponding_author":{"author":{"author_orcid":null,"middle_name":null,"organization":"Dana-Farber Cancer Institute","street":null,"town_or_city":"Boston","state_or_province":null,"post_or_zip":"02215","first_name":"Youdong","last_name":"Mao","country":"United States"}},"authors":[{"author":{"name":"Mao Y","author_orcid":null}},{"author":{"name":"Wang L","author_orcid":null}},{"author":{"name":"Gu C","author_orcid":null}},{"author":{"name":"Herschhorn A","author_orcid":null}},{"author":{"name":"Desormeaux A","author_orcid":null}},{"author":{"name":"Finzi A","author_orcid":null}},{"author":{"name":"Xiang SH","author_orcid":null}},{"author":{"name":"Sodroski JG","author_orcid":null}}],"cross_references":["EMD-5447"],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Mao Y","author_orcid":null},{"name":"Wang L","author_orcid":null},{"name":"Gu C","author_orcid":null},{"name":"Herschhorn A","author_orcid":null},{"name":"Desormeaux A","author_orcid":null},{"name":"Finzi A","author_orcid":null},{"name":"Xiang SH","author_orcid":null},{"name":"Sodroski JG","author_orcid":null}],"editors":[],"published":null,"j_or_nj_citation":true,"title":"Molecular architecture of the uncleaved HIV-1 envelope glycoprotein trimer.","volume":"110","first_page":"12438","last_page":"12443","year":"2013","language":null,"doi":"doi:10.1073/pnas.1307382110","pubmedid":"23757493","details":null,"journal":"Pnas","issue":""}],"dataset_size":"38.0 GB","experiment_type":"EMDB","scale":null,"entry_doi":"10.6019/EMPIAR-10008"}}