Tim, if I'm not wrong, if you judo type "dss" on the pymol command line you will apply dssp to your pdb and have your model checked for secondary structure elements.
Ciao, S -- Sebastiano On 30/mag/2013, at 18:35, Tim Gruene <[email protected]> wrote: > -----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-----
