Error when running initial_3Dmodel after importing class averages

[JulianMoebius]

Hi! I’m trying to use the 3D ab initio method in SIMPLE and ran into an issue I can’t track down.

I’m starting with an .mrcs file that contains 34 class averages (64 × 64). After opening the GUI and creating a new project, I imported the class averages using import_cavgs. The log looks fine:

>>> EXECUTION DIRECTORY: 1_import_cavgs
>>> DONE PROCESSING PARAMETERS
       _______ _____ _______  _____         _______
       |______   |   |  |  | |_____] |      |______
       ______| __|__ |  |  | |       |_____ |______
 
 _)_ ( _   _     ) o  _             _   _   _   o  _   _
 (_   ) ) )_)   (  ( ) ) (_( \)    )_) ) ) (_(  ( ) ) )_)
         (_                  (\   (_         _)      (_

**** IMPORT_CAVGS NORMAL STOP ****

However, when I try to start initial_3Dmodel, I get the following error:

>>> EXECUTION DIRECTORY: 3_initial_3Dmodel
>>> DONE PROCESSING PARAMETERS
ERROR! the project file does not contain enough information for e/o alignment, use a low-pass instead: LPSTART/LPSTOP; simple_commander_abinitio.f90; line:   146
ChildProcessError: `simple_exec prg=initial_3Dmodel pgrp=c1 msk=64 nparts=2 nthr=0 projfile=/home/julian/Documents/SIMPLE/beta_galac_tests/beta_galac/1_import_cavgs/beta_galac.simple` failed with code 1

I’ve tried this with multiple .mrcs files that work fine in other software, so I’m not sure where the issue is coming from. Any help or suggestions would be greatly appreciated!

Thanks!

[hael]

Hi, In SIMPLE, we do gold-standard refinement in 2D and we have FRCs associated with the class averages. These are used to automatically select the bandpass limit range used in the alignment. When you import class averages, this information is lacking. Therefore, as the error message specifies use a low-pass instead: LPSTART/LPSTOP Hence, give a starting low-pass limit in A (20 A typically works well) and a final low-pass limit (8 A if you see secondary structure in the class averages, otherwise something higher). Best, Hans From: JulianMoebius ***@***.***> Date: Tuesday, November 25, 2025 at 4:13 AM To: hael/SIMPLE ***@***.***> Cc: Subscribed ***@***.***> Subject: [EXTERNAL] [hael/SIMPLE] Error when running initial_3Dmodel after importing class averages (Issue #19) [https://avatars.githubusercontent.com/u/104631304?s=20&v=4]JulianMoebius created an issue (hael/SIMPLE#19)<#19> Hi! I’m trying to use the 3D ab initio method in SIMPLE and ran into an issue I can’t track down. I’m starting with an .mrcs file that contains 34 class averages (64 × 64). After opening the GUI and creating a new project, I imported the class averages using import_cavgs. The log looks fine:

>> EXECUTION DIRECTORY: 1_import_cavgs >> DONE PROCESSING PARAMETERS

_______ _____ _______ _____ _______ |______ | | | | |_____] | |______ ______| __|__ | | | | |_____ |______ _)_ ( _ _ ) o _ _ _ _ o _ _ (_ ) ) )_) ( ( ) ) (_( \) )_) ) ) (_( ( ) ) )_) (_ (\ (_ _) (_ **** IMPORT_CAVGS NORMAL STOP **** However, when I try to start initial_3Dmodel, I get the following error:

>> EXECUTION DIRECTORY: 3_initial_3Dmodel >> DONE PROCESSING PARAMETERS

ERROR! the project file does not contain enough information for e/o alignment, use a low-pass instead: LPSTART/LPSTOP; simple_commander_abinitio.f90; line: 146 ChildProcessError: `simple_exec prg=initial_3Dmodel pgrp=c1 msk=64 nparts=2 nthr=0 projfile=/home/julian/Documents/SIMPLE/beta_galac_tests/beta_galac/1_import_cavgs/beta_galac.simple` failed with code 1 I’ve tried this with multiple .mrcs files that work fine in other software, so I’m not sure where the issue is coming from. Any help or suggestions would be greatly appreciated! Thanks! — Reply to this email directly, view it on GitHub<#19>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAJENUVOXKTGVLBZVJ36MNT36QMSZAVCNFSM6AAAAACNDZ47PGVHI2DSMVQWIX3LMV43ASLTON2WKOZTGY3DEMJUHA3DOMQ>. You are receiving this because you are subscribed to this thread. CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

[JulianMoebius]

Thank you so much for the quick reply! Everything works now!