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Hi all, my problem is the following: I want to model a structure based on another one. Both are trimers. My sequence (corresponding to the "unknown" proteins) has additional residues at the beginning of each chain, and I have to force them to make an alpha-helix. The problem is that when I try to add the restraints using as template the original chains-including PDB file and separating chains in the .ali file, the residues numbering seems to start from the residue 1 of the template, and I can't impose anything on my sequence. I've tried too to edit the template PDB file in order to delete the information about chains and to obtain a "normal" numbering, but in this case, obviously, Modeller is not able to separate the subunits and generates strange distortions to keep in contact the boundary residues. Last possibility would be to model separately the chains and to reconstruct the trimer at the end, but the modeling changes the coordinates and I can not imagine how to reassemble the single results. Any suggestion? thanks in advance > From: > To: > Subject: confirm 392af0e853ea4879fdb3eb3ac0b3f1a1fbc59de1 > Date: Tue, 12 Feb 2008 01:55:35 -0800 > > Mailing list subscription confirmation notice for mailing list > modeller_usage > > We have received a request from giorgione.sbp.op.sissa.it for > subscription of your email address, "", to the > mailing list. To confirm that you want to > be added to this mailing list, simply reply to this message, keeping > the Subject: header intact. Or visit this web page: > > https://salilab.org/mailman/confirm/modeller_usage/392af0e853ea4879fdb3eb3ac0b3f1a1fbc59de1 > > > Or include the following line -- and only the following line -- in a > message to : > > confirm 392af0e853ea4879fdb3eb3ac0b3f1a1fbc59de1 > > Note that simply sending a `reply' to this message should work from > most mail readers, since that usually leaves the Subject: line in the > right form (additional "Re:" text in the Subject: is okay). > > If you do not wish to be subscribed to this list, please simply > disregard this message. If you think you are being maliciously > subscribed to the list, or have any other questions, send them to > . Windows Live Spaces Push the Button! Crea il tuo blog e condividi le tue esperienze col mondo! |