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Hello Yun Lin-- > I am trying to get a RMSD matrix from about 400 structures. While > using the script eginput/gb1_rdc/pairRMSD.py, I got the following > error: > pairRMSD.py(82): for j in range(i+1,len(pdbFiles)): > pairRMSD.py(83): protocol.initCoords(pdbFiles[j]) > PDBTool:read: atom not found in structure: AXIS ANI 500 X > PDBTool:read: atom not found in structure: AXIS ANI 500 Y > PDBTool:read: atom not found in structure: AXIS ANI 500 Z > PDBTool:read: atom not found in structure: AXIS ANI 500 OO > PDBTool:read: atom not found in structure: AXIS ANI 500 OO2 > PDBTool:read: atom not found in structure: AXIS ANI 500 PA1 > PDBTool:read: atom not found in structure: AXIS ANI 500 PA2 > matchInexactAtomEntry: found no match for entry AXIS 500 X > pseudo atom > matchInexactAtomEntry: found no match for entry AXIS 500 Y > pseudo atom > matchInexactAtomEntry: found no match for entry AXIS 500 Z > pseudo atom > matchInexactAtomEntry: found no match for entry AXIS 500 OO > pseudo atom > matchInexactAtomEntry: found no match for entry AXIS 500 OO2 > pseudo atom > matchInexactAtomEntry: found no match for entry AXIS 500 PA1 > pseudo atom > matchInexactAtomEntry: found no match for entry AXIS 500 PA2 > pseudo atom These messages can be ignored- they refer to pseudo-atoms. > %ALLHP-err: too much memory requested. > Subroutine DIE called . Terminating even though 400 structures is a large number, this should not exhaust memory unless there are a large number of atoms (>40,000) in these structures. It seems like there's a bad memory leak. I will investigate. > > When running the script, the memory usage of 'xplor' process ( > using 'top' command) keeps growing. Since I only need the RMSD values, > is there any way to dump the calculated data from the memory? > (Besides, my computer has 2GB memory) This script computes pairwise rmsd - just a single number, really. Do you really want to do this? To compute rmsd relative to a target structure use bin/targetRMSD. And you're correct- it isn't very efficient. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAksUR2EACgkQPK2zrJwS/lY2fQCfYFOyyj/cNMMD6lM5u7wT2mUq p/AAoIlAe5RK8e6gQA1VzdxjYZONrq4B =rtnv -----END PGP SIGNATURE-----
