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Hello Valerie-- > > I'm calculating the structure of a weak-affinity protein complex > using only PDBs and PRE data. Some of the output structures contain > the two > proteins interlocked or tangled, and sometimes even occupying the same > space. I am using the saWithPreAllNoRdc.py script, in which I > have commented out restraint commands except anything pertaining to > PRE, VDW, RAMA, ANGL, BOND. Any information on why these proteins are > colliding like this? I have also commented out the collapse command. > first, make 100% certain that your pre parameters are correct. I believe the script you are working from was used for refinement. It is probably better to instead work from a docking script (like eginput/EIN_HPr_diffTens/dock.py in Xplor-NIH 2.22, moving to eginput/diffPot/dock/dock.py in 2.23), and add the PRE bits. Doing this will be easier with the new PRE helper tools in Xplor-NIH 2.23 (hopefully out this week). best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkn/AqEACgkQPK2zrJwS/lZfaQCdFYEhiwNAnIIwC1HFFA+PNEZJ GvEAniGTZzjomAH6xTbzxl6vZcvFtYT2 =xCMq -----END PGP SIGNATURE-----
