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PostPosted: 2018.02.02 00:28 
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Joined: 2011.08.15 22:18
Posts: 20
Location: UTMB, Galveston, TX
Hello,

I am trying to use SREFLEX to allow a large macromolecular complex of about 3,800 residues to deform to optimize the fit to our SAXS data. I have run SREFLEX on smaller molecules, but the molecular size seems to be limited by the programs ability to allocate arrays. This is machine independent (Linux CentOS6/7 24 to 264 Gb RAM), so it is probably an issue with the program and the object size.

sreflex -p NMA-00A -t 10 --lm 25 --sm 0.28 --cst saxs.dat Complex.pdb
--SREFLEX LOG
--VERSION: ATSAS 2.8.0 (r8972)
--DATE and TIME: 2018-02-01 16:18:22
--INPUT SAXS data filename: saxs.dat
--INPUT PDB filename: Complex.pdb
--INPUT PDB contains 30130 ATOM entries, of which 3616 are centroids.
WARNING - Large input structure (3616 centroids), adjusting resPerBlock to 6.
--CPU cores/threads that will be used: 10
--NMA: Running initial normal mode analysis...
STOP *Working arrays allocation error*
ERROR 116 FILE 'initial/initial.vectors' NOT FOUND.

Is there any work-around to deal with large macromolecular complexes in SREFLEX?

Best regards,
Mark


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PostPosted: 2018.02.05 19:55 
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Joined: 2014.03.05 17:56
Posts: 45
Dear Mark,

thanks for reporting this problem.
I see you are using ATSAS 2.8.0, this situation has been improved in the latest version (2.8.3).
Please try again after installing the latest ATSAS.

Alternatively, you can try adding the argument " -g resPerBlock=5 " to the SREFLEX command line call.

Best,

sasha


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