Dear Jan, in principle you can (ab-)use the program mrtailor for this purpose. You provide the PDB file, the sequence alignment (the way you want it to be aligned) and it will mutate only the mismatches and leave all other residues in the PDB file untouched. There is a command line option but also the GUI mrtailor-gui at http://shelx.uni-ac.gwdg.de/~tg/research/programs/mrtailor/
Best, Tim On 11/12/2014 06:04 PM, Jan Stransky wrote: > Hi all, > I have experienced strange behavior of Align&mutate tool. I wanted to > correct few differences in sequence with it, and there is a place in the > sequence looking like this: > orginal sequence: > XYZDSUVW > new sequence: > XYZSPUVW > > which ends after Align&mutate like this: > XYZDS-UVW > XYZ-SPUVW > > and more over numbering of residues changes because of it. And that is > wrong. > Therefore, I suggest to incorporate an option "Treat sequence rigid" or > something like that, which would just found best match without any > "missing" residues. Yes, Mutate residue range did the trick, but it has > slightly different purpose, I think. > > The second problem I have noticed, that it seems that with both > mutate-sequence tools (Align&mutate, Mutate residue range), it mutates > all the residues, including those which remains same. That cause > displacement of correctly placed residues. > > Best regards, > Jan > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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