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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
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