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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 <[log in to unmask]>
> 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
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