-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Donghui,
did you actually check this stretch IS a beta-strand, given how distorted it looks? I am asking because in my experience people tend to believe what programs like pymol or molscript tell them to believe without checking the model e.g. for a hydrogen bonding network supporting the secondary structure definition. I may also remember incorrectly, but as far as I know pymol does not use the DSSP algorithm as e.g. molscript and often comes up with different boundaries for the secondary structure elements. I believe the dssp algorithm is more accurate, although this may be because I like molscript (typing) better than pymol (clicking). Regards, Tim On 05/30/2013 05:29 AM, wu donghui 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 - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRp3/cUxlJ7aRr7hoRAkV+AJ9QkNSlAhSC4VAKe2UHt+YpqSY3SwCfQ+Zw ry5vjpLD1hRVZGU7qHnajj4= =yxdy -----END PGP SIGNATURE-----
