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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 > >>refmac5 must be assuming that you number your protein according to your > > protein sequence, which is continuous. In my opinion, this is reasonable. > > Uhhh... this assumption turns perilious quickly, because there > are post-translational mods and splicing (see Concanavalin), > and biologists sometimes prefer keeping the > key residues in related structures (trypsin, fabs, etc) at > a certain residue number. This causes > sequence insertions (addressed correctly, as you say) > and gaps (not addressed correctly, my situation.) > Sure, but after any modification whatsoever the sequence of the final protein is, except for perhaps a few pathological cases, continuous. Now, I can understand, though not always agree, that biologists (I am one) prefer to give a consistent number to a particular residue in a family of proteins, but for a refinement program I still think it is reasonable to consider the numbering as continuous by default: this would be the most usual situation, I would say. In any case, knowing that you can fix the problem using TRANS (perhaps even CIS if the thing is really bizarre) is very useful, thanks! Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: [EMAIL PROTECTED] www: http://www.ysbl.york.ac.uk/~mol/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.1 (GNU/Linux) iD8DBQFE2tmRF6oOrDvhbQIRAoW9AJoCpyWRpC+R6XGzn6IGxniwwRK2UgCgoyDe RRece2CHvTn8P22eekYjbZc= =61Z2 -----END PGP SIGNATURE-----
