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 <[log in to unmask]> wrote:
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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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