Jon, This can be done conveniently within Coot. 1) SSM superpose using chain B as the reference and chain A as the moving structure. Check the "Move copy of moving structure" so you keep your original molecule. 2a) You can use "Copy fragment" under Extensions to get the loop. Then use the "Merge Molecules" to merge the loop to chain B. You may need to manually rename the chain name of the loop as merging leads to different name. 2b) If the loop is short enough, I would create a dummy loop in chain B to fill the gap first. Then use the "Replace Fragment" to update the dummy loop by the rotated loop. You may still need to rename the chain ID to B first as the rotated loop may still be called chain A. "Change Chain ID" will handle that.
This may not be the most direct way but it should do the job. Hope it works for you. Yong Jonathan Grimes <[email protected]> Sent by: Mailing list for users of COOT Crystallographic Software <[email protected]> 03/06/2012 06:33 AM Please respond to Jonathan Grimes <[email protected]> To [email protected] cc Subject Using NCS to copy between molecules I have 3 copies of a molecule A,B and C A is complete. B and C have a loop missing. Refinement has brought up nice density for the loop in chain B. I want to use the structure of the loop in chain A and make a copy and flip it in and merge with chain A. I have done this before, but cant remember how. Clue anyone pls. Thanks Jon Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: [email protected], Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547
