Hi Donghui, I don't think that is a problem in PyMOL. The cartoon representation is an idealized form of the secondary structure and does not strictly follow the atomic coordinates of the protein backbone. The strands are flattened and that's why you see the gaps between the strand and the side chain. By setting 'side_chain_helper on' the flatness of the cartoon representation is switched off and the strand follows the protein backbone and thus you get the curves. I don't think there is a solution to your 'problem'. (Well, I guess you could move your side-chains, but that's probably not what you want)
Check the pymol wiki entries 'side-chain helper' and 'cartoon flat cycles' for more info: http://www.pymolwiki.org/index.php/Cartoon_side_chain_helper Bernhard On May 29, 2013, at 8:29 PM, wu donghui <[email protected]<mailto:[email protected]>> wrote: Dear all, I found a problem when I use pymol to prepare structure interface. Strand is distorted when residue from the strand is connected to the strand by turning on "side_chain_helper on". However when side_chain_helper is off, the strand turns to normal shape but the residue from it is disconnected to the strand. I attached the picture for your help. I know there must be some tricks for this. Welcome for any input. Thanks a lot. Best, Donghui <Distorsion and connectivity in pymol for strand.pdf>
