DAMMIF/N Alignment Errors

[Hailee Scelsi]

Hello,

I'm trying to use DAMMIF/N to generate bead models for my pressure series. I've gone through the tutorial step by step for generating the GNOM .out files and running DAMMIF/N.

I've successfully run the first 3 outputs of my series, but I've repeatedly tried to continue but keep receiving these errors.

For context, I'm running 15 reconstructions, 3 simultaneous runs, Fast, checking the refine box and providing a PDB file for alignment. The errors are coming after the completion of the refinement step.

Thanks for the help!

System: Windows-10-10.0.22631-SP0
RAW version: 2.3.0
Prebuilt: True
ATSAS version: 3.2.1

Error 1:

Traceback (most recent call last):

  File "bioxtasraw\RAW.py", line 16108, in run_with_except_hook

  File "threading.py", line 982, in run

  File "bioxtasraw\RAWAnalysis.py", line 6620, in runSuperimpose

  File "bioxtasraw\RAWAnalysis.py", line 6765, in runCifsup

  File "bioxtasraw\SASFileIO.py", line 2807, in loadDamaverGlobalSummaryFile

FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Users\\ScelsiSpectre\\GaTech Dropbox\\CoS\\Chemistry\\Lieberman_Lab\\CHESS\\HP BioSAXS\\10162024\\WT pressure series\\Reconstruction data\\150mpa_dammif\\WT_150-global-summary.txt'

Error 2:
Traceback (most recent call last):

  File "bioxtasraw\RAW.py", line 16108, in run_with_except_hook

  File "threading.py", line 982, in run

  File "bioxtasraw\RAWAPI.py", line 3881, in dammin

  File "bioxtasraw\SASFileIO.py", line 3052, in loadmmCIFFile

FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Users\\ScelsiSpectre\\GaTech Dropbox\\CoS\\Chemistry\\Lieberman_Lab\\CHESS\\HP BioSAXS\\10162024\\WT pressure series\\Reconstruction data\\150mpa_dammif\\refine_WT_150-1.cif'

Error 3:
Traceback (most recent call last):

  File "bioxtasraw\RAW.py", line 16108, in run_with_except_hook

  File "threading.py", line 982, in run

  File "bioxtasraw\RAWAPI.py", line 4109, in damaver

  File "bioxtasraw\SASFileIO.py", line 2776, in loadDamaverDistancesFile

FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Users\\ScelsiSpectre\\GaTech Dropbox\\CoS\\Chemistry\\Lieberman_Lab\\CHESS\\HP BioSAXS\\10162024\\WT pressure series\\Reconstruction data\\150mpa_dammif\\WT_150-distances.txt'

[Jesse Hopkins]

Hi Hailee,

Basically, these messages are saying that RAW isn't finding the expected output files from your dammif reconstructions. There's a couple of things you can do. First, check and see whether these files exist in the directory listed (last line of each error has the directory and filename).

I'd also recommend trying two things. First, can you try saving the output to a local folder, rather than your dropbox or similar folder. We've seen some weird issues in the past when folks have tried to save output to onedrive, so it could be something similar. Second (and this could be done at the same time) you might try using a shorter output filepath. I don't know if dammif has a max limit on file path length, but it's certainly possible. So something like C:\Users\ScelsiSpectre\saxs_data_test.

Let me know if either of those helps.

All the best.

- Jesse

----

Jesse Hopkins, PhD

Deputy Director

BioCAT, Sector 18

Advanced Photon Source

--
You received this message because you are subscribed to the Google Groups "BioXTAS RAW" group.
To unsubscribe from this group and stop receiving emails from it, send an email to bioxtas_raw...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/bioxtas_raw/5f1d9210-9bf6-4635-92f0-67c4f2272234n%40googlegroups.com.

[Hailee Scelsi]

Hi Jesse,

I moved the folder out of Dropbox (thereby also giving it a shorter path) and the problem seems to be resolved.

Thanks for the help!

Hailee

You received this message because you are subscribed to a topic in the Google Groups "BioXTAS RAW" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/bioxtas_raw/9_npGYEOLD0/unsubscribe.
To unsubscribe from this group and all its topics, send an email to bioxtas_raw...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/bioxtas_raw/CAGRN2W3VmEHvqB3OVKD8AOyAiOVnKDPYL5m7ZeTv4X%3DYohPAag%40mail.gmail.com.