-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Sebastiano,
that's good to know. Thanks for the comment! Tim On 05/30/2013 06:58 PM, Sebastiano Pasqualato wrote: > > 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: > > 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/ iD8DBQFRqEykUxlJ7aRr7hoRAhcZAJ9u1OhVI1OqiRECB1wQREg9lDeLowCfXx+F tQ11l9/W+DkNNYYQWUbrWDk= =uQms -----END PGP SIGNATURE-----
