Dear Folmer,
I tried doing this workaround before and it is working as long as you don't
rename the other monomers chain from the initial chain name A to B, C, D to
address them easily and individually. After changing the chain name the
additional information is then just applied to chain A because the definition
is just given for this chain. Even if the chain name remains chain A for all 4
monomers (in the case of this example), this PDB file is not correctly
interpreted by other programs and web tools.
If pymol is never preserving these informations I guess I need to calculate and
include them myself for the three additional monomers of this example.
Regards,
Maximilian
On 2012/01/08, at 1:23, Folmer Fredslund wrote:
> Dear Maximilian,
>
> Pymol only saves the atomic coordinates. In the PDB file additional
> information is present, but none of this information is preserved.
>
> When you load the saved PDB kg Pymol will calculate the secondary structure
> by itself.
>
> I think it would be possible to copy the lines from the original PDB.
>
> Venlig hilsen
> Folmer Fredslund
> fra mobilen
>
> Den 08/01/2012 05.02 skrev "Maximilian Ebert" <[email protected]>:
> Dear list,
>
> today I realized that if I create a single PDB file of a biological unit
> (i.e. a tetramer of monomers) the secondary structure information isn't kept.
> The way I create such a file is:
>
> fetch 2RH2, type=pdb1
> split_states 2RH2,
> delete 2RH2
> alter all, segi = model[-4:]
> rewind
> save 2RH2_tetra.pdb, all
>
> If I open this file the secondary structure of each monomer in the tetramer
> visualized by "show cartoon" isn't the same as before saving (i.e.
> beta-sheets length is different etc.). Any ideas why?
>
> Thank you very much,
>
> Dipl.-Ing. Maximilian Ebert
>
> Étudiant au doctorat en biochimie
> Laboratoire du Dr. Joelle Pelletier
> Université de Montréal
>
> [email protected]
>
>
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