Hi, I have a model of a protein-protein complex, where several residues in a loop in the interface are undefined. I want to use xplor to add the loop residues, and put them in a location that does not clash with the rest of the protein or with the binding partner.
I used addAtoms2.py to generate the loop residues without disturbing the rest of the structure. The loop that was generated clashed with the binding partner, so I wanted to run some dynamics to move the loop into a more suitable position, again without disturbing the rest of the model. I found the dock.py script has some features to treat the proteins as rigid bodies, and to prevent sidechain movement, while allowing some movement in a defined part of the protein(s). So I'm trying to use the dock.py script, with lines like: dyn_fix.group( 'resid 1022:1237') dyn_fix.group( 'resid 1238:1329' ) dyn_fix.group( 'resid 1338:1428' ) dyn_fix.fix( 'resid 1022:1237') dyn_fix.fix( 'resid 1238:1329') dyn_fix.fix( 'resid 1338:1428' ) I'm trying to set the protein without the modified loop as fixed, and the N-terminal and C-terminal parts of the other protein, before and after the loop as a fixed group, and let the loop itself be moved. However, no matter what I do, a bond at the C-terminal end of the loop is always broken. Is there a more appropriate approach to finding a possible conformation of a flexible loop, while keeping all other residues in a model fixed? Thank you, Katie Edmonds -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20130605/315aede8/attachment.html>
