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Hello Xiaogang-- > Hi Charles, > > ????? As your suggestion, I use PosDiffPot to restrain the refined > structure around the reference X ray structure. But the result is > still disordered. I think it is strange. If the refined structure is > already restrained around the reference structure, at least I should > get a structure close to the reference structure. I think maybe I need > to use a high force constant for this restrain. But I do not know how > to do it. I have attached the script (refine.py) I use for refinement > and the result file(refine.out). Can you take a look and tell me how > to set the force constant or something else need to be correct? The > protein structure I want to refine is a 2 A X ray structure with about > 360 residues. > Please try increasing the refRMSD force constant by a factor of 10-100, by specifying e.g. refRMSD.setScale(100) after the term is created. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkon7O8ACgkQPK2zrJwS/lagwgCeI88tzpBfUo+z8cFUAUeQ7wKk quQAnins00mWj+NgKIRzv1RlHHqAEVgm =5aSo -----END PGP SIGNATURE-----
