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If I understand you correctly, the CCP4 program Chainsaw would do this. It uses an alignment file, which you could hand-craft to select mutate or conserve. Keyword "MODE MIXA" to select the truncate-to-beta option. HTH Martyn -----Original Message----- From: CCP4 bulletin board on behalf of [log in to unmask] Sent: Sun 4/29/2007 3:41 AM To: [log in to unmask] Subject: [ccp4bb] search-and-replace Hello everyone, I have two pdb files for molecule A (A.pdb and A_polyala.pdb) from which I would like to make a hybrid file A_semi.pdb. A_semi.pdb will have some residues with full sidechains (so derived from A.pdb) and some residues with only a C-beta atom for a sidechain (so derived from A_polyala.pdb). The residues I would like mutated are listed in file B.txt (in total about 250 residues to be mutated). I could do this by hand but I figure there must be a fater way to do it. Does anyone have any suggestions on how I might be able to do this? Is there some unix search-and-replace command line I could use to replace all lines of text in A.pdb containing ### (spaced appropriately) with those lines of text in A_polyala.pdb containing the same ###, and then have it repeat this for all ~250 residues listed in the file B.txt? Many thanks in advance, Shekeb